Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/IAO_0000005 objective specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity goal specification A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. http://purl.obolibrary.org/obo/IAO_0000184 scatter plot http://purl.obolibrary.org/obo/IAO_0000038 graph scattergraph A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. http://purl.obolibrary.org/obo/OBI_0000014 regulator role http://purl.obolibrary.org/obo/OBI_0000017 regulatory role regulator a regulatory role involved with making and/or enforcing relevant legislation and governmental orders http://purl.obolibrary.org/obo/OBI_0000018 material supplier role http://purl.obolibrary.org/obo/OBI_0000947 service provider role material provider role a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. http://purl.obolibrary.org/obo/OBI_0000023 classified data set http://purl.obolibrary.org/obo/IAO_0000100 data set data set with assigned class labels A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels. http://purl.obolibrary.org/obo/OBI_0000094 material processing http://purl.obolibrary.org/obo/OBI_0000011 planned process material transformation A planned process which results in physical changes in a specified input material http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification artifact creation objective an objective specifiction that creates an specific output object from input materials. http://purl.obolibrary.org/obo/OBI_0000648 clustered data set http://purl.obolibrary.org/obo/IAO_0000100 data set data set with assigned discovered class labels A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels. http://purl.obolibrary.org/obo/OBI_0000659 specimen collection process http://purl.obolibrary.org/obo/OBI_0000011 planned process specimen collection A planned process with the objective of collecting a specimen. http://purl.obolibrary.org/obo/OBI_0000663 class prediction data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation supervised classification data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. http://purl.obolibrary.org/obo/OBI_0000700 support vector machine http://purl.obolibrary.org/obo/OBI_0000663 class prediction data transformation SVM A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space. http://purl.obolibrary.org/obo/OBI_0000727 k-nearest neighbors http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating k-NN A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned. http://purl.obolibrary.org/obo/OBI_0000749 CART http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation classification and regression trees A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0000011 planned process data processing A planned process that produces output data from input data. http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating data projection A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m. http://purl.obolibrary.org/obo/OBI_0200051 principal components analysis dimensionality reduction http://purl.obolibrary.org/obo/OBI_0200050 dimensionality reduction pca data reduction A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones. http://purl.obolibrary.org/obo/OBI_0200111 data visualization http://purl.obolibrary.org/obo/OBI_0000011 planned process data encoding as image An planned process that creates images, diagrams or animations from the input data. http://purl.obolibrary.org/obo/OBI_0200175 class discovery data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation unsupervised classification data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. http://purl.obolibrary.org/obo/OBI_0200178 class discovery objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective clustering objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. http://purl.obolibrary.org/obo/OBI_0200179 class prediction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective classification objective A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. http://purl.obolibrary.org/obo/OBI_0200188 cross validation objective http://purl.obolibrary.org/obo/OBI_0200172 partitioning objective rotation estimation objective A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis. http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating http://purl.obolibrary.org/obo/OBI_0000011 planned process dataset creation A planned process that has a data set as its specified output. http://edamontology.org/data_0582 Ontology http://purl.obolibrary.org/obo/IAO_0000027 data item Ontologies An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. http://edamontology.org/data_2603 Microarray data http://purl.obolibrary.org/obo/IAO_0000027 data item mRNA quantification data Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification. http://edamontology.org/data_2968 Image http://purl.obolibrary.org/obo/IAO_0000027 data item Image data Biological or biomedical data has been rendered into an image, typically for display on screen. http://edamontology.org/format_1936 GenBank format http://purl.obolibrary.org/obo/IAO_0000098 data format specification GenBank Genbank entry format. http://edamontology.org/format_2549 OBO Flat File Format http://edamontology.org/format_2330 Textual format OBO flat file format OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies. http://edamontology.org/format_2585 SBML http://edamontology.org/format_2332 XML Systems Biology Markup Language Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. http://edamontology.org/operation_0224 Query and retrieval http://purl.obolibrary.org/obo/OBI_0200000 data transformation Query Search or query a data resource and retrieve entries and / or annotation. http://edamontology.org/operation_0362 Genome annotation http://purl.obolibrary.org/obo/OBI_0200000 data transformation Metagenome annotation Annotate a genome sequence with terms from a controlled vocabulary. http://edamontology.org/operation_2426 Modelling and simulation http://purl.obolibrary.org/obo/OBI_0200000 data transformation Mathematical modelling Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. http://www.ebi.ac.uk/swo/SWO_0000011 IntelliJ IDEA http://www.ebi.ac.uk/swo/SWO_0000001 software IntelliJ IntelliJ IDEA is a commercial Java IDE for developing software. http://www.ebi.ac.uk/swo/SWO_0000027 OBO-Edit http://www.ebi.ac.uk/swo/SWO_0000028 ontology engineering software OBO edit OBO-Edit is an open source ontology editor optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. http://www.ebi.ac.uk/swo/SWO_0000077 Sequence Alignment and Modeling System http://www.ebi.ac.uk/swo/SWO_0000001 software SAM Sequence Alignment and Modeling System, a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. http://www.ebi.ac.uk/swo/SWO_0000133 DAVID http://www.ebi.ac.uk/swo/SWO_0000001 software Database for Annotation, Visualization and Integrated Discovery DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB). All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies. http://www.ebi.ac.uk/swo/SWO_0000135 PSI-BLAST http://www.ebi.ac.uk/swo/SWO_1100032 BLAST Position-Specific Iterative Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as "hypothetical protein" or "similar to...". http://www.ebi.ac.uk/swo/SWO_0000138 Entrez http://www.ebi.ac.uk/swo/SWO_0000140 search engine Entrez Global Query Cross-Database Search System The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. http://www.ebi.ac.uk/swo/SWO_0000139 web content search http://edamontology.org/operation_0224 Query and retrieval website content search Web content search is the searching for information on the World Wide Web. http://www.ebi.ac.uk/swo/SWO_0000140 search engine http://www.ebi.ac.uk/swo/SWO_0000001 software web search engine A search engine is a software system that is designed to search for information on the World Wide Web. http://www.ebi.ac.uk/swo/SWO_0000141 Weka http://www.ebi.ac.uk/swo/SWO_0000001 software Waikato Environment for Knowledge Analysis Weka (Waikato Environment for Knowledge Analysis) is a suite of machine learning software, originally intended for data mining tasks, written in Java and developed at the University of Waikato, New Zealand. http://www.ebi.ac.uk/swo/SWO_0000142 PostgreSQL http://www.ebi.ac.uk/swo/SWO_0000001 software Postgres PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance. http://www.ebi.ac.uk/swo/SWO_0000153 VCell http://www.ebi.ac.uk/swo/SWO_0000001 software Virtual Cell VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing. http://www.ebi.ac.uk/swo/SWO_0000154 COBRA http://www.ebi.ac.uk/swo/SWO_0000001 software COnstraints Based Reconstruction and Analysis COBRA (COnstraint-Based Reconstruction and Analysis Toolbox) includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models. http://www.ebi.ac.uk/swo/SWO_0000155 COBRApy http://www.ebi.ac.uk/swo/SWO_0000154 COBRA COnstraints Based Reconstruction and Analysis for Python COBRA Toolbox is the version of the COBRA software for Python. http://www.ebi.ac.uk/swo/SWO_0000156 COBRA Toolbox http://www.ebi.ac.uk/swo/SWO_0000154 COBRA COnstraints Based Reconstruction and Analysis Toolbox for MATLAB COBRA Toolbox is the version of the COBRA software for Matlab. http://www.ebi.ac.uk/swo/algorithm/SWO_4000006 ODE Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm Ordinary Differential Equation Algorithm In mathematics, an ordinary differential equation or ODE is an equation containing a function of one independent variable and its derivatives. The term "ordinary" is used in contrast with the term partial differential equation which may be with respect to more than one independent variable. http://www.ebi.ac.uk/swo/algorithm/SWO_4000009 DAE Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm Differential Algebraic Equation Algorithm Differential Algebraic equations (DAEs) are a general form of (systems of) differential equations for vector–valued functions in one independent variable. In practical terms, the distinction between DAEs and ODEs is often that the solution of a DAE system depends on the derivatives of the input signal and not just the signal itself as in the case of ODEs. http://www.ebi.ac.uk/swo/algorithm/SWO_4000010 PDE Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm Partial Differential Equation Algorithm A partial differential equation (PDE) is a differential equation that contains unknown multivariable functions and their partial derivatives. This is in contrast to ordinary differential equations, which deal with functions of a single variable and their derivatives. http://www.ebi.ac.uk/swo/data/SWO_3000061 Data File Standard for Flow Cytometry http://www.ebi.ac.uk/swo/data/SWO_3000042 ASCII format FCS The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. The principal goal of the Standard is to provide a uniform file format allowing files created by one type of acquisition hardware and software to be analyzed by another type. http://www.ebi.ac.uk/swo/data/SWO_3000068 BLASTN http://www.ebi.ac.uk/swo/SWO_1100032 BLAST Nucleotide-nucleotide BLAST Nucleotide-nucleotide BLAST (blastn) is a type of BLAST software that takes a given DNA query and returns the most similar DNA sequences from the DNA database that the user specifies. http://www.ebi.ac.uk/swo/data/SWO_3000073 GMTK parameter data http://purl.obolibrary.org/obo/IAO_0000027 data item Graphical Models Toolkit parameter data GMTK parameter data is a type of data which contains the various parameter files required by GMTK to define a dynamic Bayesian network. http://www.ebi.ac.uk/swo/interface/SWO_5000002 web user interface http://www.ebi.ac.uk/swo/interface/SWO_9000052 graphical user interface WUI A Web User interface is a Graphical User Interface which is loaded and run via a Web browser rather than within the user's operating system. http://www.ebi.ac.uk/swo/interface/SWO_5000003 desktop graphical user interface http://www.ebi.ac.uk/swo/interface/SWO_9000052 graphical user interface Desktop GUI A Desktop Graphical User interface is a Graphical User Interface which is loaded and run within the user's operating system rather than via a Web browser. http://www.ebi.ac.uk/swo/interface/SWO_5000004 SOAP service http://www.ebi.ac.uk/swo/interface/SWO_9000051 web service SOAP Service A SOAP service is a Web service which provides a standard, extensible, composable framework for packaging and exchanging XML messages. The service may expose an arbitrary, application-specific set of operations. http://www.ebi.ac.uk/swo/interface/SWO_5000005 REST service http://www.ebi.ac.uk/swo/interface/SWO_9000051 web service REST Service A REST service is a Web service in which the primary purpose of the service is to manipulate XML representations of Web resources using a uniform set of "stateless" operations. RESTful APIs do not require XML-based web service protocols (SOAP and WSDL) to support their light-weight interfaces. http://www.ebi.ac.uk/swo/interface/SWO_9000051 web service http://www.ebi.ac.uk/swo/SWO_9000050 software interface Web Service A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services. http://www.ebi.ac.uk/swo/interface/SWO_9000052 graphical user interface http://www.ebi.ac.uk/swo/SWO_9000050 software interface GUI https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013. http://www.ebi.ac.uk/swo/interface/SWO_9000053 command-line interface http://www.ebi.ac.uk/swo/SWO_9000050 software interface Command-line A command-line interface is a means of interacting with a computer program where the user (or client) issues commands to the program in the form of successive lines of text (command lines). http://www.ebi.ac.uk/swo/interface/SWO_9000054 application programming interface http://www.ebi.ac.uk/swo/SWO_9000050 software interface API An application programming interface is a set of routines, protocols, and tools for building software applications. 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The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. http://www.ebi.ac.uk/swo/license/SWO_1000092 CC BY-SA 3.0 http://www.ebi.ac.uk/swo/license/SWO_1000001 Creative Commons Creative Commons Attribution-Sharealike 3.0 Unported CC BY-SA 3.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. http://www.ebi.ac.uk/swo/license/SWO_1000093 CC BY-SA 3.0 US http://www.ebi.ac.uk/swo/license/SWO_1000001 Creative Commons Creative Commons Attribution-Sharealike 3.0 United States CC BY-SA 3.0 US is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. http://www.ebi.ac.uk/swo/license/SWO_1000094 CC BY-SA 4.0 http://www.ebi.ac.uk/swo/license/SWO_1000001 Creative Commons Creative Commons Attribution-Sharealike 4.0 International CC BY-SA 4.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. http://www.ebi.ac.uk/swo/license/SWO_1000096 ODbL v1.0 http://www.ebi.ac.uk/swo/license/SWO_1000095 Open Data Commons Open Database License (ODbL) v1.0 The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL. 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[wikipedia] http://www.ebi.ac.uk/swo/data/SWO_3000025 tex http://www.ebi.ac.uk/swo/data/SWO_3000014 document exchange format LaTeX format tex is a format for documents written in the document markup language and document preparation system LaTeX. http://www.ebi.ac.uk/swo/data/SWO_3000028 OPML http://www.ebi.ac.uk/swo/data/SWO_3000026 outline document format Outline Processor Markup Language OPML (Outline Processor Markup Language) is an XML format for outlines http://www.ebi.ac.uk/swo/data/SWO_3000036 obsolete CopasiML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class .cps An XML-based file format for use with the COPASI software. http://www.ebi.ac.uk/swo/license/SWO_1000006 Academic Free License version 3 http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free License Type AFL The Academic Free License is a free software license under the definition of "free" by the GNU Project, is not copyleft, and is incompatible with the GNU GPL. http://www.ebi.ac.uk/swo/license/SWO_1000007 FreeBSD http://www.ebi.ac.uk/swo/license/SWO_1000044 GNU GPL Compatible License Type 2-clause BSD License This is the original BSD license with the advertising clause and another clause removed. 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The only change is that the EPL removes the broader patent retaliation language regarding patent infringement suits specifically against Contributors to the EPL'd program. http://www.ebi.ac.uk/swo/license/SWO_9000085 Modified BSD http://www.ebi.ac.uk/swo/license/SWO_1000044 GNU GPL Compatible License Type 3 clause BSD License The Modified BSD is a software license based on he original FreeBSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. This license is sometimes referred to as the 3-clause BSD license. According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery. http://www.ebi.ac.uk/swo/license/SWO_9000087 OPL v1.0 http://www.ebi.ac.uk/swo/license/SWO_1000008 Open source software license Open Public License Version 1.0 OPL v1.0 is not a free software license according to the definition of the GNU Project because it requires sending every published modified version to a specific initial developer. http://purl.obolibrary.org/obo/OBI_0002210 histologic grade according to the Fuhrman Nuclear Grading System http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Histologic Grade (Fuhrman Nuclear Grading System) A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. http://purl.obolibrary.org/obo/OBI_0002224 pathologic primary tumor stage for colon and rectum according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002232 pathologic primary tumor stage for lung according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread lung primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002243 pathologic primary tumor stage for kidney according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002256 pathologic primary tumor stage for ovary according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002270 pathologic lymph node stage for colon and rectum according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002279 pathologic lymph node stage for lung according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002284 pathologic lymph node stage for kidney according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002287 pathologic lymph node stage for ovary according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. http://purl.obolibrary.org/obo/OBI_0002290 pathologic distant metastases stage for colon according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: colon distant metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002298 pathologic distant metastases stage for lung according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: lung distant metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002306 pathologic distant metastases stage for kidney according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: kidney distant Metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002310 pathologic distant metastases stage for ovary according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification M: ovarian distant metastases (AJCC 7th Edition) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. http://purl.obolibrary.org/obo/OBI_0002314 clinical tumor stage group according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Clinical tumor stage group (AJCC 7th Edition) A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. http://purl.obolibrary.org/obo/OBI_0002326 International Federation of Gynecology and Obstetrics cervical cancer stage value specification http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Clinical FIGO stage A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. http://purl.obolibrary.org/obo/OBI_0002341 International Federation of Gynecology and Obstetrics ovarian cancer stage value specification http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. http://purl.obolibrary.org/obo/OBI_0002356 performance status value specification http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification Performance Status Scale A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). http://purl.obolibrary.org/obo/OBI_0002357 Eastern Cooperative Oncology Group score value specification http://purl.obolibrary.org/obo/OBI_0002356 performance status value specification ECOG score A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. http://purl.obolibrary.org/obo/OBI_0002363 Karnofsky score vaue specification http://purl.obolibrary.org/obo/OBI_0002356 performance status value specification Karnofsky Score A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. http://www.ebi.ac.uk/swo/SWO_0000032 Agilent Scan Control http://www.ebi.ac.uk/swo/SWO_0000034 Agilent Technologies Software Scan Control Application software Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions http://www.ebi.ac.uk/swo/SWO_0000039 ArrayGauge http://www.ebi.ac.uk/swo/SWO_0000001 software ArrayGauge [FUJIFILM] Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis. Its ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop. http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix http://www.ebi.ac.uk/swo/SWO_0000001 software Genepix GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use. http://www.ebi.ac.uk/swo/SWO_0000236 ImageQuant http://www.ebi.ac.uk/swo/SWO_0000001 software ImageQuant (Molecular Dynamics) This is a general image analysis program used in the study of electrophoretic separations, dot blots, slot blots, microplate assays, TLC assays, and plaque assays. ImageQuant provides a point-and-click environment for fast analysis of qualitative and quantitative assays. With tools for accurate volume integration, ImageQuant generates accurate lane profiles even for curved or slanted lanes. http://www.ebi.ac.uk/swo/SWO_0000238 ImaGene http://www.ebi.ac.uk/swo/SWO_0000001 software Imagene ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis. http://www.ebi.ac.uk/swo/SWO_0000271 MIcroarray Analysis Suite http://www.ebi.ac.uk/swo/SWO_0000001 software Affymetrix MicroArraySuite Affymetrix® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChip® platform. http://www.ebi.ac.uk/swo/SWO_0000329 QuantArray scanner software http://www.ebi.ac.uk/swo/SWO_0000001 software QuantArray QuantArray® is a powerful microarray analysis software that enables researchers to easily and accurately visualize and quantitate gene expression data. http://www.ebi.ac.uk/swo/SWO_0000418 ScanArray http://www.ebi.ac.uk/swo/SWO_0000001 software ScanArray Express [PerkinElmer] ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance. http://www.ebi.ac.uk/swo/SWO_0000424 Silicon Genetics Genespring http://www.ebi.ac.uk/swo/SWO_0000001 software SiliconGenetics GeneSpring The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment http://www.ebi.ac.uk/swo/SWO_1100011 'ANOVA' http://purl.obolibrary.org/obo/IAO_0000064 algorithm ANNOVA ANOVA or Analysis of Variance is a hypothesis testing algorithm which a variable is partitioned into components attributable to different sources of variation. http://www.ebi.ac.uk/swo/SWO_1100021 Affymetrix GeneChip Operating Software http://www.ebi.ac.uk/swo/SWO_0000001 software GeneChip Operating Software The Affymetrix GeneChip Operating Software (GCOS) is an operating system software that controls Affymetrix instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. http://www.ebi.ac.uk/swo/SWO_1100047 BioConductor Software http://www.ebi.ac.uk/swo/SWO_0000001 software Bioconductor Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages. http://www.ebi.ac.uk/swo/SWO_1100049 BlueFuse http://www.ebi.ac.uk/swo/SWO_0000001 software BlueFuse [BlueGnome] BlueFuse for Microarrays is a powerful software solution for the analysis of microarray expression and arrayCGH experiments. Operation is simple and fully automated, saving time, removing operator error and subjectivity and ensuring experimental reproducibility. http://www.ebi.ac.uk/swo/SWO_1100060 CARMAweb http://www.ebi.ac.uk/swo/SWO_0000001 software CarmaWEB CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages. http://www.ebi.ac.uk/swo/SWO_1100064 ChipReader 3.1 http://www.ebi.ac.uk/swo/SWO_0000001 software VersArray ChipReader Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime. http://www.ebi.ac.uk/swo/SWO_1100065 ChipSkipper http://www.ebi.ac.uk/swo/SWO_0000001 software ChipSkipper [EMBL] ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data http://www.ebi.ac.uk/swo/SWO_1100104 Agilent Feature Extraction Software http://www.ebi.ac.uk/swo/SWO_0000034 Agilent Technologies Software Feature Extraction software The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment http://www.ebi.ac.uk/swo/SWO_1100108 GC-RMA Quantification http://www.ebi.ac.uk/swo/SWO_0000034 Agilent Technologies Software GC-RMA Quantification (Stratagene ArrayAssist Expression Software) Single-user desktop software package for analyzing microarray data from multiple microarray platforms. http://purl.obolibrary.org/obo/APOLLO_SV_00000008 software development http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process that has specified output a software product and that involves the creation of source code. http://purl.obolibrary.org/obo/PATO_0000001 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that has temporal parts and that happens, unfolds or develops through time. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000009 datum label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. http://purl.obolibrary.org/obo/IAO_0000007 action specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity that describes an action the bearer will take. http://purl.obolibrary.org/obo/IAO_0000009 datum label http://purl.obolibrary.org/obo/IAO_0000030 information content entity A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://purl.obolibrary.org/obo/IAO_0000010 software http://purl.obolibrary.org/obo/IAO_0000104 plan specification Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. http://purl.obolibrary.org/obo/IAO_0000025 programming language http://purl.obolibrary.org/obo/IAO_0000104 plan specification A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity. http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. http://purl.obolibrary.org/obo/IAO_0000037 dot plot http://purl.obolibrary.org/obo/IAO_0000038 graph A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. http://purl.obolibrary.org/obo/IAO_0000038 graph http://purl.obolibrary.org/obo/IAO_0000309 diagram A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. http://purl.obolibrary.org/obo/IAO_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000096 source code module http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A source code module is a directive information entity that specifies, using a programming language, some algorithm. http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. http://purl.obolibrary.org/obo/IAO_0000101 image http://purl.obolibrary.org/obo/IAO_0000308 figure An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000027 data item Data about an ontology part is a data item about a part of an ontology, for example a term http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. http://purl.obolibrary.org/obo/IAO_0000129 version name http://purl.obolibrary.org/obo/IAO_0000028 symbol A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. http://purl.obolibrary.org/obo/IAO_0000178 material information bearer http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity in which a concretization of an information content entity inheres. http://purl.obolibrary.org/obo/IAO_0000179 histogram http://purl.obolibrary.org/obo/IAO_0000038 graph A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. http://purl.obolibrary.org/obo/IAO_0000180 heatmap http://purl.obolibrary.org/obo/IAO_0000038 graph A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. http://purl.obolibrary.org/obo/IAO_0000183 dendrogram http://purl.obolibrary.org/obo/IAO_0000038 graph A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. http://purl.obolibrary.org/obo/IAO_0000225 obsolescence reason specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000308 figure http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. http://purl.obolibrary.org/obo/IAO_0000309 diagram http://purl.obolibrary.org/obo/IAO_0000308 figure A figure that expresses one or more propositions http://purl.obolibrary.org/obo/IAO_0000310 document http://purl.obolibrary.org/obo/IAO_0000030 information content entity A collection of information content entities intended to be understood together as a whole http://purl.obolibrary.org/obo/IAO_0000409 denotator type http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part A denotator type indicates how a term should be interpreted from an ontological perspective. http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000015 process A process that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/OBI_0000017 regulatory role http://purl.obolibrary.org/obo/BFO_0000023 role a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. http://purl.obolibrary.org/obo/OBI_0000047 processed material http://purl.obolibrary.org/obo/BFO_0000040 material entity Is a material entity that is created or changed during material processing. http://purl.obolibrary.org/obo/OBI_0000112 specimen role http://purl.obolibrary.org/obo/BFO_0000023 role a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/BFO_0000040 material entity An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. http://purl.obolibrary.org/obo/OBI_0000450 regulatory agency http://purl.obolibrary.org/obo/OBI_0000245 organization A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. http://purl.obolibrary.org/obo/OBI_0000457 manufacturing http://purl.obolibrary.org/obo/OBI_0000094 material processing Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process http://purl.obolibrary.org/obo/OBI_0000458 manufacturing objective http://purl.obolibrary.org/obo/OBI_0000456 material transformation objective is the objective to manufacture a material of a certain function (device) http://purl.obolibrary.org/obo/OBI_0000571 manufacturer role http://purl.obolibrary.org/obo/BFO_0000023 role Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. http://purl.obolibrary.org/obo/OBI_0000684 specimen collection objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification A objective specification to obtain a material entity for potential use as an input during an investigation. http://purl.obolibrary.org/obo/OBI_0000704 decision tree induction objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. http://purl.obolibrary.org/obo/OBI_0000707 decision tree building data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. http://purl.obolibrary.org/obo/OBI_0000713 GenePattern software http://purl.obolibrary.org/obo/IAO_0000010 software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. http://purl.obolibrary.org/obo/OBI_0000726 peak matching http://purl.obolibrary.org/obo/OBI_0200000 data transformation Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation http://purl.obolibrary.org/obo/OBI_0200171 partitioning data transformation A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. http://purl.obolibrary.org/obo/OBI_0000835 manufacturer http://purl.obolibrary.org/obo/BFO_0000040 material entity A person or organization that has a manufacturer role http://purl.obolibrary.org/obo/OBI_0000947 service provider role http://purl.obolibrary.org/obo/BFO_0000023 role is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person http://purl.obolibrary.org/obo/OBI_0000953 processed specimen http://purl.obolibrary.org/obo/OBI_0100051 specimen A specimen that has been intentionally physically modified. http://purl.obolibrary.org/obo/OBI_0000963 categorical label http://purl.obolibrary.org/obo/IAO_0000009 datum label A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. http://purl.obolibrary.org/obo/OBI_0001000 questionnaire http://purl.obolibrary.org/obo/IAO_0000310 document A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification http://purl.obolibrary.org/obo/OBI_0001933 value specification A value specification that is specifies one category out of a fixed number of nominal categories http://purl.obolibrary.org/obo/OBI_0001933 value specification http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that specifies a value within a classification scheme or on a quantitative scale. http://purl.obolibrary.org/obo/OBI_0002076 collection of specimens http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that has two or more specimens as its parts. http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. http://purl.obolibrary.org/obo/OBI_0100051 specimen http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity that has the specimen role. http://purl.obolibrary.org/obo/OBI_0200033 leave one out cross validation method http://purl.obolibrary.org/obo/OBI_0000792 statistical model validation is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data http://purl.obolibrary.org/obo/OBI_0200041 k-means clustering http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed). http://purl.obolibrary.org/obo/OBI_0200042 hierarchical clustering http://purl.obolibrary.org/obo/APOLLO_SV_00000796 dataset creating A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root). http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification to transformation input data into output data http://purl.obolibrary.org/obo/OBI_0200171 partitioning data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A partitioning data transformation is a data transformation that has objective partitioning. http://purl.obolibrary.org/obo/OBI_0200172 partitioning objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set. http://purl.obolibrary.org/obo/OBI_0200190 clustered data visualization http://purl.obolibrary.org/obo/OBI_0200111 data visualization A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type. http://purl.obolibrary.org/obo/UO_0000001 length unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the distance between two points. http://purl.obolibrary.org/obo/UO_0000002 mass unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the amount of matter/energy of a physical object. http://purl.obolibrary.org/obo/UO_0000003 time unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the dimension in which events occur in sequence. http://kt.ijs.si/panovp/OntoDM#OntoDM_000034 generalization specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed. http://edamontology.org/data_1636 Heatmap http://edamontology.org/data_3768 Clustered gene expression profiles A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. http://edamontology.org/data_3768 Clustered gene expression profiles http://edamontology.org/data_2603 Microarray data Groupings of gene expression profiles according to a clustering algorithm. http://edamontology.org/format_2332 XML http://purl.obolibrary.org/obo/IAO_0000098 data format specification Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C. http://edamontology.org/format_3162 MAGE-TAB http://www.ebi.ac.uk/swo/data/SWO_3000046 tab delimited file format MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files. http://edamontology.org/format_3239 CopasiML http://edamontology.org/format_2332 XML CopasiML, the native format of COPASI. http://www.ebi.ac.uk/efo/swo/SWO_0000393 obsolete_Information processing http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Information processing is a process in which input information is analysed or transformed in order to produce information as output. http://www.ebi.ac.uk/swo/SWO_0000001 software http://purl.obolibrary.org/obo/IAO_0000104 plan specification Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations. http://www.ebi.ac.uk/swo/SWO_0000003 obsolete information processing http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class Information processing is a process in which input information is analysed or transformed in order to produce information as output. http://www.ebi.ac.uk/swo/SWO_0000004 Microsoft Excel 2007 http://www.ebi.ac.uk/swo/SWO_9000070 Microsoft Excel Microsoft Excel 2007 is a spreadsheet editing and viewing tool. http://www.ebi.ac.uk/swo/SWO_0000005 MATLAB http://www.ebi.ac.uk/swo/SWO_0000001 software MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran http://www.ebi.ac.uk/swo/SWO_0000007 OmniOutliner http://www.ebi.ac.uk/swo/SWO_0000001 software OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group http://www.ebi.ac.uk/swo/SWO_0000013 COPASI http://www.ebi.ac.uk/swo/SWO_0000001 software COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI provides an C++ API with language bindings for Perl, python, R, Java, and Octave and is able to communicate with the Systems Biology Workbench COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. http://www.ebi.ac.uk/swo/SWO_0000014 Microsoft Excel 2003 http://www.ebi.ac.uk/swo/SWO_1100127 software before Microsoft 2007 Microsoft Excel 2003 is a spreadsheet editing and viewing tool. http://www.ebi.ac.uk/swo/SWO_0000021 operating system http://www.ebi.ac.uk/swo/SWO_0000001 software An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources. http://www.ebi.ac.uk/swo/SWO_0000024 Adobe Illustrator 10 http://www.ebi.ac.uk/swo/SWO_0000026 software with image input Adobe Illustrator is a graphics editor for creating and editing vector graphics. http://www.ebi.ac.uk/swo/SWO_0000044 BLAST+ 2.2.26 http://www.ebi.ac.uk/swo/SWO_1100032 BLAST The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763) http://www.ebi.ac.uk/swo/SWO_0000051 Clustal http://www.ebi.ac.uk/swo/SWO_0000001 software Multiple alignment program for nucleic acid or protein sequences. http://www.ebi.ac.uk/swo/SWO_0000052 Clustal Omega http://www.ebi.ac.uk/swo/SWO_0000051 Clustal Clustal Omega provides improved scalability over previous Clustal versions, allowing hundreds of thousands of sequences to be aligned in a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. http://www.ebi.ac.uk/swo/SWO_0000065 CRG TCoffee http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee TCoffee is a multiple sequence alignment program with a number of different modes. http://www.ebi.ac.uk/swo/SWO_0000066 EBI TCoffee Web Tool http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. This Web tool provides both interactive access via a Web browser and programmatic SOAP Web service access. Currently only the Web service interface is modelled in OWL. http://www.ebi.ac.uk/swo/SWO_0000067 CRG RCoffee Web Tool http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee Aligns RNA sequences using predicted secondary structures by accessing the RCoffee mode of the underlying TCoffee software. http://www.ebi.ac.uk/swo/SWO_0000068 CRG TCoffee Web Tool http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. http://www.ebi.ac.uk/swo/SWO_0000069 CRG MCoffee Web Tool http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee Aligns DNA, RNA or Proteins by combining the output of popular aligners and by accessing the MCoffee mode of the underlying TCoffee software. http://www.ebi.ac.uk/swo/SWO_0000070 CRG Expresso Web Tool http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee Aligns protein sequences using structural information by accessing the 3DCoffee/Expresso mode of the underlying TCoffee software. http://www.ebi.ac.uk/swo/SWO_0000071 CRG PSICoffee Web Tool http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee Aligns distantly related proteins using homology extension (slow and accurate) by accessing the PSICoffee mode of the underlying TCoffee software. http://www.ebi.ac.uk/swo/SWO_0000072 CRG TCoffee 9.02.r1228 http://www.ebi.ac.uk/swo/SWO_0000065 CRG TCoffee The initial interface is via the command line. Depending on the options and inputs provided at the command line, an appropriate alignment takes place and is then presented to the user via a Graphical User Interface. http://www.ebi.ac.uk/swo/SWO_0000073 Q http://www.ebi.ac.uk/swo/SWO_0000001 software Q is a set of tools tailored for some specific kinds of free energy calculations, namely: (I) Free energy perturbation (FEP) simulations. (II) Empirical valence bond (EVB) calculations of reaction free energies. (III) Linear interaction energy (LIE) calculations of receptor-ligand binding affinities. http://www.ebi.ac.uk/swo/SWO_0000075 SPSS http://www.ebi.ac.uk/swo/SWO_0000001 software Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks. http://www.ebi.ac.uk/swo/SWO_0000079 Cytoscape http://www.ebi.ac.uk/swo/SWO_0000001 software Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. http://www.ebi.ac.uk/swo/SWO_0000083 Plugin http://purl.obolibrary.org/obo/BFO_0000023 role This role can be borne by any software which is a plugin for another piece of software. It can be used, for example, with an axiom such as "ParentSoftware 'uses software' some (PluginSoftware has_role some Plugin)" http://www.ebi.ac.uk/swo/SWO_0000090 Gene Expression Atlas at EBI R statistics package http://www.ebi.ac.uk/swo/SWO_0000001 software R package for producing statistics that populate the Gene Expression Atlas. https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R http://www.ebi.ac.uk/swo/SWO_0000143 data storage http://purl.obolibrary.org/obo/OBI_0200000 data transformation The storing of digital information. Often this is done for archiving and retrieval purposes. http://www.ebi.ac.uk/swo/SWO_0000145 Segway 1.2 http://www.ebi.ac.uk/swo/SWO_0000001 software The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. http://www.ebi.ac.uk/swo/SWO_0000146 Python 2.6 http://www.ebi.ac.uk/swo/SWO_0000118 Python Version 2.6 of the Python programming language. http://www.ebi.ac.uk/swo/SWO_0000147 Python 2.7 http://www.ebi.ac.uk/swo/SWO_0000118 Python Version 2.7 of the Python programming language. http://www.ebi.ac.uk/swo/SWO_0000149 Mac OS http://www.ebi.ac.uk/swo/SWO_0000021 operating system Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc. http://www.ebi.ac.uk/swo/SWO_0000151 OS X http://www.ebi.ac.uk/swo/SWO_0000149 Mac OS OS X is a Mac OS operating system which succeeds the original Mac OS, which had been Apple's primary operating system since 1984. Unlike the earlier Macintosh operating system, OS X is a Unix-based operating system. http://www.ebi.ac.uk/swo/SWO_0000152 iBioSim http://www.ebi.ac.uk/swo/SWO_0000001 software iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. http://www.ebi.ac.uk/swo/SWO_0000158 libSBML http://www.ebi.ac.uk/swo/SWO_1100075 R software LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It provides interfaces for C, C++, C#(.NET), Java, MATLAB, Octave, Perl, Python R and Ruby. LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux. http://www.ebi.ac.uk/swo/SWO_0000159 GNU Octave http://purl.obolibrary.org/obo/IAO_0000025 programming language GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. http://www.ebi.ac.uk/swo/SWO_9000005 licence clause http://purl.obolibrary.org/obo/IAO_0000030 information content entity A licence clause is a component of a licence which defines some aspect of a restriction or conversely permission in how something corresponding to a licence may be legally redistributed, partially redistrubed, extended, modified or otherwise used in some way. http://www.ebi.ac.uk/swo/SWO_9000006 Attribution clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause An Attribution clause is a license clause intended to provide a specified level of recognition of the licensor as the copyright holder of the work. This can take many forms, including the requirement to preserve any copyright notice, attribution statements and the URL (link) to the original work. The attribution requirement thus serves the dual purpose of ensuring that the publisher receives appropriate credit, and that provenance information is kept intact. There are varying strengths of these clauses, from licensors requesting not to be attributed at all to requiring attribution for all uses of the resource. http://www.ebi.ac.uk/swo/SWO_9000007 Derivatives clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause Derivatives clauses are license clauses which state what requirements on derivative resource, if any, are attached to a license. The license for a resource may or may not allow the creation of new resources derived from it. If it is allowed, such usage may be restricted in a variety of ways. http://www.ebi.ac.uk/swo/SWO_9000008 Source code clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause A source code clause is a license clause which states the restrictions placed on the source code for the licensed software, if any. The license for a piece of software may or may not allow access to the source code. If such access is allowed, usage may be restricted in a variety of ways. http://www.ebi.ac.uk/swo/SWO_9000009 Platform clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause A Platform clause is a license clause which states the platform restrictions for the licensed resource, if any. The license for a resource may or may not allow the use of any platform. If it is allowed, such usage may be restricted in a variety of ways. http://www.ebi.ac.uk/swo/SWO_9000010 Number of installations clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform. http://www.ebi.ac.uk/swo/SWO_9000011 Number of users clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause A Number of users clause is a license clause which may limit the number of users a particular licensee may allow to use the resource. http://www.ebi.ac.uk/swo/SWO_9000012 Time clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause A time clause is a license clause which states the restrictions placed on the length of time the licensed resource may be used, if any. The license for a resource may or may not allow access to the resource for an unlimited time. If such access is allowed, usage may be restricted in a variety of ways. http://www.ebi.ac.uk/swo/SWO_9000013 Usage clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause A usage clause is a license clause which states the restrictions placed on how the licensed resource may be used. The license for a resource may restrict how the licensee may use the software. If such access is allowed, usage may be restricted in a variety of ways. http://www.ebi.ac.uk/swo/SWO_9000016 No restrictions on derivatives http://www.ebi.ac.uk/swo/license/SWO_10000038 Derivatives allowed No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created. http://www.ebi.ac.uk/swo/SWO_9000017 Restrictions on derivative software http://www.ebi.ac.uk/swo/license/SWO_10000038 Derivatives allowed Restrictions on derivative software is a derivatives clause which allows the creation of derivatives but which also places some kind of restriction on how derivative software may be created. http://www.ebi.ac.uk/swo/SWO_9000018 Derivatives not allowed http://www.ebi.ac.uk/swo/SWO_9000007 Derivatives clause Derivatives not allowed clauses are derivatives clauses which state that derivative resources are never allowed using the licensed resource. http://www.ebi.ac.uk/swo/SWO_9000019 derivative code same license http://www.ebi.ac.uk/swo/SWO_9000017 Restrictions on derivative software Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license. http://www.ebi.ac.uk/swo/SWO_9000020 Source code available http://www.ebi.ac.uk/swo/SWO_9000008 Source code clause A source code available clause is a source code clause which states that the source code for the licensed software is available to the licensee. However, usage of the source code may or may not be restricted in a variety of ways. http://www.ebi.ac.uk/swo/SWO_9000021 Source code unavailable http://www.ebi.ac.uk/swo/SWO_9000008 Source code clause A source code unavailable clause is a source code clause which states that the source code for the licensed software is not available to the licensee. http://www.ebi.ac.uk/swo/SWO_9000022 Platform restricted http://www.ebi.ac.uk/swo/SWO_9000009 Platform clause Platform restricted is a platform clause which places restrictions on which platform the licensed resource may be installed on. http://www.ebi.ac.uk/swo/SWO_9000023 Platform unrestricted http://www.ebi.ac.uk/swo/SWO_9000009 Platform clause Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the resource may be licensed for. http://www.ebi.ac.uk/swo/SWO_9000024 Number of installations restricted http://www.ebi.ac.uk/swo/SWO_9000010 Number of installations clause A Number of installations restricted clause is a number of installations clause which restricts the number of times the resource may be installed by any given licensee. http://www.ebi.ac.uk/swo/SWO_9000025 Number of installations unrestricted http://www.ebi.ac.uk/swo/SWO_9000010 Number of installations clause A Number of installations unrestricted clause is a number of installations clause which does not restrict the number of times the resource may be installed by any given licensee. http://www.ebi.ac.uk/swo/SWO_9000026 Number of users restricted http://www.ebi.ac.uk/swo/SWO_9000011 Number of users clause A Number of users restricted clause is a number of users clause which restricts the number of users the resource may have for a particular licensee. This may be number of total users, or number of concurrent users. http://www.ebi.ac.uk/swo/SWO_9000027 Number of users unrestricted http://www.ebi.ac.uk/swo/SWO_9000011 Number of users clause A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed resource. http://www.ebi.ac.uk/swo/SWO_9000028 Time for use restricted http://www.ebi.ac.uk/swo/SWO_9000012 Time clause Time for use restricted is a time clause which places restrictions on the length of time the licensed resource may be used. http://www.ebi.ac.uk/swo/SWO_9000029 Time for use unrestricted http://www.ebi.ac.uk/swo/SWO_9000012 Time clause Time for use unrestrictred is a time clause which does not place any restrictions on the length of time the resource may be licensed for. http://www.ebi.ac.uk/swo/SWO_9000030 Usage unrestricted http://www.ebi.ac.uk/swo/SWO_9000013 Usage clause Usage unrestricted is a usage clause which places no restrictions on how the licensed resource may be used. http://www.ebi.ac.uk/swo/SWO_9000031 Usage restricted http://www.ebi.ac.uk/swo/SWO_9000013 Usage clause Usage restricted is a usage clause which places restrictions on how the licensed resource may be used. These restrictions will vary according to the individual license. http://www.ebi.ac.uk/swo/SWO_9000032 Non-commercial use only http://www.ebi.ac.uk/swo/SWO_9000031 Usage restricted Non-commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are not commercial entites. http://www.ebi.ac.uk/swo/SWO_9000033 Academic use only http://www.ebi.ac.uk/swo/SWO_9000031 Usage restricted Academic use only is a usage restricted clause which restricts the use of the licensed resource to academic licensees only. http://www.ebi.ac.uk/swo/SWO_9000034 derivative code linked same license http://www.ebi.ac.uk/swo/SWO_9000017 Restrictions on derivative software Derivative code linked same license is a restrictive derivatives clause where code may only be linked to in derivative software that is released under the same license. http://www.ebi.ac.uk/swo/SWO_9000050 software interface http://purl.obolibrary.org/obo/IAO_0000030 information content entity The mode of interaction with a piece of software. http://www.ebi.ac.uk/swo/algorithm/SWO_4000004 SAEM http://purl.obolibrary.org/obo/IAO_0000064 algorithm A stochastic algorithm for population pharmacology modeling http://www.ebi.ac.uk/swo/algorithm/SWO_4000005 dynamic Bayesian network model http://www.ebi.ac.uk/swo/SWO_1100041 Bayesian Model A Dynamic Bayesian Network model is a Bayesian Network which relates variables to each other over adjacent time steps. http://www.ebi.ac.uk/swo/algorithm/SWO_4000007 Gillespie's Stochastic Simulation Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm Gillespie's Stochastic Simulation Algorithm is an algorithm which generates a statistically correct trajectory (possible solution) of a stochastic equation. It can be used to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power. The algorithm is particularly useful for simulating reactions within cells where the number of reagents typically number in the tens of molecules (or less). Mathematically, it is a variety of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational systems biology http://www.ebi.ac.uk/swo/algorithm/SWO_4000008 Monte Carlo http://purl.obolibrary.org/obo/IAO_0000064 algorithm Monte Carlo is a discrete stochastic simulation algorithm and an estimation procedure algorithm. If it is necessary to know the average value of some random variable and its distribution can not be stated, and if it is possible to take samples from the distribution, we can estimate it by taking the samples, independently, and averaging them. If there are sufficiently enough samples, then the law of large numbers says the average must be close to the true value. The central limit theorem says that the average has a Gaussian distribution around the true value. http://www.ebi.ac.uk/swo/data/SWO_3000052 Interaction data http://purl.obolibrary.org/obo/IAO_0000027 data item A type of data which defines interactions between items in the file. This can be simple pairwise interactions or more complex ones. Used to provide a class of data for software requiring specific types of interaction data as input. http://www.ebi.ac.uk/swo/data/SWO_3000053 Knowledge representation http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A knowledge representation role is a role borne by a data format which utilizes formalisms to make complex systems easier to design and build. Knowledge representation is the field of artificial intelligence devoted to representing information about the world in a form that a computer system can utilize to solve complex tasks. http://www.ebi.ac.uk/swo/data/SWO_3000057 CDF ASCII format http://www.ebi.ac.uk/swo/data/SWO_3000042 ASCII format The CDF ASCII format is an ASCII data format specification created by Affymetrix similar to the Windows INI format. This format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. http://www.ebi.ac.uk/swo/data/SWO_3000058 BAR http://edamontology.org/format_2333 binary format BAR is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined). The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software. http://www.ebi.ac.uk/swo/data/SWO_3000059 CEL ASCII format http://www.ebi.ac.uk/swo/data/SWO_3000042 ASCII format CEL ASCII format is ASCII data format specification created by Affymetrix similar to the Windows INI format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. http://www.ebi.ac.uk/swo/data/SWO_3000060 Affymetrix-compliant data http://purl.obolibrary.org/obo/IAO_0000027 data item Affymetrix-compliant data is data produced in a format compatible with Affymetrix software. This is a defined class where other data classes will be inferred to be members if they have a data format specification which has been published by Affymetrix. http://www.ebi.ac.uk/swo/data/SWO_3000062 FCS3.0 http://www.ebi.ac.uk/swo/data/SWO_3000061 Data File Standard for Flow Cytometry FCS3.0 is version 3.0 of the Data File Standard for Flow Cytometry. It contains a mechanism for handling data sets of 100 megabytes and larger, support for UNICODE text for keyword values, support for cyclic redundancy check (CRC) validation for each data set, a requirement for the inclusion of information describing the method of signal amplification and increased support for the inclusion of time as a measurement parameter. http://www.ebi.ac.uk/swo/data/SWO_3000065 DNA nucleotide sequence http://www.ebi.ac.uk/swo/data/SWO_3000066 biological sequence data A nucleic acid sequence that indicate the order of nucleotides within some DNA. http://www.ebi.ac.uk/swo/data/SWO_3000066 biological sequence data http://purl.obolibrary.org/obo/IAO_0000027 data item Data about primary biological sequence information, such as DNA neucleotide sequences. http://www.ebi.ac.uk/swo/data/SWO_3000067 amino acid protein sequence data http://www.ebi.ac.uk/swo/data/SWO_3000066 biological sequence data Data which contains information about amino acid sequences of proteins. http://www.ebi.ac.uk/swo/data/SWO_3000070 tabix file format http://www.ebi.ac.uk/swo/data/SWO_3000069 sequence feature format Tabix indexes a TAB-delimited genome position file and creates an index file when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. http://www.ebi.ac.uk/swo/data/SWO_3000071 genomedata format http://purl.obolibrary.org/obo/IAO_0000098 data format specification Genomedata provides a way to store and access large-scale functional genomics data in a format which is both space-efficient and allows efficient random-access. Genomedata archives are implemented as one or more HDF5 files, either as single files or as directory archives. HDF5 archives are self describing, like XML, but may also contain more complex structures such contain binary data. http://www.ebi.ac.uk/swo/data/SWO_3000072 BedGraph http://edamontology.org/format_2330 Textual format The bedGraph format is a line-oriented text file format. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line are the track data in four column BED format. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state. http://www.ebi.ac.uk/swo/data/SWO_3000074 MathML 2.0 http://edamontology.org/format_2332 XML MathML 2.0 is an XML format which is a low-level specification for describing mathematics as a basis for machine to machine communication. It is a W3C Recommendation and was released on 21 Feb 2001. A product of the W3C Math working group, it provides a much needed foundation for the inclusion of mathematical expressions in Web pages. http://www.ebi.ac.uk/swo/data/SWO_3000075 FieldML http://edamontology.org/format_2332 XML FieldML is an XML-based language for describing time-varying and spatially-varying fields. The aims of the language design process are to keep the language concise, consistent, intuitive and flexible. http://www.ebi.ac.uk/swo/data/SWO_3000076 WKn http://www.ebi.ac.uk/swo/data/SWO_3000001 spreadsheet format WKn is a collective name for a spreadsheet format created for Lotus 1-2-3. http://www.ebi.ac.uk/swo/interface/SWO_5000006 JSON web service http://www.ebi.ac.uk/swo/interface/SWO_9000051 web service A web service in which calls invoked return JSON. http://www.ebi.ac.uk/swo/license/SWO_10000035 Distribution clause http://www.ebi.ac.uk/swo/SWO_9000005 licence clause Distribution clauses are license clauses which state the requirements on how the licensed resource is redistributed. The license for a resource may or may not allow the redistribution of that resource. If it is allowed, such usage may be restricted in a variety of ways. http://www.ebi.ac.uk/swo/license/SWO_10000036 Distribution restricted http://www.ebi.ac.uk/swo/license/SWO_10000035 Distribution clause Distribution restricted is a distribution clause which places restrictions on how the licensed resource may be distributed by third parties. These restrictions may be complete, e.g. no further redistribution, or partial. http://www.ebi.ac.uk/swo/license/SWO_10000037 Distribution unrestricted http://www.ebi.ac.uk/swo/license/SWO_10000035 Distribution clause Distribution unrestricted is a distribution clause which states that the licensed resource can be redistributed by a third party in whatever manner that party wishes. http://www.ebi.ac.uk/swo/license/SWO_10000038 Derivatives allowed http://www.ebi.ac.uk/swo/SWO_9000007 Derivatives clause Derivatives allowed clauses are derivatives clauses which state that derivative resources are allowed using the licensed resource. Even when allowed, such a clause may or may not restrict the usage of the licensed resource in a variety of ways. http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free License Type http://www.ebi.ac.uk/swo/license/SWO_1000008 Open source software license A licensed is a free license according to GNU if the users have the four essential freedoms: The freedom to run the program, for any purpose (freedom 0). The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this. The freedom to redistribute copies so you can help your neighbor (freedom 2). The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this. A program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so. “Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies. http://www.ebi.ac.uk/swo/license/SWO_1000044 GNU GPL Compatible License Type http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free License Type GNU GPL Compatible License Type is a GNU Project Free License Type which is also compatible with one or more versions of the GNU GPL http://www.ebi.ac.uk/swo/license/SWO_1000045 Copyleft http://www.ebi.ac.uk/swo/SWO_9000019 derivative code same license Copyleft is a derivative code same license clause which says that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. In other words, it requires that all derivative code uses the same license, but further limits the type of license to one which gives everyone the rights to use, modify, and redistribute the program's code, or any program derived from it, but only if the distribution terms are unchanged. To copyleft a program, you first state that it is copyrighted; then the distribution terms described above are added. This makes copyleft a legal instrument ensuring that the code and the freedoms become legally inseparable. http://www.ebi.ac.uk/swo/license/SWO_1000051 Attribution required http://www.ebi.ac.uk/swo/SWO_9000006 Attribution clause Attribution required is an attribution clause which states that attribution of the type specified in the license must be provided whenever the resource is used. http://www.ebi.ac.uk/swo/license/SWO_1000055 Mozilla Public License Version 2.0 http://www.ebi.ac.uk/swo/license/SWO_9000088 MPL MPL v2.0 a free software license as defined by the GNU Project. Section 3.3 provides indirect compatibility between this license and the GNU GPL version 2.0, the GNU LGPL version 2.1, the GNU AGPL version 3.0, and all later versions of those licenses. The MPL allows covered source code to be mixed with other files under a different, even proprietary license. However, code files licensed under the MPL must remain under the MPL and freely available in source form. http://www.ebi.ac.uk/swo/license/SWO_1000057 Artistic License 2.0 http://www.ebi.ac.uk/swo/license/SWO_1000056 Artistic License The Artistic License v 2.0 is a free software license by the definition of the GNU Project and compatible with the GPL thanks to the relicensing option in section 4(c)(ii) (as compared with the Artistic License 1.0). http://www.ebi.ac.uk/swo/license/SWO_1000058 Purchase cost http://www.ebi.ac.uk/swo/SWO_9000005 licence clause Purchase cost is a license clause which states whether there is a cost involved with a particular usage or licensing of a resource. http://www.ebi.ac.uk/swo/license/SWO_1000059 Free http://www.ebi.ac.uk/swo/license/SWO_1000058 Purchase cost Free is a type of purchase cost clause which, when applied, means that there is no cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages are free. http://www.ebi.ac.uk/swo/license/SWO_1000060 Not Free http://www.ebi.ac.uk/swo/license/SWO_1000058 Purchase cost Not Free is a type of purchase cost clause which, when applied, means that there is a cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages incur a purchase cost. http://www.ebi.ac.uk/swo/license/SWO_1000061 free to use license http://www.ebi.ac.uk/swo/SWO_0000002 software license A license which allows any form of usage of the artifact. http://www.ebi.ac.uk/swo/license/SWO_1000066 Attribution not required http://www.ebi.ac.uk/swo/SWO_9000006 Attribution clause Attribution not required is an attribution clause which states that no attribution need be provided whenever the resource is used. http://www.ebi.ac.uk/swo/license/SWO_1000099 FlowRepository Open Access Terms of Use http://www.ebi.ac.uk/swo/license/SWO_1000009 License without restrictions on derivatives The FlowRepository Open Access Terms of Use license allows any individual to access the licensed product (originally the Flow Cytometry Data Repository) for any purpose. There are no restrictions on the use or redistribution of the data associated with this license, though it makes the statement that some data covered may also be included under more restrictive licensing. http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License http://www.ebi.ac.uk/swo/SWO_0000002 software license A vendor-specific license is a license which was, at least originally, created by a specific organization to be used just on the resources created within that organization. This is a hierarchy of convenience rather than of shared philosophy. Many of the licenses have since been taken up by other groups whose licensing requirements matched those of the originating organization. http://www.ebi.ac.uk/swo/license/SWO_1000104 NIDA NIH Data Access Policy http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The NIDA NIH Data Access Policy specifies under what legal requirements NIDA NIH data may be accessed. 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There are also limits on how long records may be stored with the licensee, and how records may be linked. http://www.ebi.ac.uk/swo/license/SWO_1000107 CellFinder Copyright http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The created contents and works provided under this license by CellFinder are subject to the German copyright law. Third-party contributions are marked as such. Reproduction, adaptation, dissemination and any kind of exploitation outside the limits of the copyright require the written consent of the author or creator. Downloads and copies of these pages are only permitted for private, non-commercial use. 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Any redistribution or reproduction of part or all of the contents in any form is prohibited other than the following: you may print or download to a local hard disk extracts for your use only, with a daily limit of 50 webpages; and you may copy the content to individual third parties for their use, but only if you acknowledge the website as the source of the material. You may not, except with our express written permission, distribute or commercially exploit the content. http://www.ebi.ac.uk/swo/license/SWO_1000118 LOINC RELMA Terms of Use http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License LOINC RELMA Terms of Use is a vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. An unlimited number of copies of the licensed material may be used. http://www.ebi.ac.uk/swo/license/SWO_1000119 MIACA Full Copyright http://www.ebi.ac.uk/swo/license/SWO_1000008 Open source software license MIACA Full Copyright is a vendor-specific license which allows the document it references to be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the MIACA Standards Initiative or other organizations, except as needed for the purpose of developing MIACA Standards Initiative Recommendations in which case the procedures for copyrights defined in the MIACA Document process must be followed, or as required to translate it into languages other than English. http://www.ebi.ac.uk/swo/license/SWO_1000120 ORCID MIT-Style License (MIT) http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The ORCID MIT-style license is identical to the MIT License, except for the addition of the following two clauses: 1. "The above license does not apply to the branding or the "look and feel" of the websites located at the orcid.org URL even if elements thereof are contained in the Software."; 2. "Except to provide the copyright notice required above or as allowed under ORCID Inc.'s Trademark Use Policy (available at http://orcid.org, under "Policies"), you may not use the name of ORCID, Inc., ORCID, its marks and logo, to advertise, promote or suggest any affiliation with or endorsement by ORCID, Inc. in connection with your use of the Software.". The MIT License is is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. http://www.ebi.ac.uk/swo/license/SWO_1000121 NIH Genomic Data Sharing Policy http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The NIH Genomic Data Sharing Policy specifies under what legal requirements NIH genomic data may be accessed. Access to human data is through a tiered model involving unrestricted- and controlled-data access mechanisms. Requests for controlled-access data are reviewed by NIH Data Access Committees (DACs). http://www.ebi.ac.uk/swo/license/SWO_1000122 Facebase Data Access Policy http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The Facebase Data Access Policy specifies under what legal requirements Facebase data may be accessed. Non-sensitive data is available for use for all purposes and usages. As consent must be aquired for sensitive (or closed) data, this license only covers the use of the open data (a separate agreement must be entered into for restricted access data). http://www.ebi.ac.uk/swo/license/SWO_1000123 ORCID Terms of Use http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The ORCID Terms of Use is a vendor-specific license for describing how the data in the ORCID resource may be used. ORCID data can be sublicensed, reproduced, stored, transmitted, distributed, publicly performed and publicly displayed for non-commercial and commercial uses. http://www.ebi.ac.uk/swo/license/SWO_1000125 SciCrunch Terms and Conditions http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The SciCrunch Terms and Conditions specifies under what legal requirements SciCrunch data may be accessed. Broadly speaking, the site conforms, both for data and for the site documents themselves, to the CC BY 3.0 license. However, particular details for this resource (other than attribution requirements) are unclear. http://www.ebi.ac.uk/swo/license/SWO_1000126 ProDom Commercial License http://www.ebi.ac.uk/swo/license/SWO_1000137 Fee-Based Commercial License The ProDom Commercial License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes for a fee. Non-commercial use does not require licensing or a fee, and is covered by a separate license. http://www.ebi.ac.uk/swo/license/SWO_1000129 RegenBase Terms of Use http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The RegenBase Terms of Use is a vendor-specific license which requires attribution and which does not meet the requirements for open source code, as there is a statement saying that the user will NOT translate, reverse engineer, decompile or disassemble the SYSTEM, or disclose the SYSTEM or any underlying information or technology to any third party. http://www.ebi.ac.uk/swo/license/SWO_1000130 SABIO-RK Non-Commercial Purpose License http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The SABIO-RK Non-Commercial Purpose License covers use of the Database for Non-Commercial Purpose only, and appropriate attribution must be given. Non-Commercial Purpose means the use of the Database solely for internal non-commercial research and academic purposes. As consent must be aquired for commercial use, a separate agreement must be entered into for commercial use and is not covered here. http://www.ebi.ac.uk/swo/license/SWO_1000131 Terms of Use for EMBL-EBI Services http://www.ebi.ac.uk/swo/license/SWO_1000009 License without restrictions on derivatives The Terms of Use for EMBL-EBI Services reflect EMBL-EBI’s commitment to OpenScience through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. They impose no additional constraints on the use of the contributed data than those provided by the data owner.
EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated on the appropriate web page. http://www.ebi.ac.uk/swo/license/SWO_1000133 UMLS Metathesaurus License http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The UMLS Metathesaurus License is a vendor-specific license which allows redistribution (as part of a larger computer application) as long as the original data is attributed correctly and a summary of data use provided each year. There is no cost to use the service, and may be used both commercially and non-commercially. Users must inform the resource if it is redistributed within a computer application. http://www.ebi.ac.uk/swo/license/SWO_1000134 MHAS Data Policy http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The MHAS Data Policy is a vendor-specific license which requires that users attribute the data properly. The data is accessible free of charge to all commercial and non-commercial users. http://www.ebi.ac.uk/swo/license/SWO_1000136 Commercial use only http://www.ebi.ac.uk/swo/SWO_9000031 Usage restricted Commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are commercial entites. http://www.ebi.ac.uk/swo/license/SWO_1000137 Fee-Based Commercial License http://www.ebi.ac.uk/swo/SWO_0000002 software license Fee-Based Commercial License is a license which, among its license clauses, states that commercial entities may use the resource for a fee. http://www.ebi.ac.uk/swo/license/SWO_1000138 BRENDA License http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The BRENDA License is a vendor-specific license which allows access to the official website and its data free of charge. Any inclusion of BRENDA components into other data bases, or redistribution of BRENDA requires a license. To obtain commercial in-house versions please contact our distributor Biobase GmbH ( http://www.biobase-international.com). In-house versions for academic users are available from Enzymeta GmbH (http://www.enzymeta.de). The copyright of the printed version is held by Springer publishers. Users of the website may retrieve a copy of the data but must not alter the BRENDA data or charge money for a copy of it, and must not distribute any BRENDA data without prior permission of the copyright holder. As there are separate licenses for in-house versions of BRENDA, please note that this license only describes the website-accessible version of BRENDA. http://www.ebi.ac.uk/swo/license/SWO_1000140 Non-Commercial No-Fee License http://www.ebi.ac.uk/swo/SWO_0000002 software license Non-Commercial No-Fee License is a license which, among its license clauses, states that non-commercial entities may use the resource without a purchase or usage cost. http://www.ebi.ac.uk/swo/license/SWO_1000141 DrugBank Academic License http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License DrugBank is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes (including internal use) requires a license. We ask that users who download significant portions of the database cite the DrugBank paper in any resulting publications. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use). http://www.ebi.ac.uk/swo/license/SWO_1000142 UCSC Genome Browser Commercial Software License http://www.ebi.ac.uk/swo/license/SWO_1000137 Fee-Based Commercial License The UCSC Genome Browser Commercial Software License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes under specific restrictions for a fee. The licensee shall not have the right to create Derivative Works of the Licensed Products, and the Licensee shall not have the right to sublicense, sell, transfer, or assign the Licensed Products. Non-commercial use does not require licensing or a fee, and is covered by a separate license. http://www.ebi.ac.uk/swo/license/SWO_1000143 Permission required for commercial use http://www.ebi.ac.uk/swo/license/SWO_1000136 Commercial use only Permission required for commercial use is a clause which restricts the use of the licensed resource only to licensees who are commercial entites which have received explicit permission in the manner stipulated by the resource. http://www.ebi.ac.uk/swo/license/SWO_1000144 Permission required for derivative work http://www.ebi.ac.uk/swo/SWO_9000017 Restrictions on derivative software Permission required for derivative work is a clause which restricts the production of derivative work based on the licensed resource only to licensees who have received explicit permission in the manner stipulated by the resource. http://www.ebi.ac.uk/swo/license/SWO_1000145 Xenbase Academic Conditions of Use http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License Data are to be used only for purposes of research and education. Commercial use is prohibited without written permission from Xenbase. The contributor(s) of unpublished data should be explicitly acknowledged in any publication that incorporates, or is based in part or entirely on these data. Xenbase should be explicitly acknowledged when data used in any publication, has been in part or solely derived from analysis of data from this website. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use). http://www.ebi.ac.uk/swo/license/SWO_1000146 RIKEN Copyright http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The RIKEN copyright is a vendor-specific license which states that all text, photographs, diagrams, and other materials on their website are copyrighted by RIKEN unless explicitly specified otherwise on the website. It is prohibited to use, reproduce, or modify any of the material without RIKEN's permission. http://www.ebi.ac.uk/swo/license/SWO_1000147 Design Science License http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free License Type The Design Science License is a license intended to be a general "copyleft" that can be applied to any kind of work that has protection under copyright. This license states those certain conditions under which a work published under its terms may be copied, distributed, and modified. Unlike other open source licenses, the DSL was intended to be used on any type of copyrightable work, including documentation and source code. It was the first "generalized copyleft" license. This is a free and copyleft license meant for general data. THe GNU Project does not recommend it for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL; however, they consider it appropriate for other kinds of data. The DSL was written by Michael Stutz. The DSL came out in the 1990s, before the formation of the Creative Commons. According to Wikipedia, once the Creative Commons arrived, Stutz considered the DSL experiment "over" and no longer recommended its use. http://www.ebi.ac.uk/swo/license/SWO_1000148 University of Concordia Terms of Use http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The University of Concordia Terms of Use is a vendor-specific license which states that no document appearing on this website or any other website owned, operated or controlled by Concordia may be copied, sold, reproduced, republished, downloaded, posted, transmitted or distributed by any means with the exception of downloading or printing the contents of the site for personal, non-commercial use. This use must bear in mind that Concordia reserves its copyright and its rights to exclusivity over the material. http://www.ebi.ac.uk/swo/license/SWO_1000149 OME Software Conditons of Use http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License All OME formats and software are freely available, and all OMERO and Bio-Formats source code is available under GNU public "copyleft" licenses or through commercial license from Glencoe Software. FLIMfit is also now available under a GNU public "copyleft" license. For questions about the GNU license refer to the Frequently Asked Questions about the GNU Licenses page. Bio-Formats - under the terms of the GNU public "copyleft" license, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive BSD-2 license which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the supported formats table. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from Glencoe Software; please contact them at bioformats@glencoesoftware.com to discuss your requirements. The core OME Model Schema files (.XSD) use the Creative Commons Attribution 4.0 International License, and as such you are free to share or adapt them as long as you attribute the OME consortium as follows; "This work is derived in part from the OME specification. Copyright (C) 2002-2016 Open Microscopy Environment". See further information about using OME-XML in your work. This website is also covered by the Creative Commons Attribution 4.0 International License - you are free to share or adapt content as long as you credit the Open Microscopy Environment. The exception to this is the screenshots and videos which can only be used for non-commercial purposes, see Attributions below. http://www.ebi.ac.uk/swo/license/SWO_1000150 ImmPort Conditions of Use http://www.ebi.ac.uk/swo/license/SWO_1000103 Vendor-specific License The ImmPort Conditions of Use is a vendor-specific license which allows the use of ImmPort data for any legal purpose except for those prohibited elsewhere in this agreement. There are very few prohibitions, and no requirement for attribution. http://www.ebi.ac.uk/swo/license/SWO_9000059 Distribution with notices http://www.ebi.ac.uk/swo/license/SWO_10000035 Distribution clause Distribution with notices is a distribution clause in which distribution is unrestricted, except that all distributions must retain certain licence information (e.g., copyright notices). http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status http://purl.obolibrary.org/obo/IAO_0000030 information content entity Development status is an information content entity which indicates the maturity of a software entity within the context of the software life cycle. http://www.ebi.ac.uk/swo/maturity/SWO_9000062 alpha http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status Alpha is a development status which is applied to software by the developer/publisher during initial development and testing. Software designated alpha is commonly unstable and prone to crashing. It may or may not be released publicly. http://www.ebi.ac.uk/swo/maturity/SWO_9000063 beta http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status Beta is a development status which is generally applied to software by the developer/publisher once the majority of features have been implemented, but when the software may still contain bugs or cause crashes or data loss. Software designated beta is often released publicly, either on a general release or to a specific subset of users called beta testers. http://www.ebi.ac.uk/swo/maturity/SWO_9000064 Release candidate http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status A release candidate (RC) is a beta version with potential to be a final product, which is ready to release unless significant bugs emerge. http://www.ebi.ac.uk/swo/maturity/SWO_9000066 Obsolete http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status Sofware is no longer being supplied by the developers/publishers http://www.ebi.ac.uk/swo/maturity/SWO_9000069 Superseded http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status An updated version of the software is available. http://www.ebi.ac.uk/swo/maturity/SWO_9000071 First release http://www.ebi.ac.uk/swo/maturity/SWO_9000065 Live The first release of a piece of software. A first release does not imply any particular levels of maturity other than is this is the first instance of this software to be considered released. http://www.ebi.ac.uk/swo/maturity/SWO_9000072 Latest release http://www.ebi.ac.uk/swo/maturity/SWO_9000065 Live The latest release of a piece of software. This does not imply any levels of maturity other than indicating this is the most recent release. http://www.ebi.ac.uk/swo/maturity/SWO_9000073 Maintained http://www.ebi.ac.uk/swo/maturity/SWO_9000061 Development status Software has developers actively maintaining it (fixing bugs) http://www.ebi.ac.uk/swo/objective/SWO_4000009 laboratory information management http://purl.obolibrary.org/obo/OBI_0200000 data transformation Manage Laboratory information such is commonly performed by LIMS software. http://www.ebi.ac.uk/swo/objective/SWO_4000010 manage computer operations http://purl.obolibrary.org/obo/OBI_0200000 data transformation the objective of performing the actions of an operation system such as managing the software running a computer and the interactions with the system resources and hardware. http://www.ebi.ac.uk/swo/objective/SWO_4000011 text editing http://purl.obolibrary.org/obo/OBI_0200000 data transformation Text editing is the objective of editing plain text files. http://www.ebi.ac.uk/swo/objective/SWO_7000005 averaging http://purl.obolibrary.org/obo/OBI_0200000 data transformation An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. http://www.ebi.ac.uk/swo/objective/SWO_7000006 center calculation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. http://www.ebi.ac.uk/swo/objective/SWO_7000007 class discovery http://purl.obolibrary.org/obo/OBI_0200000 data transformation A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. http://www.ebi.ac.uk/swo/objective/SWO_7000008 class prediction http://purl.obolibrary.org/obo/OBI_0200000 data transformation A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. http://www.ebi.ac.uk/swo/objective/SWO_7000010 correction http://purl.obolibrary.org/obo/OBI_0200000 data transformation A correction is where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself. http://www.ebi.ac.uk/swo/objective/SWO_7000011 background correction http://www.ebi.ac.uk/swo/objective/SWO_7000010 correction A background correction is where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. http://www.ebi.ac.uk/swo/objective/SWO_7000012 error correction http://www.ebi.ac.uk/swo/objective/SWO_7000010 correction An error correction is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. http://www.ebi.ac.uk/swo/objective/SWO_7000014 curve fitting http://purl.obolibrary.org/obo/OBI_0200000 data transformation curve fitting is a data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. http://www.ebi.ac.uk/swo/objective/SWO_7000015 data normalization http://purl.obolibrary.org/obo/OBI_0200000 data transformation A normalization is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. http://www.ebi.ac.uk/swo/objective/SWO_7000016 decision tree induction http://purl.obolibrary.org/obo/OBI_0200000 data transformation A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. http://www.ebi.ac.uk/swo/objective/SWO_7000017 descriptive statistical calculation http://purl.obolibrary.org/obo/OBI_0200000 data transformation A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. http://www.ebi.ac.uk/swo/objective/SWO_7000019 feature extraction http://purl.obolibrary.org/obo/OBI_0200000 data transformation A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. http://www.ebi.ac.uk/swo/organization/SWO_9000055 software publishing process http://purl.obolibrary.org/obo/BFO_0000015 process The process of publishing software. Typically this process involves a software publisher performing acts such as licensing, marketing, publicising and/or providing support for a product. http://www.ebi.ac.uk/swo/organization/SWO_9000056 software development http://purl.obolibrary.org/obo/OBI_0200000 data transformation The process of developing software, typically involving the design, implementation and testing of software. http://www.ebi.ac.uk/swo/SWO_1100133 Stavrox http://www.ebi.ac.uk/swo/SWO_0000001 software StavroX software identifies cross-linked peptides. http://www.ebi.ac.uk/swo/SWO_1100134 ProteomicsTools http://www.ebi.ac.uk/swo/SWO_0000001 software ProteomicsTools software suite contains a bunch of tools used in proteomics research, including identification, result parsing, quantification, and modification. http://www.ebi.ac.uk/swo/SWO_1100135 Chromeleon http://www.ebi.ac.uk/swo/SWO_0000001 software Chromeleon software provides full integration of Thermo Scientific gas chromatography (GC-MS/MS), liquid chromatography (LC-MS/MS), and ion chromatography (IC-MS) instruments. http://www.ebi.ac.uk/swo/SWO_1100136 AnalyzerPro http://www.ebi.ac.uk/swo/SWO_0000001 software AnalyzerPro​ is a productivity software application for both low and high resolution LC-MS and GC-MS data with support for multiple vendors’ data. This comprehensive post-processing utility provides optimized workflows for sample-to-sample comparison, target component analysis, quantitation and library searching for data generated from any LC-MS and GC-MS platform http://www.ebi.ac.uk/swo/SWO_1100137 SWATH Software http://www.ebi.ac.uk/swo/SWO_0000001 software SWATH is the only data independent acquisition (DIA) technique that allows comprehensive detection and quantitation of virtually every detectable compound in a sample (MS/MSALL). This provides confidence in your quantitative results and virtually eliminates the risk of missing a critical component. SWATH Acquisition strategy can only be achieved through the power and speed of SCIEX TripleTOF® and QTOF technology. http://www.ebi.ac.uk/swo/SWO_1100138 Supernovo http://www.ebi.ac.uk/swo/SWO_0000001 software SupernovoTM is a unique, hands-free solution for end-to-end de novo sequencing of monoclonal antibodies (mAbs), enabling high throughput protein discovery. http://www.ebi.ac.uk/swo/SWO_1100139 PEAKS DB http://www.ebi.ac.uk/swo/SWO_0000001 software Protein Identification Software including an LC-MS/MS search engine, modification search and PTM profiling, sequence variant search, integration with de novo sequencing, and support for all types of fragment ions. http://www.ebi.ac.uk/swo/SWO_1100140 HTSeq http://www.ebi.ac.uk/swo/SWO_0000001 software HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. http://www.ebi.ac.uk/swo/SWO_1100141 RNA-SeQC http://www.ebi.ac.uk/swo/SWO_0000001 software RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis. http://www.ebi.ac.uk/swo/SWO_1100142 RSeQC http://www.ebi.ac.uk/swo/SWO_0000001 software RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. http://www.ebi.ac.uk/swo/SWO_1100143 SAMtools http://www.ebi.ac.uk/swo/SWO_0000001 software SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. http://www.ebi.ac.uk/swo/SWO_1100144 FastQC http://www.ebi.ac.uk/swo/SWO_0000001 software FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. http://www.ebi.ac.uk/swo/SWO_1100145 CutAdapt http://www.ebi.ac.uk/swo/SWO_0000001 software Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. http://purl.obolibrary.org/obo/GO_0016301 kinase activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. http://edamontology.org/format_1665 Taverna workflow format http://edamontology.org/format_2332 XML Format of Taverna workflows. http://edamontology.org/format_2331 HTML http://www.ebi.ac.uk/swo/data/SWO_3000013 web page specification html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web. http://www.ebi.ac.uk/swo/SWO_0000002 software license http://purl.obolibrary.org/obo/IAO_0000030 information content entity A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence. http://www.ebi.ac.uk/swo/SWO_0000008 Racket http://purl.obolibrary.org/obo/IAO_0000025 programming language Racket is a Scheme-based language interpreter and programming environment http://www.ebi.ac.uk/swo/SWO_0000118 Python http://purl.obolibrary.org/obo/IAO_0000025 programming language Python is a widely used general-purpose, high-level programming language. Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C. The language provides constructs intended to enable clear programs on both a small and large scale.Python supports multiple programming paradigms, including object-oriented, imperative and functional programming or procedural styles. http://www.ebi.ac.uk/swo/data/SWO_3000001 spreadsheet format http://purl.obolibrary.org/obo/IAO_0000098 data format specification A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered. http://www.ebi.ac.uk/swo/data/SWO_3000002 XLS spreadsheet http://www.ebi.ac.uk/swo/data/SWO_3000001 spreadsheet format A spreadsheet data format designed for Microsoft Excel. http://www.ebi.ac.uk/swo/data/SWO_3000003 XML spreadsheet http://www.ebi.ac.uk/swo/data/SWO_3000001 spreadsheet format A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity. http://www.ebi.ac.uk/swo/data/SWO_3000006 RDF http://purl.obolibrary.org/obo/IAO_0000098 data format specification The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web. http://www.ebi.ac.uk/swo/data/SWO_3000007 RDF-XML http://www.ebi.ac.uk/swo/data/SWO_3000006 RDF A serialisation of RDF into an XML format. http://www.ebi.ac.uk/swo/data/SWO_3000009 DWG http://www.ebi.ac.uk/swo/data/SWO_3000008 image format DWG ("drawing") is a binary file format used for storing two and three dimensional design data and metadata http://www.ebi.ac.uk/swo/data/SWO_3000010 DXF http://www.ebi.ac.uk/swo/data/SWO_3000008 image format DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs. http://www.ebi.ac.uk/swo/data/SWO_3000011 BMP http://www.ebi.ac.uk/swo/data/SWO_3000020 raster image format The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter). http://www.ebi.ac.uk/swo/data/SWO_3000012 CGM http://www.ebi.ac.uk/swo/data/SWO_3000020 raster image format Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632. http://www.ebi.ac.uk/swo/data/SWO_3000020 raster image format http://www.ebi.ac.uk/swo/data/SWO_3000008 image format A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel. http://www.ebi.ac.uk/swo/data/SWO_3000021 vector image format http://www.ebi.ac.uk/swo/data/SWO_3000008 image format A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering. http://www.ebi.ac.uk/swo/data/SWO_3000024 PostScript http://www.ebi.ac.uk/swo/data/SWO_3000014 document exchange format PostScript is a format used for describing documents. http://www.ebi.ac.uk/swo/data/SWO_3000026 outline document format http://purl.obolibrary.org/obo/IAO_0000098 data format specification A format specification for data used or produced by outliner software http://www.ebi.ac.uk/swo/data/SWO_3000027 OmniOutline format http://www.ebi.ac.uk/swo/data/SWO_3000026 outline document format A proprietary format for documents created and edited using OmniOutliner outliner software, http://www.ebi.ac.uk/swo/data/SWO_3000029 JPEG 2000 http://www.ebi.ac.uk/swo/data/SWO_3000020 raster image format JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia] http://www.ebi.ac.uk/swo/data/SWO_3000032 Microsoft Word doc http://www.ebi.ac.uk/swo/data/SWO_3000030 word processing document format A file format for word processing documents for Microsoft Word. http://www.ebi.ac.uk/swo/data/SWO_3000034 .java file http://www.ebi.ac.uk/swo/data/SWO_3000033 programming language format A source code file format which is specified to be used with the Java programming language. http://www.ebi.ac.uk/swo/data/SWO_3000035 .class file http://www.ebi.ac.uk/swo/data/SWO_3000033 programming language format A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine. http://www.ebi.ac.uk/swo/data/SWO_3000038 OWL-XML http://edamontology.org/format_2332 XML The Web Ontology Language (OWL) in XML serialization http://www.ebi.ac.uk/swo/data/SWO_3000039 OWL2-XML http://edamontology.org/format_2332 XML Web Ontology Language version 2 in XML Serialization http://www.ebi.ac.uk/swo/data/SWO_3000046 tab delimited file format http://www.ebi.ac.uk/swo/data/SWO_3000043 plain text file format Tab delimited file format is a plain text file format where each field value of a record is separated from the next by a tab stop character. http://www.ebi.ac.uk/swo/data/SWO_3000049 SIF http://edamontology.org/format_2330 Textual format SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces). http://www.ebi.ac.uk/swo/data/SWO_3000050 GML http://edamontology.org/format_2332 XML GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages http://www.ebi.ac.uk/swo/data/SWO_3000051 XGMML http://edamontology.org/format_2332 XML XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML. http://www.ebi.ac.uk/swo/license/SWO_1000005 Apache License Version 2.0 http://www.ebi.ac.uk/swo/license/SWO_1000009 License without restrictions on derivatives This is a free software license under the definition of "free" by the GNU Project, and is compatible with version 3 of the GNU GPL. http://www.ebi.ac.uk/swo/license/SWO_9000082 Artistic License 1.0 http://www.ebi.ac.uk/swo/license/SWO_1000056 Artistic License The Artistic License v1.0 is not considered a free software license by the definition of the GNU Project because it is too vague; some passages are "too clever for their own good", and their meaning is not clear. The GNU Project recommends that it is not used except as part of the disjunctive license of Perl. http://purl.obolibrary.org/obo/OBI_0002205 histologic grade according to AJCC 7th edition http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. http://purl.obolibrary.org/obo/OBI_0002215 histologic grade for ovarian tumor http://purl.obolibrary.org/obo/OBI_0001930 categorical value specification A categorical value specification that is a histologic grade assigned to a ovarian tumor. http://purl.obolibrary.org/obo/OBI_0002216 histologic grade for ovarian tumor according to a two-tier grading system http://purl.obolibrary.org/obo/OBI_0002215 histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. http://purl.obolibrary.org/obo/OBI_0002219 histologic grade for ovarian tumor according to the World Health Organization http://purl.obolibrary.org/obo/OBI_0002215 histologic grade for ovarian tumor A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). http://www.ontodm.com/OntoDM-core/OntoDM_419460 single generalization specification http://kt.ijs.si/panovp/OntoDM#OntoDM_000034 generalization specification A single generalization specification is a generalization specification and denotes a type of generalization that is produced by a single generalization data mining algorithm. This algorithm produces only one generalization at its output. http://www.ebi.ac.uk/swo/SWO_0000035 'AnnotationDbi' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides user interface and database connection code for annotation data packages using SQLite data storage. http://www.ebi.ac.uk/swo/SWO_0000037 Applied Biosystems 1700 Expression Array System Software http://www.ebi.ac.uk/swo/SWO_0000001 software Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are: Sensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA. Content: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated. Pipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results. http://www.ebi.ac.uk/swo/SWO_0000040 ArrayNorm http://www.ebi.ac.uk/swo/SWO_0000001 software ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis. http://www.ebi.ac.uk/swo/SWO_0000041 'ArrayTools' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. http://www.ebi.ac.uk/swo/SWO_0000042 ArrayVision http://www.ebi.ac.uk/swo/SWO_0000001 software This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting. http://www.ebi.ac.uk/swo/SWO_0000048 BAC http://www.ebi.ac.uk/swo/SWO_1100075 R software This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments http://www.ebi.ac.uk/swo/SWO_0000049 Binning clustering method http://purl.obolibrary.org/obo/IAO_0000064 algorithm binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory eciency by avoiding the calculation of an all-against-all distance matrix. http://www.ebi.ac.uk/swo/SWO_0000084 CEL binary format http://edamontology.org/format_2333 binary format CEL binary format is a binary data format specification created by Affymetrix where values are stored in little-endian format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. http://www.ebi.ac.uk/swo/SWO_0000163 GGtools http://www.ebi.ac.uk/swo/SWO_1100075 R software This package deals with hapmap SNP reports, GWAS, etc. http://www.ebi.ac.uk/swo/SWO_0000164 GLAD http://www.ebi.ac.uk/swo/SWO_1100075 R software Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified. http://www.ebi.ac.uk/swo/SWO_0000166 GLEAMS software http://www.ebi.ac.uk/swo/SWO_0000001 software Microarray image quantification is performed using GLEAMS software http://www.ebi.ac.uk/swo/SWO_0000168 GOstats http://www.ebi.ac.uk/swo/SWO_1100075 R software A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations http://www.ebi.ac.uk/swo/SWO_0000170 GSEABase http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). http://www.ebi.ac.uk/swo/SWO_0000171 GSEAlm http://www.ebi.ac.uk/swo/SWO_1100075 R software Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. http://www.ebi.ac.uk/swo/SWO_0000175 GeneData Expressionist Analyst v4.0.5 http://www.ebi.ac.uk/swo/SWO_0000001 software Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data. http://www.ebi.ac.uk/swo/SWO_0000188 GeneR http://www.ebi.ac.uk/swo/SWO_1100075 R software Package manipulating nucleotidic sequences (Embl, Fasta, GenBank) http://www.ebi.ac.uk/swo/SWO_0000189 GeneRegionScan http://www.ebi.ac.uk/swo/SWO_1100075 R software A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data http://www.ebi.ac.uk/swo/SWO_0000190 GeneRfold http://www.ebi.ac.uk/swo/SWO_1100075 R software Package manipulating sequences with fold routines http://www.ebi.ac.uk/swo/SWO_0000191 GeneSelectMMD http://www.ebi.ac.uk/swo/SWO_1100075 R software Gene selection based on a mixture of marginal distributions http://www.ebi.ac.uk/swo/SWO_0000192 GeneSelector http://www.ebi.ac.uk/swo/SWO_1100075 R software The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. http://www.ebi.ac.uk/swo/SWO_0000193 GeneSpring http://www.ebi.ac.uk/swo/SWO_1100075 R software Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects http://www.ebi.ac.uk/swo/SWO_0000195 GeneTac Analyser http://www.ebi.ac.uk/swo/SWO_0000001 software Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 16 capillaries operating in parallel, offers high-quality data and efficient sample processing http://www.ebi.ac.uk/swo/SWO_0000196 GeneTraffic http://www.ebi.ac.uk/swo/SWO_1100075 R software Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw) http://www.ebi.ac.uk/swo/SWO_0000201 GeneticsBase http://www.ebi.ac.uk/swo/SWO_1100075 R software This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions. http://www.ebi.ac.uk/swo/SWO_0000202 GeneticsDesign http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains functions useful for designing genetics studies, including power and sample-size calculations. http://www.ebi.ac.uk/swo/SWO_0000203 GeneticsPed http://www.ebi.ac.uk/swo/SWO_1100075 R software Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable http://www.ebi.ac.uk/swo/SWO_0000205 GenomeGraphs http://www.ebi.ac.uk/swo/SWO_1100075 R software Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system. http://www.ebi.ac.uk/swo/SWO_0000206 GlobalAncova http://www.ebi.ac.uk/swo/SWO_1100075 R software GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. http://www.ebi.ac.uk/swo/SWO_0000207 GOSemSim http://www.ebi.ac.uk/swo/SWO_1100075 R software Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast. http://www.ebi.ac.uk/swo/SWO_0000208 GraphAT http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions and data used in Balasubramanian, et al. (2004) http://www.ebi.ac.uk/swo/SWO_0000209 GraphAlignment http://www.ebi.ac.uk/swo/SWO_1100075 R software Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. http://www.ebi.ac.uk/swo/SWO_0000210 GridGrinder http://www.ebi.ac.uk/swo/SWO_0000001 software Software for microarray image analysis. http://www.ebi.ac.uk/swo/SWO_0000213 HELP http://www.ebi.ac.uk/swo/SWO_1100075 R software The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications http://www.ebi.ac.uk/swo/SWO_0000214 HEM http://www.ebi.ac.uk/swo/SWO_1100075 R software This package fits heterogeneous error models for analysis of microarray data http://www.ebi.ac.uk/swo/SWO_0000219 Hidden Variable Dynamic Modelling HVDM) http://purl.obolibrary.org/obo/IAO_0000064 algorithm Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets. http://www.ebi.ac.uk/swo/SWO_0000222 Harshlight http://www.ebi.ac.uk/swo/SWO_1100075 R software The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem. http://www.ebi.ac.uk/swo/SWO_0000224 Heatplus http://www.ebi.ac.uk/swo/SWO_1100075 R software Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display. http://www.ebi.ac.uk/swo/SWO_0000225 HilbertVis http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions to visualize long vectors of integer data by means of Hilbert curves http://www.ebi.ac.uk/swo/SWO_0000226 HilbertVisGUI http://www.ebi.ac.uk/swo/SWO_1100075 R software An interactive tool to visualize long vectors of integer data by means of Hilbert curves http://www.ebi.ac.uk/swo/SWO_0000230 IRanges http://www.ebi.ac.uk/swo/SWO_1100075 R software The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions. http://www.ebi.ac.uk/swo/SWO_0000231 ITALICS http://www.ebi.ac.uk/swo/SWO_1100075 R software A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set http://www.ebi.ac.uk/swo/SWO_0000241 Initial microarray data processing (data filtering, local normalisation and quality control) http://www.ebi.ac.uk/swo/SWO_0000001 software These scripts are for primer design and initial microarray data processing and are available as .zip files: http://www.ebi.ac.uk/swo/SWO_0000245 Jaguar http://www.ebi.ac.uk/swo/SWO_0000001 software Image analysis software http://www.ebi.ac.uk/swo/SWO_0000246 KCsmart http://www.ebi.ac.uk/swo/SWO_1100075 R software Multi sample aCGH analysis package using kernel convolution http://www.ebi.ac.uk/swo/SWO_0000247 KEGGSOAP http://www.ebi.ac.uk/swo/SWO_1100075 R software A package that provides a client interface to the KEGG SOAP server http://www.ebi.ac.uk/swo/SWO_0000248 KEGGgraph http://www.ebi.ac.uk/swo/SWO_1100075 R software KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. http://www.ebi.ac.uk/swo/SWO_0000251 Kolmogorov Smirnov rank-sum based algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm KS measures how biased the ranks of a subset of items are among the ranks of the entire set http://www.ebi.ac.uk/swo/SWO_0000252 LBE http://www.ebi.ac.uk/swo/SWO_1100075 R software LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. http://www.ebi.ac.uk/swo/SWO_0000254 LMGene http://www.ebi.ac.uk/swo/SWO_1100075 R software LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package http://www.ebi.ac.uk/swo/SWO_0000258 LPE http://www.ebi.ac.uk/swo/SWO_1100075 R software This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. http://www.ebi.ac.uk/swo/SWO_0000259 LPEadj http://www.ebi.ac.uk/swo/SWO_1100075 R software Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment. http://www.ebi.ac.uk/swo/SWO_0000260 publisher role http://purl.obolibrary.org/obo/BFO_0000023 role A publisher role is a role borne by an organization or individual in which they are responsible for making software available to a particular consumer group. Such organizations or individuals do need to be involved in the development of the software. http://www.ebi.ac.uk/swo/SWO_0000266 MAANOVA v1.2 package for MATLAB http://www.ebi.ac.uk/swo/SWO_0000001 software Tools for analyzing Micro Array experiments http://www.ebi.ac.uk/swo/SWO_0000269 MANOR http://www.ebi.ac.uk/swo/SWO_1100075 R software We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. http://www.ebi.ac.uk/swo/SWO_0000278 MCR algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples. http://www.ebi.ac.uk/swo/SWO_0000279 MCRestimate http://www.ebi.ac.uk/swo/SWO_1100075 R software This package includes a function for combining preprocessing and classification methods to calculate misclassification errors http://www.ebi.ac.uk/swo/SWO_0000280 MEDME http://www.ebi.ac.uk/swo/SWO_1100075 R software MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments http://www.ebi.ac.uk/swo/SWO_0000283 MLInterfaces http://www.ebi.ac.uk/swo/SWO_1100075 R software Uniform interfaces to machine learning code for data in Bioconductor containers http://www.ebi.ac.uk/swo/SWO_0000284 MMD http://purl.obolibrary.org/obo/IAO_0000064 algorithm MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes), http://www.ebi.ac.uk/swo/SWO_0000285 MVCClass http://www.ebi.ac.uk/swo/SWO_1100075 R software Creates classes used in model-view-controller (MVC) design http://www.ebi.ac.uk/swo/SWO_0000288 MantelCorr http://www.ebi.ac.uk/swo/SWO_1100075 R software Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data) http://www.ebi.ac.uk/swo/SWO_0000289 MassSpecWavelet http://www.ebi.ac.uk/swo/SWO_1100075 R software Processing Mass Spectrometry spectrum by using wavelet based algorithm http://www.ebi.ac.uk/swo/SWO_0000292 MeasurementError.cor http://www.ebi.ac.uk/swo/SWO_1100075 R software Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation http://www.ebi.ac.uk/swo/SWO_0000293 MergeMaid http://www.ebi.ac.uk/swo/SWO_1100075 R software The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival. http://www.ebi.ac.uk/swo/SWO_0000294 Mfuzz http://www.ebi.ac.uk/swo/SWO_1100075 R software Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface) http://www.ebi.ac.uk/swo/SWO_0000295 MiPP http://www.ebi.ac.uk/swo/SWO_1100075 R software This package finds optimal sets of genes that seperate samples into two or more classes. http://www.ebi.ac.uk/swo/SWO_0000305 Nested Effects Models http://purl.obolibrary.org/obo/IAO_0000064 algorithm This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing http://www.ebi.ac.uk/swo/SWO_0000307 OCplus http://www.ebi.ac.uk/swo/SWO_1100075 R software This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). http://www.ebi.ac.uk/swo/SWO_0000308 OLIN http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data http://www.ebi.ac.uk/swo/SWO_0000309 OLINgui http://www.ebi.ac.uk/swo/SWO_1100075 R software Graphical user interface for the OLIN package http://www.ebi.ac.uk/swo/SWO_0000310 Optiquant http://www.ebi.ac.uk/swo/SWO_0000001 software Computer software for image acquisition, analysis and reporting, for use in the life sciences http://www.ebi.ac.uk/swo/SWO_0000311 OrderedList http://www.ebi.ac.uk/swo/SWO_1100075 R software Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. http://www.ebi.ac.uk/swo/SWO_0000312 OutlierD http://www.ebi.ac.uk/swo/SWO_1100075 R software This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data. http://www.ebi.ac.uk/swo/SWO_0000314 PAnnBuilder http://www.ebi.ac.uk/swo/SWO_1100075 R software Processing annotation data from public data repositories and building annoation data packages. http://www.ebi.ac.uk/swo/SWO_0000316 PCpheno http://www.ebi.ac.uk/swo/SWO_1100075 R software Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways. http://www.ebi.ac.uk/swo/SWO_0000317 PGSEA http://www.ebi.ac.uk/swo/SWO_1100075 R software Parametric Analysis of Gene Set Enrichment http://www.ebi.ac.uk/swo/SWO_0000318 'PLM' http://purl.obolibrary.org/obo/IAO_0000064 algorithm it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis http://www.ebi.ac.uk/swo/SWO_0000319 PLPE http://www.ebi.ac.uk/swo/SWO_1100075 R software This package performs tests for paired high-throughput data. http://www.ebi.ac.uk/swo/SWO_0000322 PROcess http://www.ebi.ac.uk/swo/SWO_1100075 R software A package for processing protein mass spectrometry data. http://www.ebi.ac.uk/swo/SWO_0000323 Propagation of uncertainty in microarray analysis http://purl.obolibrary.org/obo/IAO_0000064 algorithm Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions http://www.ebi.ac.uk/swo/SWO_0000324 Pathways 2.01 software http://www.ebi.ac.uk/swo/SWO_0000001 software The background intensity data from the spot quantification programs may be used to correct spot intensity. This software measures background globally as: BGLow (low background), BGAvg (Average background), BGRms (root mean square background). http://www.ebi.ac.uk/swo/SWO_0000333 RBGL http://www.ebi.ac.uk/swo/SWO_1100075 R software A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. http://www.ebi.ac.uk/swo/SWO_0000335 RBioinf http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions and datasets and examples to accompany the monograph R For Bioinformatics. http://www.ebi.ac.uk/swo/SWO_0000337 Recursive Feature Elimination (RFE) http://purl.obolibrary.org/obo/IAO_0000064 algorithm for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC) http://www.ebi.ac.uk/swo/SWO_0000338 RLMM http://www.ebi.ac.uk/swo/SWO_1100075 R software A Genotype Calling Algorithm for Affymetrix SNP Arrays http://www.ebi.ac.uk/swo/SWO_0000343 RMAExpress http://www.ebi.ac.uk/swo/SWO_0000001 software RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays. http://www.ebi.ac.uk/swo/SWO_0000346 RMAGEML http://www.ebi.ac.uk/swo/SWO_1100075 R software This package can be used to handle MAGEML documents in Bioconductor http://www.ebi.ac.uk/swo/SWO_0000347 RNAither http://www.ebi.ac.uk/swo/SWO_1100075 R software RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes http://www.ebi.ac.uk/swo/SWO_0000348 ROC http://www.ebi.ac.uk/swo/SWO_1100075 R software utilities for ROC, with uarray focus http://www.ebi.ac.uk/swo/SWO_0000349 RWebServices http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment. http://www.ebi.ac.uk/swo/SWO_0000350 RankProd http://www.ebi.ac.uk/swo/SWO_1100075 R software Rank Product method for identifying differentially expressed genes with application in meta-analysis http://www.ebi.ac.uk/swo/SWO_0000352 RbcBook1 http://www.ebi.ac.uk/swo/SWO_1100075 R software Support for Springer monograph on Bioconductor http://www.ebi.ac.uk/swo/SWO_0000353 Rdbi http://www.ebi.ac.uk/swo/SWO_1100075 R software Generic database methods http://www.ebi.ac.uk/swo/SWO_0000354 RdbiPgSQL http://www.ebi.ac.uk/swo/SWO_1100075 R software Provides methods for accessing data stored in PostgreSQL tables. http://www.ebi.ac.uk/swo/SWO_0000355 Rdisop http://www.ebi.ac.uk/swo/SWO_1100075 R software Decomposition of Isotopic Patterns http://www.ebi.ac.uk/swo/SWO_0000356 RefPlus http://www.ebi.ac.uk/swo/SWO_1100075 R software The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods. http://www.ebi.ac.uk/swo/SWO_0000358 Resourcerer http://www.ebi.ac.uk/swo/SWO_1100075 R software This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. http://www.ebi.ac.uk/swo/SWO_0000359 Rgraphviz http://www.ebi.ac.uk/swo/SWO_1100075 R software Provides plotting capabilities for R graph objects http://www.ebi.ac.uk/swo/SWO_0000360 Ringo http://www.ebi.ac.uk/swo/SWO_1100075 R software The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects http://www.ebi.ac.uk/swo/SWO_0000361 Rintact http://www.ebi.ac.uk/swo/SWO_1100075 R software Queries and data structures for protein interactions http://www.ebi.ac.uk/swo/SWO_0000362 Rmagpie http://www.ebi.ac.uk/swo/SWO_1100075 R software Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. http://www.ebi.ac.uk/swo/SWO_0000365 Rosetta Resolver http://www.ebi.ac.uk/swo/SWO_0000001 software The Rosetta Resolver® system provides a central analysis center and repository for biologists, statisticians, and bioinformaticians for the evaluation of gene expression data from microarrays and qPCR studies. http://www.ebi.ac.uk/swo/SWO_0000367 RpsiXML http://www.ebi.ac.uk/swo/SWO_1100075 R software Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously. http://www.ebi.ac.uk/swo/SWO_0000368 Rredland http://www.ebi.ac.uk/swo/SWO_1100075 R software interface to redland RDF utilities http://www.ebi.ac.uk/swo/SWO_0000369 Rtreemix http://www.ebi.ac.uk/swo/SWO_1100075 R software Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc. http://www.ebi.ac.uk/swo/SWO_0000370 Ruuid http://www.ebi.ac.uk/swo/SWO_1100075 R software A package to provide UUID values in R http://www.ebi.ac.uk/swo/SWO_0000373 SAGx http://www.ebi.ac.uk/swo/SWO_1100075 R software A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed. http://www.ebi.ac.uk/swo/SWO_0000375 SAS/STAT Software, Version 8 http://www.ebi.ac.uk/swo/SWO_0000001 software Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis. http://www.ebi.ac.uk/swo/SWO_0000377 SBMLR http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples. http://www.ebi.ac.uk/swo/SWO_0000382 SIM http://www.ebi.ac.uk/swo/SWO_1100075 R software Finds associations between DNA copy number and gene expression. http://www.ebi.ac.uk/swo/SWO_0000383 SLGI http://www.ebi.ac.uk/swo/SWO_1100075 R software A variety of data files and functions for the analysis of genetic interactions http://www.ebi.ac.uk/swo/SWO_0000384 SLqPCR http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH http://www.ebi.ac.uk/swo/SWO_0000385 SMAP http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions and classes for DNA copy number profiling of array-CGH data http://www.ebi.ac.uk/swo/SWO_0000387 SNPchip http://www.ebi.ac.uk/swo/SWO_1100075 R software This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing. http://www.ebi.ac.uk/swo/SWO_0000388 SPIA http://www.ebi.ac.uk/swo/SWO_1100075 R software This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study. http://www.ebi.ac.uk/swo/SWO_0000389 Semantic Similarity Measures http://purl.obolibrary.org/obo/IAO_0000064 algorithm Semantic Similarity Measures- Four methods proposed by Resnik[Philip, 1999], Jiang[Jiang and Conrath, 1997], Lin[Lin, 1998] and Schlicker[Schlicker et al., 2006] respectively have presented to determine the semantic similarities of two GO terms based on the annotation statistics of their common ancestor terms. Wang [Wang et al., 2007] proposed a new method to measure the similarities based on the graph structure of GO. http://www.ebi.ac.uk/swo/SWO_0000390 SSPA http://www.ebi.ac.uk/swo/SWO_1100075 R software Sample size and power analysis for microarray data, where two groups are analysed. http://www.ebi.ac.uk/swo/SWO_0000392 software developer role http://purl.obolibrary.org/obo/BFO_0000023 role Software developer role is a role borne by an organization or individual in which they are responsible for authoring software. http://www.ebi.ac.uk/swo/SWO_0000396 software developer organization http://purl.obolibrary.org/obo/OBI_0000245 organization An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing. http://www.ebi.ac.uk/swo/SWO_0000397 software publisher organization http://purl.obolibrary.org/obo/OBI_0000245 organization An organization or legal entity (including single person) that is responsible for publishing software. Publishing here includes tasks such as designing and producing physical products, technical customer support, licensing arrangements and marketing. http://www.ebi.ac.uk/swo/SWO_0000398 50-50 MANOVA algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm Classical multivariate analysis-of-variance tests perform poorly in cases with several highly correlated responses and the tests collapse when the number of responses exceeds the number of observations. This paper presents a new method which handles this problem. The dimensionality of the data is reduced by using principal component decompositions and the final tests are still based on the classical test statistics and their distributions. The methodology is illustrated with an example from the production of sausages with responses from near infrared reflectance spectroscopy. A closely related method for testing relationships in uniresponse regression with collinear explanatory variables is also presented. The new test, which is called the 50-50 F-test, uses the first k components to calculate SSMODEL. The next d components are not involved in SSERROR and they are called buffer components. http://www.ebi.ac.uk/swo/SWO_0000405 ArrayExpress Bioconductor http://www.ebi.ac.uk/swo/SWO_1100079 MAGE-TAB inputting software ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects. http://www.ebi.ac.uk/swo/SWO_0000416 ScISI http://www.ebi.ac.uk/swo/SWO_1100075 R software Package to create In Silico Interactomes http://www.ebi.ac.uk/swo/SWO_0000417 ScanAlyze http://www.ebi.ac.uk/swo/SWO_0000001 software Processes fluorescent images of microarrays http://www.ebi.ac.uk/swo/SWO_0000421 Scanning software G2565AA version A6.3.1 http://www.ebi.ac.uk/swo/SWO_0000420 scanning software High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results http://www.ebi.ac.uk/swo/SWO_0000422 ShortRead http://www.ebi.ac.uk/swo/SWO_1100075 R software Base classes, functions, and methods for representation of high-throughput, short-read sequencing data. http://www.ebi.ac.uk/swo/SWO_0000429 Spotfinder [TIGR] http://www.ebi.ac.uk/swo/SWO_0000001 software TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression http://www.ebi.ac.uk/swo/SWO_0000430 Spotfire http://www.ebi.ac.uk/swo/SWO_0000001 software Spotfire’s interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability. http://www.ebi.ac.uk/swo/SWO_0000432 TAS Software http://www.ebi.ac.uk/swo/SWO_1100022 Affymetrix Software Tiling Analysis Software (TAS) is a freely downloadable tool for analysis, with which one can perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, and can derive an interval overlap report and/or computation of summary statistics. http://www.ebi.ac.uk/swo/SWO_0000435 TargetSearch http://www.ebi.ac.uk/swo/SWO_1100075 R software This packages provides a targeted pre-processing method for GC-MS data. http://www.ebi.ac.uk/swo/SWO_0000438 TypeInfo http://www.ebi.ac.uk/swo/SWO_1100075 R software A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions http://www.ebi.ac.uk/swo/SWO_0000442 VanillaICE http://www.ebi.ac.uk/swo/SWO_1100075 R software Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays http://www.ebi.ac.uk/swo/SWO_0000446 XDE http://www.ebi.ac.uk/swo/SWO_1100075 R software XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression http://www.ebi.ac.uk/swo/SWO_0000447 XDotsReader http://www.ebi.ac.uk/swo/SWO_0000001 software Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification http://www.ebi.ac.uk/swo/SWO_0000450 Array Comparative Genomic Hybridization http://www.ebi.ac.uk/swo/SWO_1100075 R software The aCGH package functions for reading data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. http://www.ebi.ac.uk/swo/SWO_0000451 Acuity http://www.ebi.ac.uk/swo/SWO_0000001 software Acuity is the complete enterprise microarray informatics platform for microarray data storage, data filtering and data analysis. It analysis tools for quality, visualizations for discovery and Data Management for Security. http://www.ebi.ac.uk/swo/SWO_0000452 affxparser http://www.ebi.ac.uk/swo/SWO_1100075 R software affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. http://www.ebi.ac.uk/swo/SWO_0000453 affyContam http://www.ebi.ac.uk/swo/SWO_1100075 R software affyContam is software which provides the in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics. In essence, it creates structured corruption within CEL data to demonstrate QA effectiveness. http://www.ebi.ac.uk/swo/SWO_0000454 affyImGUI http://www.ebi.ac.uk/swo/SWO_1100075 R software A Graphical User Interface for affy analysis using the limma Microarray package http://www.ebi.ac.uk/swo/SWO_0000455 'affyPLM' http://www.ebi.ac.uk/swo/SWO_0000461 affypdnn A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. http://www.ebi.ac.uk/swo/SWO_0000456 affyPara http://www.ebi.ac.uk/swo/SWO_1100075 R software The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data. http://www.ebi.ac.uk/swo/SWO_0000457 affyQCReport http://www.ebi.ac.uk/swo/SWO_1100075 R software This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. http://www.ebi.ac.uk/swo/SWO_0000458 affyTiling http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays. http://www.ebi.ac.uk/swo/SWO_0000459 'affycoretools' http://www.ebi.ac.uk/swo/SWO_1100075 R software Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see http://www.ebi.ac.uk/swo/SWO_0000460 affyio http://www.ebi.ac.uk/swo/SWO_1100075 R software Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. http://www.ebi.ac.uk/swo/SWO_0000461 affypdnn http://www.ebi.ac.uk/swo/SWO_1100075 R software The package contains functions to perform the PDNN method described by Li Zhang et al. http://www.ebi.ac.uk/swo/SWO_0000463 altcdfenvs http://www.ebi.ac.uk/swo/SWO_1100075 R software altcdfenvs is a software package for alternative CDF environments (aka probeset mappings) and contains convenience data structures and functions to handle cdfenvs. http://www.ebi.ac.uk/swo/SWO_0000465 annaffy http://www.ebi.ac.uk/swo/SWO_1100075 R software This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria. http://www.ebi.ac.uk/swo/SWO_0000466 'annotate' http://www.ebi.ac.uk/swo/SWO_1100075 R software Using R enviroments for annotation. http://www.ebi.ac.uk/swo/SWO_0000468 annotationTools http://www.ebi.ac.uk/swo/SWO_1100075 R software This package functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). http://www.ebi.ac.uk/swo/SWO_0000470 'apComplex' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package functions to estimate a bipartite graph of protein complex membership using AP-MS data. http://www.ebi.ac.uk/swo/SWO_0000471 aroma.light http://www.ebi.ac.uk/swo/SWO_1100075 R software This package functions as methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. http://www.ebi.ac.uk/swo/SWO_0000472 arrayMvout http://www.ebi.ac.uk/swo/SWO_1100075 R software This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate http://www.ebi.ac.uk/swo/SWO_0000473 arrayQuality http://www.ebi.ac.uk/swo/SWO_1100075 R software This package functions for performing print-run and array level quality assessment. http://www.ebi.ac.uk/swo/SWO_0000474 arrayQualityMetrics http://www.ebi.ac.uk/swo/SWO_1100075 R software This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels. http://www.ebi.ac.uk/swo/SWO_0000476 arrayWoRx http://www.ebi.ac.uk/swo/SWO_0000001 software Applied Precision MicroArray Scanner Model arrayWoRx Comprehensive system that fully automates the image capture and quantitation of microarrays. by integrating Slid handling, fluorescent microscopy, and sophisticated spot scan and analysis software the systems detects and measures the fluorescence intensity at each of the specified elements in a microarray. The intensity data can be presented as image data, graphical representation, or as numerical data. http://www.ebi.ac.uk/swo/SWO_0000479 'beadarray' http://www.ebi.ac.uk/swo/SWO_1100075 R software The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. http://www.ebi.ac.uk/swo/SWO_0000480 'beadarraySNP' http://www.ebi.ac.uk/swo/SWO_1100075 R software Importing data from Illumina SNP experiments and performing copy number calculations and reports. http://www.ebi.ac.uk/swo/SWO_0000481 'betr' http://www.ebi.ac.uk/swo/SWO_1100075 R software betr is a software package which implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data. http://www.ebi.ac.uk/swo/SWO_0000482 bgafun http://www.ebi.ac.uk/swo/SWO_1100075 R software BGAfun is a method to identify specifity determining residues in protein families http://www.ebi.ac.uk/swo/SWO_0000483 bgx http://www.ebi.ac.uk/swo/SWO_1100075 R software Bayesian integrated analysis of Affymetrix GeneChips http://www.ebi.ac.uk/swo/SWO_0000485 bioDist http://www.ebi.ac.uk/swo/SWO_1100075 R software The bioDist package contains some distance functions that have been shown to be useful in a number of dierent biological or bioinformatic problems. The return values are typically instances of the S3 class dist. http://www.ebi.ac.uk/swo/SWO_0000486 'biocDatasets' http://www.ebi.ac.uk/swo/SWO_1100075 R software Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal. http://www.ebi.ac.uk/swo/SWO_0000487 'biocGraph' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides examples and code that make use of the different graph related packages produced by Bioconductor. http://www.ebi.ac.uk/swo/SWO_0000488 'biocViews' http://www.ebi.ac.uk/swo/SWO_1100075 R software Categorized views of R package repositories http://www.ebi.ac.uk/swo/SWO_0000489 biomaRT http://www.ebi.ac.uk/swo/SWO_1100075 R software The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. http://www.ebi.ac.uk/swo/SWO_0000491 'bridge' http://www.ebi.ac.uk/swo/SWO_1100075 R software The bridge package consists of several functions for testing for dierential expression among mul- tiple samples http://www.ebi.ac.uk/swo/SWO_0000494 'cellHTS' http://www.ebi.ac.uk/swo/SWO_1100075 R software Bioconductor package concerned with analysis of cell-based RNA interference screens http://www.ebi.ac.uk/swo/SWO_0000495 'cellHTS2' http://www.ebi.ac.uk/swo/SWO_1100075 R software Analysis of cell-based RNA interference screens http://www.ebi.ac.uk/swo/SWO_0000496 cghMCR http://www.ebi.ac.uk/swo/SWO_1100075 R software Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform. http://www.ebi.ac.uk/swo/SWO_0000498 cls http://edamontology.org/format_2330 Textual format Categorical (e.g tumor vs normal) class file format http://www.ebi.ac.uk/swo/SWO_0000499 'clusterStab' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. http://www.ebi.ac.uk/swo/SWO_0000501 'codelink' http://www.ebi.ac.uk/swo/SWO_1100075 R software This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. http://www.ebi.ac.uk/swo/SWO_0000504 convert http://www.ebi.ac.uk/swo/SWO_1100075 R software Define coerce methods for microarray data objects. http://www.ebi.ac.uk/swo/SWO_0000505 copa http://www.ebi.ac.uk/swo/SWO_1100075 R software COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. http://www.ebi.ac.uk/swo/SWO_0000506 cosmo http://www.ebi.ac.uk/swo/SWO_1100075 R software cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively. http://www.ebi.ac.uk/swo/SWO_0000507 cosmoGUI http://www.ebi.ac.uk/swo/SWO_1100075 R software cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. http://www.ebi.ac.uk/swo/SWO_0000509 database creation http://purl.obolibrary.org/obo/OBI_0200000 data transformation An objective in which the aim is to create a new database instance. http://www.ebi.ac.uk/swo/SWO_0000510 crlmm http://www.ebi.ac.uk/swo/SWO_1100075 R software Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0. http://www.ebi.ac.uk/swo/SWO_0000512 ctc http://www.ebi.ac.uk/swo/SWO_1100075 R software Tools for export and import classification trees and clusters to other programs http://www.ebi.ac.uk/swo/SWO_0000513 dChip http://www.ebi.ac.uk/swo/SWO_0000001 software Analysis and visualization of gene expression and SNP microarrays http://www.ebi.ac.uk/swo/SWO_0000514 daMA http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. http://www.ebi.ac.uk/swo/SWO_0000520 'diffGeneAnalysis' http://www.ebi.ac.uk/swo/SWO_1100075 R software Analyze microarray data http://www.ebi.ac.uk/swo/SWO_0000521 'domainsignatures' http://www.ebi.ac.uk/swo/SWO_1100075 R software Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure. http://www.ebi.ac.uk/swo/SWO_0000522 'dualKS' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package implements a Kolmogorov Smirnov rank-sum based algorithm for training and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes. http://www.ebi.ac.uk/swo/SWO_0000523 dyebias http://www.ebi.ac.uk/swo/SWO_1100075 R software Gene-specific dye-bias correction of two-color microarray data using the GASSCO method http://www.ebi.ac.uk/swo/SWO_0000525 ecolitk http://www.ebi.ac.uk/swo/SWO_1100075 R software Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. http://www.ebi.ac.uk/swo/SWO_0000526 edd http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides tools for evaluating cohort distributions of gene expression levels http://www.ebi.ac.uk/swo/SWO_0000527 'edgeR' http://www.ebi.ac.uk/swo/SWO_1100075 R software Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries. http://www.ebi.ac.uk/swo/SWO_0000528 exonmap http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target. http://www.ebi.ac.uk/swo/SWO_0000529 'explorase' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package explores and analyzes *omics data with R and GGobi http://www.ebi.ac.uk/swo/SWO_0000530 'externalVector' http://www.ebi.ac.uk/swo/SWO_1100075 R software Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided http://www.ebi.ac.uk/swo/SWO_0000532 factDesign http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. http://www.ebi.ac.uk/swo/SWO_0000533 fbat http://www.ebi.ac.uk/swo/SWO_1100075 R software This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program http://www.ebi.ac.uk/swo/SWO_0000534 fdrame http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma http://www.ebi.ac.uk/swo/SWO_0000536 flagme http://www.ebi.ac.uk/swo/SWO_1100075 R software Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data http://www.ebi.ac.uk/swo/SWO_0000537 flowClust http://www.ebi.ac.uk/swo/SWO_1100075 R software Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed http://www.ebi.ac.uk/swo/SWO_0000538 flowCore http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides S4 data structures and basic functions to deal with flow cytometry data. http://www.ebi.ac.uk/swo/SWO_0000539 flowFlowJo http://www.ebi.ac.uk/swo/SWO_1100075 R software FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. http://www.ebi.ac.uk/swo/SWO_0000540 flowQ http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides quality control and quality assessment tools for flow cytometry data. http://www.ebi.ac.uk/swo/SWO_0000541 flowStats http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package. http://www.ebi.ac.uk/swo/SWO_0000542 flowUtils http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides utilities for flow cytometry data. http://www.ebi.ac.uk/swo/SWO_0000543 flowViz http://www.ebi.ac.uk/swo/SWO_1100075 R software Provides visualization tools for flow cytometry data http://www.ebi.ac.uk/swo/SWO_0000544 gaga http://www.ebi.ac.uk/swo/SWO_1100075 R software This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling). http://www.ebi.ac.uk/swo/SWO_0000545 'gaggle' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains functions connecting R with the Gaggle http://www.ebi.ac.uk/swo/SWO_0000546 gcRMA quantification http://www.ebi.ac.uk/swo/SWO_0000001 software Bioconductor package concerned with background adjustment using sequence information http://www.ebi.ac.uk/swo/SWO_0000547 gcrma http://www.ebi.ac.uk/swo/SWO_1100075 R software Background adjustment using sequence information http://www.ebi.ac.uk/swo/SWO_0000548 gct http://www.ebi.ac.uk/swo/data/SWO_3000046 tab delimited file format Gene Cluster Text file format http://www.ebi.ac.uk/swo/SWO_0000549 'genArise' http://www.ebi.ac.uk/swo/SWO_1100075 R software genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. http://www.ebi.ac.uk/swo/SWO_0000550 gene2pathway http://www.ebi.ac.uk/swo/SWO_1100075 R software The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained. http://www.ebi.ac.uk/swo/SWO_0000551 geneRecommender http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. http://www.ebi.ac.uk/swo/SWO_0000555 genefilter http://www.ebi.ac.uk/swo/SWO_1100075 R software Some basic functions for filtering genes http://www.ebi.ac.uk/swo/SWO_0000556 genemeta http://www.ebi.ac.uk/swo/SWO_1100075 R software http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html http://www.ebi.ac.uk/swo/SWO_0000557 geneplotter http://www.ebi.ac.uk/swo/SWO_1100075 R software Some basic functions for plotting genetic data http://www.ebi.ac.uk/swo/SWO_0000558 genomeIntervals http://www.ebi.ac.uk/swo/SWO_1100075 R software Tools for operation on genomic intervals. http://www.ebi.ac.uk/swo/SWO_0000560 Global test http://purl.obolibrary.org/obo/IAO_0000064 algorithm global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments. http://www.ebi.ac.uk/swo/SWO_0000561 globaltest http://www.ebi.ac.uk/swo/SWO_1100075 R software Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest. http://www.ebi.ac.uk/swo/SWO_0000563 goProfiles http://www.ebi.ac.uk/swo/SWO_1100075 R software The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'. http://www.ebi.ac.uk/swo/SWO_0000564 goTools http://www.ebi.ac.uk/swo/SWO_1100075 R software Wraper functions for description/comparison of oligo ID list using Gene Ontology database http://www.ebi.ac.uk/swo/SWO_0000565 gpls http://www.ebi.ac.uk/swo/SWO_1100075 R software Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. http://www.ebi.ac.uk/swo/SWO_0000567 graph http://www.ebi.ac.uk/swo/SWO_1100075 R software A package that implements some simple graph handling capabilities. http://www.ebi.ac.uk/swo/SWO_0000572 hexbin http://www.ebi.ac.uk/swo/SWO_1100075 R software Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods. http://www.ebi.ac.uk/swo/SWO_0000574 hopach http://www.ebi.ac.uk/swo/SWO_1100075 R software The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). http://www.ebi.ac.uk/swo/SWO_0000577 hypergraph http://www.ebi.ac.uk/swo/SWO_1100075 R software A package that implements some simple capabilities for representing and manipulating hypergraphs. http://www.ebi.ac.uk/swo/SWO_0000578 Icens http://www.ebi.ac.uk/swo/SWO_1100075 R software Many functions for computing the NPMLE for censored and truncated data. http://www.ebi.ac.uk/swo/SWO_0000579 idiogram http://www.ebi.ac.uk/swo/SWO_1100075 R software A package for plotting genomic data by chromosomal location http://www.ebi.ac.uk/swo/SWO_0000581 impute http://www.ebi.ac.uk/swo/SWO_1100075 R software Imputation for microarray data (currently KNN only) http://www.ebi.ac.uk/swo/SWO_0000582 iterativeBMA http://www.ebi.ac.uk/swo/SWO_1100075 R software The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402). http://www.ebi.ac.uk/swo/SWO_0000583 iterativeBMAsurv http://www.ebi.ac.uk/swo/SWO_1100075 R software The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data. http://www.ebi.ac.uk/swo/SWO_0000590 keggorth http://www.ebi.ac.uk/swo/SWO_1100075 R software Test package for a pathway 'ontology' http://www.ebi.ac.uk/swo/SWO_0000591 lapmix http://www.ebi.ac.uk/swo/SWO_1100075 R software lapmix is a software package for the identification of differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. http://www.ebi.ac.uk/swo/SWO_0000593 limma http://www.ebi.ac.uk/swo/SWO_1100075 R software Data analysis, linear models and differential expression for microarray data. http://www.ebi.ac.uk/swo/SWO_0000594 limmaGUI http://www.ebi.ac.uk/swo/SWO_1100075 R software A Graphical User Interface for the limma Microarray package http://www.ebi.ac.uk/swo/SWO_0000599 logicFS http://www.ebi.ac.uk/swo/SWO_1100075 R software Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification. http://www.ebi.ac.uk/swo/SWO_0000601 logitT http://www.ebi.ac.uk/swo/SWO_1100075 R software The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R. http://www.ebi.ac.uk/swo/SWO_0000603 lumi http://www.ebi.ac.uk/swo/SWO_1100075 R software The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. http://www.ebi.ac.uk/swo/SWO_0000604 maCorrPlot http://www.ebi.ac.uk/swo/SWO_1100075 R software Graphically displays correlation in microarray data that is due to insufficient normalization http://www.ebi.ac.uk/swo/SWO_0000605 maDB http://www.ebi.ac.uk/swo/SWO_1100075 R software maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays. http://www.ebi.ac.uk/swo/SWO_0000606 maSigPro http://www.ebi.ac.uk/swo/SWO_1100075 R software maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. http://www.ebi.ac.uk/swo/SWO_0000607 maanova http://www.ebi.ac.uk/swo/SWO_1100075 R software Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree. http://www.ebi.ac.uk/swo/SWO_0000608 macat http://www.ebi.ac.uk/swo/SWO_1100075 R software This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'. http://www.ebi.ac.uk/swo/SWO_0000609 made4 http://www.ebi.ac.uk/swo/SWO_1100075 R software Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4. http://www.ebi.ac.uk/swo/SWO_0000610 maigesPack http://www.ebi.ac.uk/swo/SWO_1100075 R software This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data http://www.ebi.ac.uk/swo/SWO_0000611 makePlatformDesign http://www.ebi.ac.uk/swo/SWO_1100075 R software makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo. http://www.ebi.ac.uk/swo/SWO_0000612 makecdfenv http://www.ebi.ac.uk/swo/SWO_1100075 R software This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. http://www.ebi.ac.uk/swo/SWO_0000613 marray http://www.ebi.ac.uk/swo/SWO_1100075 R software Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. http://www.ebi.ac.uk/swo/SWO_0000616 matchprobes http://www.ebi.ac.uk/swo/SWO_1100075 R software Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment. For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that. http://www.ebi.ac.uk/swo/SWO_0000617 mdqc http://www.ebi.ac.uk/swo/SWO_1100075 R software MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. http://www.ebi.ac.uk/swo/SWO_0000619 metaArray http://www.ebi.ac.uk/swo/SWO_1100075 R software 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform http://www.ebi.ac.uk/swo/SWO_0000621 metahdep http://www.ebi.ac.uk/swo/SWO_1100075 R software Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies http://www.ebi.ac.uk/swo/SWO_0000622 miRNApath http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes. http://www.ebi.ac.uk/swo/SWO_0000623 microRNA http://www.ebi.ac.uk/swo/SWO_1100075 R software microRNA is a software package which provides data resources for microRNAs and various functions for manipulating them. http://www.ebi.ac.uk/swo/SWO_0000625 minet http://www.ebi.ac.uk/swo/SWO_1100075 R software This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented. http://www.ebi.ac.uk/swo/SWO_0000628 Multiple testing http://purl.obolibrary.org/obo/IAO_0000064 algorithm multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. http://www.ebi.ac.uk/swo/SWO_0000630 multtest http://www.ebi.ac.uk/swo/SWO_1100075 R software Resampling-based multiple hypothesis testing http://www.ebi.ac.uk/swo/SWO_0000632 nem http://www.ebi.ac.uk/swo/SWO_1100075 R software Nested Effects Models to reconstruct phenotypic hierarchies http://www.ebi.ac.uk/swo/SWO_0000635 nnNorm http://www.ebi.ac.uk/swo/SWO_1100075 R software This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. http://www.ebi.ac.uk/swo/SWO_0000636 nudge http://www.ebi.ac.uk/swo/SWO_1100075 R software Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample) http://www.ebi.ac.uk/swo/SWO_0000637 occugene http://www.ebi.ac.uk/swo/SWO_1100075 R software Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries. http://www.ebi.ac.uk/swo/SWO_0000638 oligo http://www.ebi.ac.uk/swo/SWO_1100075 R software A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. http://www.ebi.ac.uk/swo/SWO_0000639 oligoClasses http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package. http://www.ebi.ac.uk/swo/SWO_0000641 oneChannelGUI http://www.ebi.ac.uk/swo/SWO_1100075 R software This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis. http://www.ebi.ac.uk/swo/SWO_0000642 ontoTools http://www.ebi.ac.uk/swo/SWO_1100075 R software tools for working with ontologies and graphs http://www.ebi.ac.uk/swo/SWO_0000645 pamr http://www.ebi.ac.uk/swo/SWO_1100075 R software Some functions for sample classification in microarrays http://www.ebi.ac.uk/swo/SWO_0000646 panp http://www.ebi.ac.uk/swo/SWO_1100075 R software A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. http://www.ebi.ac.uk/swo/SWO_0000647 parody http://www.ebi.ac.uk/swo/SWO_1100075 R software Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics http://www.ebi.ac.uk/swo/SWO_0000649 pathRender http://www.ebi.ac.uk/swo/SWO_1100075 R software build graphs from pathway databases, render them by Rgraphviz http://www.ebi.ac.uk/swo/SWO_0000650 pcaMethods http://www.ebi.ac.uk/swo/SWO_1100075 R software A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. http://www.ebi.ac.uk/swo/SWO_0000651 pcot2 http://www.ebi.ac.uk/swo/SWO_1100075 R software PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons. http://www.ebi.ac.uk/swo/SWO_0000653 pdInfoBuilder http://www.ebi.ac.uk/swo/SWO_1100075 R software Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. http://www.ebi.ac.uk/swo/SWO_0000654 pdmclass http://www.ebi.ac.uk/swo/SWO_1100075 R software This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression. http://www.ebi.ac.uk/swo/SWO_0000656 pgUtils http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism. http://www.ebi.ac.uk/swo/SWO_0000657 pickgene http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions to Analyze Microarray (Gene Expression) Data. http://www.ebi.ac.uk/swo/SWO_0000658 pkgDepTools http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained. http://www.ebi.ac.uk/swo/SWO_0000659 plgem http://www.ebi.ac.uk/swo/SWO_1100075 R software PLGEM is useful for detecting differential expression in microarray and proteomics datasets. http://www.ebi.ac.uk/swo/SWO_0000660 plier http://www.ebi.ac.uk/swo/SWO_1100075 R software The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. http://www.ebi.ac.uk/swo/SWO_0000662 plw http://www.ebi.ac.uk/swo/SWO_1100075 R software Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). http://www.ebi.ac.uk/swo/SWO_0000665 ppiStats http://www.ebi.ac.uk/swo/SWO_1100075 R software Tools for the analysis of protein interaction data. http://www.ebi.ac.uk/swo/SWO_0000666 prada http://www.ebi.ac.uk/swo/SWO_1100075 R software Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). http://www.ebi.ac.uk/swo/SWO_0000667 preprocessCore http://www.ebi.ac.uk/swo/SWO_1100075 R software A library of core preprocessing routines http://www.ebi.ac.uk/swo/SWO_0000669 puma http://www.ebi.ac.uk/swo/SWO_1100075 R software Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. http://www.ebi.ac.uk/swo/SWO_0000671 qpcrNorm http://www.ebi.ac.uk/swo/SWO_1100075 R software The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. http://www.ebi.ac.uk/swo/SWO_0000672 qpgraph http://www.ebi.ac.uk/swo/SWO_1100075 R software Reverse engineering of molecular regulatory networks with qp-graphs http://www.ebi.ac.uk/swo/SWO_0000675 quantsmooth http://www.ebi.ac.uk/swo/SWO_1100075 R software Quantile smoothing and genomic visualization of array data http://www.ebi.ac.uk/swo/SWO_0000676 qvalue http://www.ebi.ac.uk/swo/SWO_1100075 R software This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. http://www.ebi.ac.uk/swo/SWO_0000677 rHVDM http://www.ebi.ac.uk/swo/SWO_1100075 R software Hidden Variable Dynamic Modeling http://www.ebi.ac.uk/swo/SWO_0000678 rMAT http://www.ebi.ac.uk/swo/SWO_1100075 R software R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. http://www.ebi.ac.uk/swo/SWO_0000679 rama http://www.ebi.ac.uk/swo/SWO_1100075 R software The rama package consists of several functions for robust estimation of two color microarray intensities with replicates http://www.ebi.ac.uk/swo/SWO_0000683 rbsurv http://www.ebi.ac.uk/swo/SWO_1100075 R software This package selects genes associated with survival. http://www.ebi.ac.uk/swo/SWO_0000685 reb http://www.ebi.ac.uk/swo/SWO_1100075 R software A set of functions to dentify regional expression biases http://www.ebi.ac.uk/swo/SWO_0000686 rflowcyt http://www.ebi.ac.uk/swo/SWO_1100075 R software Statistical tools and data structures for analytic flow cytometry http://www.ebi.ac.uk/swo/SWO_0000688 rsbml http://www.ebi.ac.uk/swo/SWO_1100075 R software R support for SBML, using libsbml http://www.ebi.ac.uk/swo/SWO_0000689 rtracklayer http://www.ebi.ac.uk/swo/SWO_1100075 R software R interface to genome browsers and their annotation tracks http://www.ebi.ac.uk/swo/SWO_0000690 safe http://www.ebi.ac.uk/swo/SWO_1100075 R software SAFE is a resampling-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. http://www.ebi.ac.uk/swo/SWO_0000691 sagenhaft http://www.ebi.ac.uk/swo/SWO_1100075 R software This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison http://www.ebi.ac.uk/swo/SWO_0000692 seqLogo http://www.ebi.ac.uk/swo/SWO_1100075 R software seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo http://www.ebi.ac.uk/swo/SWO_0000693 sigPathway http://www.ebi.ac.uk/swo/SWO_1100075 R software Conducts pathway analysis by calculating the NT_k and NE_k statistics http://www.ebi.ac.uk/swo/SWO_0000694 siggenes http://www.ebi.ac.uk/swo/SWO_1100075 R software Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). http://www.ebi.ac.uk/swo/SWO_0000696 simpleaffy http://www.ebi.ac.uk/swo/SWO_1100075 R software Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures http://www.ebi.ac.uk/swo/SWO_0000697 simulatorAPMS http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions to computationally simulate the AP-MS technology based on wet-lab data. http://www.ebi.ac.uk/swo/SWO_0000698 sizepower http://www.ebi.ac.uk/swo/SWO_1100075 R software This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. http://www.ebi.ac.uk/swo/SWO_0000699 xmapbridge http://www.ebi.ac.uk/swo/SWO_1100075 R software xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format. http://www.ebi.ac.uk/swo/SWO_0000700 snapCGH http://www.ebi.ac.uk/swo/SWO_1100075 R software Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. http://www.ebi.ac.uk/swo/SWO_0000701 snpMatrix http://www.ebi.ac.uk/swo/SWO_1100075 R software Implements classes and methods for large-scale SNP association studies http://www.ebi.ac.uk/swo/SWO_0000703 spikeLI http://www.ebi.ac.uk/swo/SWO_1100075 R software Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool http://www.ebi.ac.uk/swo/SWO_0000704 spkTools http://www.ebi.ac.uk/swo/SWO_1100075 R software The package contains functions that can be used to compare expression measures on different array platforms. http://www.ebi.ac.uk/swo/SWO_0000705 splicegear http://www.ebi.ac.uk/swo/SWO_1100075 R software A set of tools to work with alternative splicing http://www.ebi.ac.uk/swo/SWO_0000706 splots http://www.ebi.ac.uk/swo/SWO_1100075 R software The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format. http://www.ebi.ac.uk/swo/SWO_0000707 spotSegmentation http://www.ebi.ac.uk/swo/SWO_1100075 R software Spot segmentation via model-based clustering and gridding for blocks within microarray slides http://www.ebi.ac.uk/swo/SWO_0000710 sscore http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains an implementation of the S-Score algorithm http://www.ebi.ac.uk/swo/SWO_0000711 ssize http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions for computing and displaying sample size information for gene expression arrays. http://www.ebi.ac.uk/swo/SWO_0000712 stam http://www.ebi.ac.uk/swo/SWO_1100075 R software The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects. http://www.ebi.ac.uk/swo/SWO_0000713 Statistical tests http://purl.obolibrary.org/obo/IAO_0000064 algorithm A statistical test is an algorithm for making quantitative decisions to determine which outcomes of a study would lead to a rejection of the null hypothesis for a pre-specified level of significance. http://www.ebi.ac.uk/swo/SWO_0000714 stepNorm http://www.ebi.ac.uk/swo/SWO_1100075 R software Stepwise normalization functions for cDNA microarray data. http://www.ebi.ac.uk/swo/SWO_0000716 tilingArray http://www.ebi.ac.uk/swo/SWO_1100075 R software Transcript mapping with high-density oligonucleotide tiling arrays http://www.ebi.ac.uk/swo/SWO_0000717 timecourse http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions for data analysis and graphical displays for developmental microarray time course data. http://www.ebi.ac.uk/swo/SWO_0000719 topGO http://www.ebi.ac.uk/swo/SWO_1100075 R software topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. http://www.ebi.ac.uk/swo/SWO_0000720 tspair http://www.ebi.ac.uk/swo/SWO_1100075 R software Top Scoring Pairs for Microarray Classification http://www.ebi.ac.uk/swo/SWO_0000721 twilight http://www.ebi.ac.uk/swo/SWO_1100075 R software Estimation of local false discovery rate http://www.ebi.ac.uk/swo/SWO_0000723 vbmp http://www.ebi.ac.uk/swo/SWO_1100075 R software Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. http://www.ebi.ac.uk/swo/SWO_0000725 vsn http://www.ebi.ac.uk/swo/SWO_1100075 R software The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references http://www.ebi.ac.uk/swo/SWO_0000726 weaver http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. http://www.ebi.ac.uk/swo/SWO_0000727 webbioc http://www.ebi.ac.uk/swo/SWO_1100075 R software An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. http://www.ebi.ac.uk/swo/SWO_0000728 widgetTools http://www.ebi.ac.uk/swo/SWO_1100075 R software This packages contains tools to support the construction of tcltk widgets http://www.ebi.ac.uk/swo/SWO_0000729 xcms http://www.ebi.ac.uk/swo/SWO_1100075 R software Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling. http://www.ebi.ac.uk/swo/SWO_0000730 xps http://www.ebi.ac.uk/swo/SWO_1100075 R software Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays http://www.ebi.ac.uk/swo/SWO_0000731 yaqcaffy http://www.ebi.ac.uk/swo/SWO_1100075 R software Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. http://www.ebi.ac.uk/swo/SWO_1100001 50-50 MANOVA http://www.ebi.ac.uk/swo/SWO_1100115 matlab software 50-50 Manova is software in which the 50-50 MANOVA algorithm is implemented. http://www.ebi.ac.uk/swo/SWO_1100002 ABarray http://www.ebi.ac.uk/swo/SWO_1100075 R software The ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be tranformed into expression data matrix. http://www.ebi.ac.uk/swo/SWO_1100003 'ACME' http://purl.obolibrary.org/obo/IAO_0000064 algorithm The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe. http://www.ebi.ac.uk/swo/SWO_1100004 Algorithms for Calculating Microarray Enrichment http://www.ebi.ac.uk/swo/SWO_1100075 R software ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. http://www.ebi.ac.uk/swo/SWO_1100005 Affymetrix Expression Console http://www.ebi.ac.uk/swo/SWO_0000001 software Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms http://www.ebi.ac.uk/swo/SWO_1100010 ANCOVA http://purl.obolibrary.org/obo/IAO_0000064 algorithm The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR http://www.ebi.ac.uk/swo/SWO_1100018 'AffyCompatible' http://www.ebi.ac.uk/swo/SWO_1100075 R software The AffyCompatible package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files. http://www.ebi.ac.uk/swo/SWO_1100019 'AffyExpress' http://www.ebi.ac.uk/swo/SWO_1100075 R software The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. http://www.ebi.ac.uk/swo/SWO_1100023 Agi4x44PreProcess http://www.ebi.ac.uk/swo/SWO_1100075 R software Preprocessing of Agilent 4x44 array data http://www.ebi.ac.uk/swo/SWO_1100029 'BCRANK' http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search http://www.ebi.ac.uk/swo/SWO_1100030 BGL http://purl.obolibrary.org/obo/IAO_0000064 algorithm BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering http://www.ebi.ac.uk/swo/SWO_1100031 'BGmix' http://www.ebi.ac.uk/swo/SWO_1100075 R software Bayesian models for differential gene expression http://www.ebi.ac.uk/swo/SWO_1100032 BLAST http://www.ebi.ac.uk/swo/SWO_0000001 software The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. http://www.ebi.ac.uk/swo/SWO_1100035 BPMAP http://edamontology.org/format_2333 binary format BPMAP is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The BPMAP format contains information relating to the design of the Affymetrix tiling arrays. http://www.ebi.ac.uk/swo/SWO_1100036 BRB-ArrayTools http://www.ebi.ac.uk/swo/SWO_0000001 software BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis. http://www.ebi.ac.uk/swo/SWO_1100037 'BSgenome' http://www.ebi.ac.uk/swo/SWO_1100075 R software This document describes the process of forging a BSgenome data package. It is intended for Bioconductor users who want to make a new BSgenome data package http://www.ebi.ac.uk/swo/SWO_1100038 BZScan http://www.ebi.ac.uk/swo/SWO_0000001 software BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures. It can work either in a fully automatic "batch mode" or at different levels of manual operation. http://www.ebi.ac.uk/swo/SWO_1100040 BasReader 3.01 http://www.ebi.ac.uk/swo/SWO_0000001 software This program may be used to read out image data from all scanners of the FujiFilm BAS series (BAS1000, BAS1500, BAS1800, BAS2000, BAS2500, BAS3000, BAS5000) and the FujiFilm FLA scanners (FLA-2000, FLA-3000). http://www.ebi.ac.uk/swo/SWO_1100042 Beadstudio http://www.ebi.ac.uk/swo/SWO_0000001 software BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications http://www.ebi.ac.uk/swo/SWO_1100043 'BicARE' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package is dedicated to biclustering analysis which allows to discover sets of genes that have the same expression pattern accross a set of samples http://www.ebi.ac.uk/swo/SWO_1100044 'BioMVCClass' http://www.ebi.ac.uk/swo/SWO_1100075 R software Creates classes used in model-view-controller (MVC) design that uses Biobase http://www.ebi.ac.uk/swo/SWO_1100045 'Biobase' http://www.ebi.ac.uk/swo/SWO_1100075 R software Functions that are needed by many other packages or which replace R functions http://www.ebi.ac.uk/swo/SWO_1100046 'BiocCaseStudies' http://www.ebi.ac.uk/swo/SWO_1100075 R software Software and data to support the case studies. http://www.ebi.ac.uk/swo/SWO_1100048 'Biostrings' http://www.ebi.ac.uk/swo/SWO_1100075 R software Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences. http://www.ebi.ac.uk/swo/SWO_1100050 'BufferedMatrix' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package creates a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. http://www.ebi.ac.uk/swo/SWO_1100051 'BufferedMatrixMethods' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package involves microarray Data related methods that utlize BufferedMatrix objects http://www.ebi.ac.uk/swo/SWO_1100052 'CALIB' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes. http://www.ebi.ac.uk/swo/SWO_1100053 'CAMERA' http://www.ebi.ac.uk/swo/SWO_1100075 R software Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments http://www.ebi.ac.uk/swo/SWO_1100054 CDF binary format http://edamontology.org/format_2333 binary format The CDF binary format is a binary data format specification created by Affymetrix was created for faster access and smaller file size in comparison to the CDF ASCII format. The values in the file are stored in little-endian format. CDF binary format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. http://www.ebi.ac.uk/swo/SWO_1100055 'CMA' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment. http://www.ebi.ac.uk/swo/SWO_1100056 CMA http://purl.obolibrary.org/obo/IAO_0000064 algorithm CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting) http://www.ebi.ac.uk/swo/SWO_1100057 'CORREP' http://www.ebi.ac.uk/swo/SWO_1100075 R software Multivariate correlation estimation and statistical inference. http://www.ebi.ac.uk/swo/SWO_1100058 CRLMM algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance. http://www.ebi.ac.uk/swo/SWO_1100062 Category http://www.ebi.ac.uk/swo/SWO_1100075 R software A collection of tools for performing category analysis. http://www.ebi.ac.uk/swo/SWO_1100063 'ChemmineR' http://www.ebi.ac.uk/swo/SWO_1100075 R software ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services. http://www.ebi.ac.uk/swo/SWO_1100067 multiscan http://www.ebi.ac.uk/swo/SWO_1100075 R software A multiscan is an R package for combining multiple scans http://www.ebi.ac.uk/swo/SWO_1100068 affy http://www.ebi.ac.uk/swo/SWO_1100075 R software The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. http://www.ebi.ac.uk/swo/SWO_1100069 affycomp http://www.ebi.ac.uk/swo/SWO_1100075 R software The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. http://www.ebi.ac.uk/swo/SWO_1100070 PCMG http://purl.obolibrary.org/obo/IAO_0000064 algorithm PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex. http://www.ebi.ac.uk/swo/SWO_1100073 Annotation-Driven Clustering http://www.ebi.ac.uk/swo/SWO_1100075 R software adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. http://www.ebi.ac.uk/swo/SWO_1100075 R software http://www.ebi.ac.uk/swo/SWO_0000001 software Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. http://www.ebi.ac.uk/swo/SWO_1100076 BCRANK http://purl.obolibrary.org/obo/IAO_0000064 algorithm BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. http://www.ebi.ac.uk/swo/SWO_1100077 Cosmo http://purl.obolibrary.org/obo/IAO_0000064 algorithm cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture http://www.ebi.ac.uk/swo/SWO_1100082 Non-linear functional regression model http://purl.obolibrary.org/obo/IAO_0000064 algorithm non-linear functional regression model with both additive and multiplicative error terms http://www.ebi.ac.uk/swo/SWO_1100083 'CoCiteStats' http://www.ebi.ac.uk/swo/SWO_1100075 R software A collection of software tools for dealing with co-citation data. http://www.ebi.ac.uk/swo/SWO_1100084 CodeLink Expression Analysis Software http://www.ebi.ac.uk/swo/SWO_0000001 software This software has a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, these tools help optimize performance in an expression profiling study. http://www.ebi.ac.uk/swo/SWO_1100085 CodeLink Expression Scanning Software http://www.ebi.ac.uk/swo/SWO_0000001 software Slides are scanned using CodeLink Expression Scanning Software http://www.ebi.ac.uk/swo/SWO_1100087 Cyber-T http://www.ebi.ac.uk/swo/SWO_0000001 software Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic. http://www.ebi.ac.uk/swo/SWO_1100088 'DEDS' http://www.ebi.ac.uk/swo/SWO_1100075 R software This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. http://www.ebi.ac.uk/swo/SWO_1100089 'DFP' http://www.ebi.ac.uk/swo/SWO_1100075 R software This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values. http://www.ebi.ac.uk/swo/SWO_1100090 Discriminant Fuzzy Pattern Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High' http://www.ebi.ac.uk/swo/SWO_1100093 'DNAcopy' http://www.ebi.ac.uk/swo/SWO_1100075 R software Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number http://www.ebi.ac.uk/swo/SWO_1100094 'EBImage' http://www.ebi.ac.uk/swo/SWO_1100075 R software EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. http://www.ebi.ac.uk/swo/SWO_1100095 'EBarrays' http://www.ebi.ac.uk/swo/SWO_1100075 R software EBarrays provides tools for the analysis of replicated/unreplicated microarray data. http://www.ebi.ac.uk/swo/SWO_1100098 Expert 2100 http://www.ebi.ac.uk/swo/SWO_0000034 Agilent Technologies Software Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools. http://www.ebi.ac.uk/swo/SWO_1100099 FACS data http://purl.obolibrary.org/obo/IAO_0000027 data item FACS data is data which describes flow cytometry data sets. http://www.ebi.ac.uk/swo/SWO_1100106 GACK http://www.ebi.ac.uk/swo/SWO_0000001 software Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK. http://www.ebi.ac.uk/swo/SWO_1100109 GEMTools 2.4 http://www.ebi.ac.uk/swo/SWO_0000001 software Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery. http://www.ebi.ac.uk/swo/SWO_1100111 GEOmetadb http://www.ebi.ac.uk/swo/SWO_1100075 R software The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. http://www.ebi.ac.uk/swo/SWO_1100112 GEOquery http://www.ebi.ac.uk/swo/SWO_1100075 R software The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data. http://www.ebi.ac.uk/swo/SWO_1100113 GGBase http://www.ebi.ac.uk/swo/SWO_1100075 R software This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc. http://www.ebi.ac.uk/swo/SWO_1100116 AtlasImage http://www.ebi.ac.uk/swo/SWO_0000001 software Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays. http://www.ebi.ac.uk/swo/SWO_1100117 CBS http://purl.obolibrary.org/obo/IAO_0000064 algorithm The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm. http://www.ebi.ac.uk/swo/SWO_1100119 'CGHbase' http://www.ebi.ac.uk/swo/SWO_1100075 R software Contains functions and classes that are needed by arrayCGH packages. http://www.ebi.ac.uk/swo/SWO_1100120 'CGHcall' http://www.ebi.ac.uk/swo/SWO_1100075 R software Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. http://www.ebi.ac.uk/swo/SWO_1100121 'CGHregions' http://www.ebi.ac.uk/swo/SWO_1100075 R software Dimension Reduction for Array CGH Data with Minimal Information Loss http://www.ebi.ac.uk/swo/SWO_1100122 CHP binary format http://edamontology.org/format_2333 binary format CHP binary format is a binary data format specification created by Affymetrix, stored in little-endian format and used to store expression, resequencing and genotyping results from algorithms implemented in the GCOS 1.2, 1.3 and 1.4 and BRLMM Analysis Tool software applications. http://www.ebi.ac.uk/swo/SWO_1100124 'DynDoc' http://www.ebi.ac.uk/swo/SWO_1100075 R software A set of functions to create and interact with dynamic documents and vignettes. http://www.ebi.ac.uk/swo/SWO_1100128 bcbio http://www.ebi.ac.uk/swo/SWO_0000001 software bcbio provides a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology. http://www.ebi.ac.uk/swo/SWO_1100129 shinyNGS http://www.ebi.ac.uk/swo/SWO_0000001 software Shinyngs is an R package designed to facilitate downstream analysis of RNA-seq and similar expression data with various exploratory plots and data mining tools. http://www.ebi.ac.uk/swo/SWO_1100130 Seurat http://www.ebi.ac.uk/swo/SWO_0000001 software Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. http://www.ebi.ac.uk/swo/SWO_1100131 Graphpad Prism http://www.ebi.ac.uk/swo/SWO_0000001 software GraphPad Prism is a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers. http://www.ebi.ac.uk/swo/SWO_1100132 Salmon http://www.ebi.ac.uk/swo/SWO_0000001 software Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data. http://www.ontodm.com/OntoDM-core/OntoDM_000037 ensemble specification http://kt.ijs.si/panovp/OntoDM#OntoDM_000034 generalization specification A ensemble of generalizations specification is a generalization specification and denotes a type of generalization that is produced by a ensemble algorithm. This algorithm produces a set of generalizations at its output. http://www.ontodm.com/OntoDM-core/OntoDM_000072 clustering algorithm http://www.ontodm.com/OntoDM-core/OntoDM_731692 single generalization algorithm Clustering algorithm is a data mining algorithm that solves a clustering task and as a result produces a clustering. http://www.ontodm.com/OntoDM-core/OntoDM_000078 pattern specification http://www.ontodm.com/OntoDM-core/OntoDM_419460 single generalization specification A patten specification is a single generalization specification and denotes a pattern P on type T which is a boolean funtion on objects of type T. http://www.ontodm.com/OntoDM-core/OntoDM_000112 clustering specification http://www.ontodm.com/OntoDM-core/OntoDM_419460 single generalization specification Clustering specification is a single generalization specification is a generalization specification and denotes a type of generalization that models the mapping of a set of objects S of type T from S to a set of natural numbers {1,...K}. This generalization is obtained by appliing a clustering algorithm on a set of data. http://www.ontodm.com/OntoDM-core/OntoDM_000160 predictive modeling algorithm http://www.ontodm.com/OntoDM-core/OntoDM_731692 single generalization algorithm Predictive modeling algorithm is a data mining algorithm that solves a predictive modeling task and as a result produces a predictive model. http://www.ontodm.com/OntoDM-core/OntoDM_000192 pattern discovery algorithm http://www.ontodm.com/OntoDM-core/OntoDM_731692 single generalization algorithm Pattern discovery algorithm is a data mining algorithm that solves a pattern discovery task and as a result produces a set of patterns. http://www.ontodm.com/OntoDM-core/OntoDM_000228 predictive model specification http://www.ontodm.com/OntoDM-core/OntoDM_419460 single generalization specification Predictive model specification is a single generalization specification and denotes a type of generalization that represents a mapping taking objects of type Td and returns objects of type To. http://www.ontodm.com/OntoDM-core/OntoDM_000285 probability distribution specification http://www.ontodm.com/OntoDM-core/OntoDM_419460 single generalization specification A probability distribution specification is a single generalization specification and denotes a type of generalization that is a mapping from objects of type T to non-negative reals. This generalization is an output of a probability distribution estimation algorithm. http://purl.obolibrary.org/obo/OBI_0002989 material supplier http://purl.obolibrary.org/obo/BFO_0000040 material entity A person or organization that provides material supplies to other people or organizations. http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires human being http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria http://purl.obolibrary.org/obo/OBI_0100026 organism eubacteria http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata bony vertebrates http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/OBI_0100026 organism eukaryotes http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi tetrapods http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda amniotes http://purl.obolibrary.org/obo/NCBITaxon_33208 Metazoa http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta multicellular animals http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota mammals http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria vertebrates http://www.ebi.ac.uk/swo/data/SWO_3000083 .mgf http://edamontology.org/format_2330 Textual format MASCOT generic format http://www.ebi.ac.uk/swo/data/SWO_3000022 SVG http://www.ebi.ac.uk/swo/data/SWO_3000021 vector image format Scalable Vector Graphics http://www.ebi.ac.uk/swo/data/SWO_3000023 AI http://www.ebi.ac.uk/swo/data/SWO_3000021 vector image format Adobe Illustrator format http://www.ebi.ac.uk/swo/data/SWO_3000077 .gz http://purl.obolibrary.org/obo/IAO_0000098 data format specification GZipped format http://www.ebi.ac.uk/swo/data/SWO_3000078 .zip http://purl.obolibrary.org/obo/IAO_0000098 data format specification Zipped format http://www.ebi.ac.uk/swo/data/SWO_3000080 RIFF http://purl.obolibrary.org/obo/IAO_0000098 data format specification Resource Interchange File Format http://www.ebi.ac.uk/swo/data/SWO_3000081 .bw http://purl.obolibrary.org/obo/IAO_0000098 data format specification BigWig format http://www.ebi.ac.uk/swo/data/SWO_3000082 .csv http://edamontology.org/format_2330 Textual format Comma-separated value format http://www.ebi.ac.uk/swo/data/SWO_3000084 .mysql http://edamontology.org/format_2330 Textual format MySQL format http://www.ebi.ac.uk/swo/data/SWO_3000085 .sql http://edamontology.org/format_2330 Textual format SQL format http://www.ebi.ac.uk/swo/license/SWO_1000001 Creative Commons http://www.ebi.ac.uk/swo/SWO_0000002 software license CC http://www.ebi.ac.uk/swo/license/SWO_1000003 MPL v1.1 http://www.ebi.ac.uk/swo/license/SWO_9000088 MPL Mozilla Public License Version 1.1 http://www.ebi.ac.uk/swo/license/SWO_1000004 GNU GPL http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free License Type GNU General Public License http://www.ebi.ac.uk/swo/license/SWO_9000086 LPPL http://www.ebi.ac.uk/swo/license/SWO_1000043 GNU Project Free License Type Latex Project Public License http://www.ebi.ac.uk/swo/license/SWO_9000088 MPL http://www.ebi.ac.uk/swo/license/SWO_1000008 Open source software license Mozilla Public License http://www.ebi.ac.uk/swo/SWO_0000179 GenePix 4100A http://www.ebi.ac.uk/swo/SWO_0000181 GenePix GenePix 4100A [Axon Instruments] http://www.ebi.ac.uk/swo/SWO_0000181 GenePix http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix GenePix [Axon Instruments] http://www.ebi.ac.uk/swo/SWO_0000187 GenePix Pro [Axon Instruments] http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro Axon GenePix Pro http://www.ebi.ac.uk/swo/SWO_0000199 GenePix Pro 4.0 http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro Genepix Pro 4.0 http://www.ebi.ac.uk/swo/SWO_0000200 GenePix Pro 3.0 http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro Genepix pro 3.0 http://www.ebi.ac.uk/swo/SWO_0000272 MicroArraySuite 5.0 http://www.ebi.ac.uk/swo/SWO_0000271 MIcroarray Analysis Suite MAS 5.0 software http://www.ebi.ac.uk/swo/SWO_0000419 ScanArray v3.1 software http://www.ebi.ac.uk/swo/SWO_0000418 ScanArray ScanArray version 3.1 http://www.ebi.ac.uk/swo/SWO_0000518 dcf http://edamontology.org/format_2330 Textual format debian control file format http://www.ebi.ac.uk/swo/SWO_0000566 gpr format http://www.ebi.ac.uk/swo/data/SWO_3000046 tab delimited file format GenePix Pro Results file format http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/UO_0000005 temperature unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000006 substance unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000051 concentration unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000095 volume unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000105 frequency unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000270 volumetric flow rate unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000280 rate unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://www.ebi.ac.uk/swo/SWO_0000134 MLXTRAN http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000136 NMTRAN http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000012 Java http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000091 ActionScript http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000092 Ada http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000093 AppleScript http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000094 Assembly http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000095 C http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000096 C Sharp http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000097 C++ http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000098 COBOL http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000099 ColdFusion http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000100 D http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000101 Delphi http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000102 Dylan http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000103 Eiffel http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000104 Forth http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000105 Fortran http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000106 Groovy http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000107 Haskell http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000108 JavaScript http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000109 LabVIEW http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000110 Lisp http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000111 Lua http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000112 Maple http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000113 Mathematica http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000114 Pascal http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000115 Perl http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000116 PHP http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000117 Prolog http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000119 REXX http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000120 Ruby http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000121 SAS http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000122 Scala http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000123 Scheme http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000124 Shell http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000125 Smalltalk http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000126 SQL http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000127 Turing http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000128 Verilog http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000129 VHDL http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000130 Visual Basic http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000160 GWT http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000161 S language http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000162 Excel http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000274 MATLAB language http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000415 R language http://purl.obolibrary.org/obo/IAO_0000025 programming language http://www.ebi.ac.uk/swo/SWO_0000233 ILLUMINA data http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000253 LC-MS data http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000270 MAQC data http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000282 Mutual information matrix (MIM) http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000406 Gene list http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000408 Clustered data set http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000469 Annotation data packages http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000484 Bitmap object http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000554 Gene expression dataset http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000575 HTML report http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000620 Meta data http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000640 OMICS data http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000661 Graph plot http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_0000670 qPCR data http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_1100008 ALL/AML data set http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_1100012 AP-MS data http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_1100080 Text data set http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_1100081 CSV data set http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_1100092 Digital gene expression (DGE) datasets http://purl.obolibrary.org/obo/IAO_0000027 data item http://www.ebi.ac.uk/swo/SWO_1100110 GEO data type http://purl.obolibrary.org/obo/IAO_0000027 data item http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_511616 data visualization algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM_361570 data processing algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000148 Firth's bias reduction procedure http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000165 Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000169 Gene Recommender algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000172 Gamma-Gamma hierarchical model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000173 Gaussian locally weighted regression http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000174 Gene-Set Enrichment Analysis http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000212 Hexagon binning algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000215 Heterogeneous Error Model (HEM) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000216 Hubert’s gamma http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000217 Hidden Markov Model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000218 Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000220 HaarSeg algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000221 Hardy-Weinberg equilibrium http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000227 Hypergeometric probability http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000229 Iteratively ReWeighted Least Squares http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000243 Jaccard’s index http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000250 'KLD' http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000255 Locally Moderated Weighted-t (LMW) method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000256 Lognormal Normal Model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000257 Lognormal Normal with Modied Variance Model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000261 Langmuir Isotherm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000262 Laplace mixture model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000263 Library Search Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000264 Loess algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000265 Logic regression http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000267 Median Average Difference Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000276 Multivariate correlation estimator http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000277 Markov Chain Monte Carlo http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000281 'MI' http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000287 Mahalanobis distance http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000296 Misclassification-Penalized Posteriors (MiPP) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000298 Mixed model equations http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000304 'Needleman-Wunsch' http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000306 Nonlinear Estimation by Iterative Partial Least Squares http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000313 Presence-Absence calls with Negative Probesets (PANP) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000315 Pearson correlation estimator http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000320 Probe level Locally moderated Weighted median-t (PLW) method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000321 PPC algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000326 Power Law Global Error Model (PLGEM) analysis method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000328 PLIER (Probe Logarithmic Error Intensity Estimate) method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000332 Radial basis function http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000334 R interface to boost graph library algorithm (RBGL) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000336 Random effects model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000339 Regression model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000340 RMA http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000341 RMA+ http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000342 RMA++ http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000364 Robust likelihood-based survival modeling http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000371 S-Score algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000372 Serial Analysis of Gene Expression (SAGE) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000374 SAM http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000386 SNPRMA algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000391 SVDimpute algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000423 Signaling Pathway Impact Analysis (SPIA) algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000425 Similarity score http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000426 'Smith-Waterman' http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000437 Theodore Ts’o’s http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000441 Variance-stabilizing transformation (VST) algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000444 WilcEbam http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000445 Wilcoxon http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000477 Associative T method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000478 AvgNRRs http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000490 Bootstrap http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000503 Concordance http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000524 Dynamic programming algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000531 f-test http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000552 Gene array analysis algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000573 Hierarchical clustering http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000576 Hypergeometric enrichment http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000584 Iterative local regression and model selection http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000587 k-cores http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000588 k-means http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000589 k-nearest neighbour classification http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000592 Likelihood method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000595 Linear modelling http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000597 Local-pooled-error http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000602 Logit-t algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000614 'MAS5' http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000618 M-estimation regression http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000626 mrnet algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000627 Multinomial probit regression with Gaussian Process priors http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000629 Multivariate t mixture models http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000631 Negative binomial distribution http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000633 Neural networks models http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000664 Position weight matrix (PWM ) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000673 Quantile normalization http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000674 Quantile regression techniques http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000680 Rank-invariant set normalization http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000681 Rank product non-parametric method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000695 Sim method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000715 't-test' http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_0000722 Two-stage measurement error model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100000 2-sample pooled t-test http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100007 Average log expression across arrays (ALE) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100009 AMDIS http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100013 ARACNE algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100015 AWS algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100033 Iterative Bayesian Model Averaging (BMA) http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100034 Base-Pair-Distance Kernel http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100039 BaldiLongT http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100041 Bayesian Model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100059 Continuous Wavelet Transform (CWT)-based peak detection algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100061 Category analysis http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100072 Chi-square http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100078 F test http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100086 Complex Estimation Algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100091 DFW http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100096 Expectation-Maximization(EM) algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100097 Empirical Bayes rule http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100100 FARMS http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100101 FC http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100102 'FDR' http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100103 Fixed effect model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100105 Fischer's Exact Test http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100107 GASSCO method http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100114 Gamma Gamma Model http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100118 CBS algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100123 CLR algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ebi.ac.uk/swo/SWO_1100125 FoxDimmicT http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://www.ontodm.com/OntoDM-core/OntoDM_000038 data mining algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://edamontology.org/format_2330 Textual format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://edamontology.org/format_2333 binary format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000064 NONMEM data format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000008 image format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000013 web page specification http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000014 document exchange format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000030 word processing document format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000033 programming language format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000079 audio format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000449 Xba.CQV and Xba.regions http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000497 chamber slide format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000508 covdesc file http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000516 .data http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000519 design file http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000562 gmt format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000598 log file http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000600 logicFS dataset http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000644 pair file http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000655 pedigree data file http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000708 sproc http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/SWO_0000709 sqlite http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://www.ebi.ac.uk/swo/data/SWO_3000069 sequence feature format http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2157 Archaea http://purl.obolibrary.org/obo/OBI_0100026 organism http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_778151 data processing task http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_40000002 matrix manipulation http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000001 spreadsheet editing http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000003 document outlining http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000004 image compression http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000005 ontology engineering http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000006 word processing http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000008 simulation and analysis of biochemical networks http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000012 file rendering http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000013 annotation editing http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000014 biological data processing http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000016 molecular sequence analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_4000017 citation management http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_7000013 cross validation http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/objective/SWO_7000018 differential expression analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/SWO_0000467 data annotation http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/SWO_0000502 dataset comparison http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/SWO_0000553 gene expression analysis http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/SWO_0000648 parse http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/swo/SWO_1100074 distance calculation http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ontodm.com/OntoDM-core/OntoDM_000098 data mining task http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://www.ebi.ac.uk/efo/swo/SWO_0000687 obsolete .rma format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://urigen_local_uri/963a1b3b-49f2-4ef9-8f37-5e9cd5403b2a/http://www.ebi.ac.uk/swo/data/SWO_3000069 obsolete sequence feature format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://kt.ijs.si/panovp/OntoDM#OntoDM_953101 data visualization task http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/Class_6 obsolete matlab software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000004 obsolete 50-50 MANOVA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000005 obsolete ABarray http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000007 obsolete Algorithms for Calculating Microarray Enrichment http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000008 obsolete Affymetrix Expression Console http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000009 obsolete AIDA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000019 obsolete Absolute Expression Analysis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000020 obsolete Absolute Expression Analysis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000021 obsolete 'AffyCompatible' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000022 obsolete 'AffyExpress' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000024 obsolete Affymetrix GCOS v1.2 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000025 obsolete Affymetrix GeneChip Operating Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000026 obsolete Affymetrix Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000027 obsolete Agi4x44PreProcess http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000028 obsolete Agilent Feature Extraction 5.1.1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000029 obsolete Agilent Feature Extraction software version 7.1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000030 obsolete Agilent Feature Extraction software version 7.5 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000031 obsolete Agilent Feature Extraction software version A.5.1.1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000032 obsolete Agilent Scan Control http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000034 obsolete Agilent Technologies Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000035 obsolete 'AnnotationDbi' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000037 obsolete Applied Biosystems 1700 Expression Array System Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000039 obsolete ArrayGauge http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000040 obsolete ArrayNorm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000041 obsolete 'ArrayTools' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000042 obsolete ArrayVision http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000044 obsolete ArrayVision 6.0 (Imaging Research Inc.) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000045 obsolete Array_vision_(Interfocus) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000046 obsolete AtlasImage http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000047 obsolete Axon GenePix Pro 3 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000048 obsolete BAC http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000050 obsolete 'BCRANK' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000053 obsolete 'BGmix' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000054 obsolete BLAST http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000058 obsolete BRB-ArrayTools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000059 obsolete 'BSgenome' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000060 obsolete BZScan http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000063 obsolete BasReader 3.01 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000065 obsolete Beadstudio http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000066 obsolete 'BicARE' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000068 obsolete 'BioMVCClass' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000070 obsolete 'Biobase' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000071 obsolete 'BiocCaseStudies' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000072 obsolete BioConductor Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000075 obsolete 'Biostrings' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000076 obsolete BlueFuse http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000077 obsolete 'BufferedMatrix' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000078 obsolete 'BufferedMatrixMethods' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000079 obsolete 'CALIB' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000080 obsolete 'CAMERA' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000085 obsolete 'CGHbase' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000086 obsolete 'CGHcall' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000087 obsolete 'CGHregions' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000090 obsolete 'CMA' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000092 obsolete 'CORREP' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000096 obsolete CARMAweb http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000098 obsolete Category http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000099 obsolete 'ChemmineR' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000100 obsolete ChipReader 3.1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000101 obsolete ChipSkipper http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000102 obsolete ChipSkipper V0.99 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000103 obsolete multiscan http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000104 obsolete affy http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000105 obsolete affycomp http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000109 obsolete Annotation-Driven Clustering http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000111 obsolete R software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000115 obsolete MAGE-TAB inputting software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000116 obsolete Text data set http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000117 obsolete CSV data set http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000120 obsolete 'CoCiteStats' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000121 obsolete CodeLink Expression Analysis Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000122 obsolete CodeLink Expression Scanning Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000124 obsolete Cyber-T http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000125 obsolete 'DEDS' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000126 obsolete 'DFP' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000130 obsolete 'DNAcopy' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000132 obsolete 'DynDoc' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000133 obsolete 'EBImage' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000134 obsolete 'EBarrays' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000138 obsolete Expert 2100 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000147 obsolete Agilent Feature Extraction Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000152 obsolete GACK http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000154 obsolete GC-RMA Quantification http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000155 obsolete GEMTools 2.4 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000158 obsolete GEOmetadb http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000159 obsolete GEOquery http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000161 obsolete GGBase http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000163 obsolete GGtools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000164 obsolete GLAD http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000166 obsolete GLEAMS software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000167 obsolete GMS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000168 obsolete GOstats http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000170 obsolete GSEABase http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000171 obsolete GSEAlm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000175 obsolete GeneData Expressionist Analyst v4.0.5 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000176 obsolete Gene Pix http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000177 obsolete GenePix 3.0.6 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000178 obsolete GenePix 4.1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000179 obsolete GenePix 4100A http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000180 obsolete GenePix 5.0.1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000181 obsolete GenePix http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000182 obsolete GenePix Pro http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000183 obsolete GenePix Pro 3 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000184 obsolete GenePix Pro 5.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000185 obsolete GenePix Pro 6.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000186 obsolete GenePix Pro 6 [Axon Instruments] http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000187 obsolete GenePix Pro [Axon Instruments] http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000188 obsolete GeneR http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000189 obsolete GeneRegionScan http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000190 obsolete GeneRfold http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000191 obsolete GeneSelectMMD http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000192 obsolete GeneSelector http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000193 obsolete GeneSpring http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000194 obsolete GeneSpringGX http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000195 obsolete GeneTac Analyser http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000196 obsolete GeneTraffic http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000199 obsolete GenePix Pro 4.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000200 obsolete GenePix Pro 3.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000201 obsolete GeneticsBase http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000202 obsolete GeneticsDesign http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000203 obsolete GeneticsPed http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000205 obsolete GenomeGraphs http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000206 obsolete GlobalAncova http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000207 obsolete GOSemSim http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000208 obsolete GraphAT http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000209 obsolete GraphAlignment http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000210 obsolete GridGrinder http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000213 obsolete HELP http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000214 obsolete HEM http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000222 obsolete Harshlight http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000224 obsolete Heatplus http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000225 obsolete HilbertVis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000226 obsolete HilbertVisGUI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000228 obsolete ICS-501 (version 2.3) Image Capture System http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000230 obsolete IRanges http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000231 obsolete ITALICS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000234 obsolete ImaGene4.1 software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000235 obsolete ImaGene 3.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000236 obsolete ImageQuant http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000237 obsolete ImageReader http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000238 obsolete ImaGene http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000239 obsolete Imagene v4.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000241 obsolete Initial microarray data processing (data filtering, local normalisation and quality control) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000245 obsolete Jaguar http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000246 obsolete KCsmart http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000247 obsolete KEGGSOAP http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000248 obsolete KEGGgraph http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000252 obsolete LBE http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000254 obsolete LMGene http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000258 obsolete LPE http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000259 obsolete LPEadj http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000260 obsolete publisher role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000266 obsolete MAANOVA v1.2 package for MATLAB http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000269 obsolete MANOR http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000271 obsolete MIcroarray Analysis Suite http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000272 obsolete MicroArraySuite 5.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000275 obsolete MAVI Pro http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000279 obsolete MCRestimate http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000280 obsolete MEDME http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000283 obsolete MLInterfaces http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000285 obsolete MVCClass http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000288 obsolete MantelCorr http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000289 obsolete MassSpecWavelet http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000292 obsolete MeasurementError.cor http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000293 obsolete MergeMaid http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000294 obsolete Mfuzz http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000295 obsolete MiPP http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000297 obsolete MicroArraySuite 4.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000307 obsolete OCplus http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000308 obsolete OLIN http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000309 obsolete OLINgui http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000310 obsolete Optiquant http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000311 obsolete OrderedList http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000312 obsolete OutlierD http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000314 obsolete PAnnBuilder http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000316 obsolete PCpheno http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000317 obsolete PGSEA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000319 obsolete PLPE http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000322 obsolete PROcess http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000324 obsolete Pathways 2.01 software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000327 obsolete Probe Cell Analysis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000329 obsolete QuantArray scanner software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000330 obsolete QuantArray, PackaardBiochip technologies http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000331 obsolete QuantArray version 2 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000333 obsolete RBGL http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000335 obsolete RBioinf http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000338 obsolete RLMM http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000343 obsolete RMAExpress http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000344 obsolete RMAExpress 2.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000345 obsolete RMAExpress quantification http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000346 obsolete RMAGEML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000347 obsolete RNAither http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000348 obsolete ROC http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000349 obsolete RWebServices http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000350 obsolete RankProd http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000352 obsolete RbcBook1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000353 obsolete Rdbi http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000354 obsolete RdbiPgSQL http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000355 obsolete Rdisop http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000356 obsolete RefPlus http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000358 obsolete Resourcerer http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000359 obsolete Rgraphviz http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000360 obsolete Ringo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000361 obsolete Rintact http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000362 obsolete Rmagpie http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000365 obsolete Rosetta Resolver http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000367 obsolete RpsiXML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000368 obsolete Rredland http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000369 obsolete Rtreemix http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000370 obsolete Ruuid http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000373 obsolete SAGx http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000375 obsolete SAS/STAT Software, Version 8 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000377 obsolete SBMLR http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000379 obsolete_SBML file http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000382 obsolete SIM http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000383 obsolete SLGI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000384 obsolete SLqPCR http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000385 obsolete SMAP http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000387 obsolete SNPchip http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000388 obsolete SPIA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000390 obsolete SSPA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000392 obsolete software developer role http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000396 obsolete software developer organization http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000397 obsolete software publisher organization http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000399 obsolete_html http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000405 obsolete ArrayExpress Bioconductor http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000416 obsolete ScISI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000417 obsolete ScanAlyze http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000418 obsolete ScanArray http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000419 obsolete ScanArray v3.1 software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000420 obsolete scanning software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000421 obsolete Scanning software G2565AA version A6.3.1 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000422 obsolete ShortRead http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000424 obsolete Silicon Genetics Genespring http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000428 obsolete Spot quantification http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000429 obsolete Spotfinder [TIGR] http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000430 obsolete Spotfire http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000432 obsolete TAS Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000434 obsolete_TIFF image http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000435 obsolete TargetSearch http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000438 obsolete TypeInfo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000442 obsolete VanillaICE http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000446 obsolete XDE http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000447 obsolete XDotsReader http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000448 obsolete_XML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000450 obsolete Array Comparative Genomic Hybridization http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000451 obsolete Acuity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000452 obsolete affxparser http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000453 obsolete affyContam http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000454 obsolete affyImGUI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000455 obsolete 'affyPLM' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000456 obsolete affyPara http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000457 obsolete affyQCReport http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000458 obsolete affyTiling http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000459 obsolete 'affycoretools' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000460 obsolete affyio http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000461 obsolete affypdnn http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000463 obsolete altcdfenvs http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000465 obsolete annaffy http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000466 obsolete 'annotate' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000468 obsolete annotationTools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000470 obsolete 'apComplex' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000471 obsolete aroma.light http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000472 obsolete arrayMvout http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000473 obsolete arrayQuality http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000474 obsolete arrayQualityMetrics http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000475 obsolete arrayWoRx 2.0 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000476 obsolete arrayWoRx http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000479 obsolete 'beadarray' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000480 obsolete 'beadarraySNP' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000481 obsolete 'betr' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000482 obsolete bgafun http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000483 obsolete bgx http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000484 obsolete Bitmap object http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000485 obsolete bioDist http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000486 obsolete 'biocDatasets' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000487 obsolete 'biocGraph' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000488 obsolete 'biocViews' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000489 obsolete biomaRT http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000491 obsolete 'bridge' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000494 obsolete 'cellHTS' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000495 obsolete 'cellHTS2' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000496 obsolete cghMCR http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000499 obsolete 'clusterStab' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000500 obsolete_Clustering algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000501 obsolete 'codelink' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000502 obsolete dataset comparison http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000504 obsolete convert http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000505 obsolete copa http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000506 obsolete cosmo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000507 obsolete cosmoGUI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000510 obsolete crlmm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000512 obsolete ctc http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000513 obsolete dChip http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000514 obsolete daMA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000520 obsolete 'diffGeneAnalysis' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000521 obsolete 'domainsignatures' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000522 obsolete 'dualKS' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000523 obsolete dyebias http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000525 obsolete ecolitk http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000526 obsolete edd http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000527 obsolete 'edgeR' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000528 obsolete exonmap http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000529 obsolete 'explorase' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000530 obsolete 'externalVector' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000532 obsolete factDesign http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000533 obsolete fbat http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000534 obsolete fdrame http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000536 obsolete flagme http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000537 obsolete flowClust http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000538 obsolete flowCore http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000539 obsolete flowFlowJo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000540 obsolete flowQ http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000541 obsolete flowStats http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000542 obsolete flowUtils http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000543 obsolete flowViz http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000544 obsolete gaga http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000545 obsolete 'gaggle' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000546 obsolete gcRMA quantification http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000547 obsolete gcrma http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000549 obsolete 'genArise' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000550 obsolete gene2pathway http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000551 obsolete geneRecommender http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000555 obsolete genefilter http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000556 obsolete genemeta http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000557 obsolete geneplotter http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000558 obsolete genomeIntervals http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000561 obsolete globaltest http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000563 obsolete goProfiles http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000564 obsolete goTools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000565 obsolete gpls http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000567 obsolete graph http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000571 obsolete_Heatmap http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000572 obsolete hexbin http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000574 obsolete hopach http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000575 obsolete HTML report http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000577 obsolete hypergraph http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000578 obsolete Icens http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000579 obsolete idiogram http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000581 obsolete impute http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000582 obsolete iterativeBMA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000583 obsolete iterativeBMAsurv http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000585 obsolete_.java file http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000586 obsolete_jpeg http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000590 obsolete keggorth http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000591 obsolete lapmix http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000593 obsolete limma http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000594 obsolete limmaGUI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000599 obsolete logicFS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000601 obsolete logitT http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000603 obsolete lumi http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000604 obsolete maCorrPlot http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000605 obsolete maDB http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000606 obsolete maSigPro http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000607 obsolete maanova http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000608 obsolete macat http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000609 obsolete made4 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000610 obsolete maigesPack http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000611 obsolete makePlatformDesign http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000612 obsolete makecdfenv http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000613 obsolete marray http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000616 obsolete matchprobes http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000617 obsolete mdqc http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000619 obsolete metaArray http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000621 obsolete metahdep http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000622 obsolete miRNApath http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000623 obsolete microRNA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000625 obsolete minet http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000630 obsolete multtest http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000632 obsolete nem http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000635 obsolete nnNorm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000636 obsolete nudge http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000637 obsolete occugene http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000638 obsolete oligo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000639 obsolete oligoClasses http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000641 obsolete oneChannelGUI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000642 obsolete ontoTools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000645 obsolete pamr http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000646 obsolete panp http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000647 obsolete parody http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000648 obsolete parse http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000649 obsolete pathRender http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000650 obsolete pcaMethods http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000651 obsolete pcot2 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000652 obsolete_pdf http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000653 obsolete pdInfoBuilder http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000654 obsolete pdmclass http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000656 obsolete pgUtils http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000657 obsolete pickgene http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000658 obsolete pkgDepTools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000659 obsolete plgem http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000660 obsolete plier http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000661 obsolete Graph plot http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000662 obsolete plw http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000663 obsolete_png http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000665 obsolete ppiStats http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000666 obsolete prada http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000667 obsolete preprocessCore http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000668 obsolete_ps http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000669 obsolete puma http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000671 obsolete qpcrNorm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000672 obsolete qpgraph http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000675 obsolete quantsmooth http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000676 obsolete qvalue http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000677 obsolete rHVDM http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000678 obsolete rMAT http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000679 obsolete rama http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000683 obsolete rbsurv http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000685 obsolete reb http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000686 obsolete rflowcyt http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000688 obsolete rsbml http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000689 obsolete rtracklayer http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000690 obsolete safe http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000691 obsolete sagenhaft http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000692 obsolete seqLogo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000693 obsolete sigPathway http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000694 obsolete siggenes http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000696 obsolete simpleaffy http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000697 obsolete simulatorAPMS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000698 obsolete sizepower http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000699 obsolete xmapbridge http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000700 obsolete snapCGH http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000701 obsolete snpMatrix http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000703 obsolete spikeLI http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000704 obsolete spkTools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000705 obsolete splicegear http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000706 obsolete splots http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000707 obsolete spotSegmentation http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000710 obsolete sscore http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000711 obsolete ssize http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000712 obsolete stam http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000714 obsolete stepNorm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000716 obsolete tilingArray http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000717 obsolete timecourse http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000718 obsolete tkWidgets http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000719 obsolete topGO http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000720 obsolete tspair http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000721 obsolete twilight http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000723 obsolete vbmp http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000725 obsolete vsn http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000726 obsolete weaver http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000727 obsolete webbioc http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000728 obsolete widgetTools http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000729 obsolete xcms http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000730 obsolete xps http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000731 obsolete yaqcaffy http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/objective/SWO_4000007 obsolete software development http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/objective/SWO_4000015 obsolete modelling http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/ontology obsolete_ontology http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/software_before_Microsoft_2007 obsolete software before Microsoft 2007 http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000107 obsolete Feature Extraction Software http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000003 obsolete 2-sample pooled t-test http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000006 obsolete 'ACME' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000010 obsolete Average log expression across arrays (ALE) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000011 obsolete ALL/AML data set http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000012 obsolete AMDIS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000013 obsolete ANCOVA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000014 obsolete 'ANOVA' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000015 obsolete AP-MS data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000016 obsolete ARACNE algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000017 obsolete ARR http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000018 obsolete AWS algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000049 obsolete Binning clustering method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000051 obsolete_BED format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000052 obsolete BGL http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000055 obsolete Iterative Bayesian Model Averaging (BMA) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000056 obsolete Base-Pair-Distance Kernel http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000057 obsolete BPMAP http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000062 obsolete BaldiLongT http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000064 obsolete Bayesian Model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000081 obsolete CBS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000082 obsolete CBS algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000083 obsolete CDF binary format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000084 obsolete CEL binary format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000088 obsolete CHP binary format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000089 obsolete CLR algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000091 obsolete CMA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000094 obsolete CRLMM algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000095 obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000097 obsolete Category analysis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000106 obsolete PCMG http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000108 obsolete Chi-square http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000110 obsolete distance calculation http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000112 obsolete BCRANK http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000113 obsolete Cosmo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000114 obsolete F test http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000118 obsolete Non-linear functional regression model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000123 obsolete Complex Estimation Algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000127 obsolete Discriminant Fuzzy Pattern Algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000128 obsolete DFW http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000129 obsolete Digital gene expression (DGE) datasets http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000135 obsolete Expectation-Maximization(EM) algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000137 obsolete Empirical Bayes rule http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000139 obsolete_FACS ( fluorescence-activated cell sorter) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000140 obsolete FACS data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000141 obsolete FARMS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000142 obsolete_FASTA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000143 obsolete FC http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000144 obsolete_FCS http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000145 obsolete 'FDR' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000146 obsolete Fixed effect model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000148 obsolete Firth's bias reduction procedure http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000149 obsolete Fischer's Exact Test http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000150 obsolete FoxDimmicT http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000153 obsolete GASSCO method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000156 obsolete GEO data type http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000157 obsolete GEO Matrix Series format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000162 obsolete Gamma Gamma Model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000165 obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000169 obsolete Gene Recommender algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000172 obsolete Gamma-Gamma hierarchical model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000173 obsolete Gaussian locally weighted regression http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000174 obsolete Gene-Set Enrichment Analysis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000212 obsolete Hexagon binning algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000215 obsolete Heterogeneous Error Model (HEM) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000216 obsolete Hubert’s gamma http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000217 obsolete Hidden Markov Model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000218 obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000219 obsolete Hidden Variable Dynamic Modelling HVDM) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000220 obsolete HaarSeg algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000221 obsolete Hardy-Weinberg equilibrium http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000227 obsolete Hypergeometric probability http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000229 obsolete Iteratively ReWeighted Least Squares http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000233 obsolete ILLUMINA data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000243 obsolete Jaccard’s index http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000249 obsolete KGML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000250 obsolete 'KLD' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000251 obsolete Kolmogorov Smirnov rank-sum based algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000253 obsolete LC-MS data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000255 obsolete Locally Moderated Weighted-t (LMW) method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000256 obsolete Lognormal Normal Model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000257 obsolete Lognormal Normal with Modied Variance Model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000261 obsolete Langmuir Isotherm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000262 obsolete Laplace mixture model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000263 obsolete Library Search Algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000264 obsolete Loess algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000265 obsolete Logic regression http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000267 obsolete Median Average Difference Algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000268 obsolete_MAGE-ML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000270 obsolete MAQC data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000274 obsolete MATLAB language http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000276 obsolete Multivariate correlation estimator http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000277 obsolete Markov Chain Monte Carlo http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000278 obsolete MCR algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000281 obsolete 'MI' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000282 obsolete Mutual information matrix (MIM) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000284 obsolete MMD http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000287 obsolete Mahalanobis distance http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000296 obsolete Misclassification-Penalized Posteriors (MiPP) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000298 obsolete Mixed model equations http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000304 obsolete 'Needleman-Wunsch' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000305 obsolete Nested Effects Models http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000306 obsolete Nonlinear Estimation by Iterative Partial Least Squares http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000313 obsolete Presence-Absence calls with Negative Probesets (PANP) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000315 obsolete Pearson correlation estimator http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000318 obsolete 'PLM' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000320 obsolete Probe level Locally moderated Weighted median-t (PLW) method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000321 obsolete PPC algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000323 obsolete Propagation of uncertainty in microarray analysis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000326 obsolete Power Law Global Error Model (PLGEM) analysis method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000328 obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000332 obsolete Radial basis function http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000334 obsolete R interface to boost graph library algorithm (RBGL) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000336 obsolete Random effects model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000337 obsolete Recursive Feature Elimination (RFE) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000339 obsolete Regression model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000340 obsolete RMA http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000341 obsolete RMA+ http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000342 obsolete RMA++ http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000363 obsolete Rnw http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000364 obsolete Robust likelihood-based survival modeling http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000371 obsolete S-Score algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000372 obsolete Serial Analysis of Gene Expression (SAGE) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000374 obsolete SAM http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000378 obsolete SBMLR format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000380 obsolete_SBML model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000381 obsolete SDF format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000386 obsolete SNPRMA algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000389 obsolete Semantic Similarity Measures http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000391 obsolete SVDimpute algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000398 obsolete 50-50 MANOVA algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000406 obsolete Gene list http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000408 obsolete Clustered data set http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000409 obsolete R data frame http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000415 obsolete R language http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000423 obsolete Signaling Pathway Impact Analysis (SPIA) algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000425 obsolete Similarity score http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000426 obsolete 'Smith-Waterman' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000437 obsolete Theodore Ts’o’s http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000441 obsolete Variance-stabilizing transformation (VST) algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000444 obsolete WilcEbam http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000445 obsolete Wilcoxon http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000449 obsolete Xba.CQV and Xba.regions http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000467 obsolete data annotation http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000469 obsolete Annotation data packages http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000477 obsolete Associative T method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000478 obsolete AvgNRRs http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000490 obsolete Bootstrap http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000493 obsolete cdt http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000497 obsolete chamber slide format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000498 obsolete cls http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000503 obsolete Concordance http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000508 obsolete covdesc file http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000509 obsolete database creation http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000516 obsolete .data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000518 obsolete dcf http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000519 obsolete design file http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000524 obsolete Dynamic programming algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000531 obsolete f-test http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000548 obsolete gct http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000552 obsolete Gene array analysis algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000553 obsolete gene expression analysis http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000554 obsolete Gene expression dataset http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000559 obsolete_gff format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000560 obsolete Global test http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000562 obsolete gmt format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000566 obsolete gpr format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000569 obsolete gtr http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000570 obsolete gxl format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000573 obsolete Hierarchical clustering http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000576 obsolete Hypergeometric enrichment http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000580 obsolete_Image http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000584 obsolete Iterative local regression and model selection http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000587 obsolete k-cores http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000588 obsolete k-means http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000589 obsolete k-nearest neighbour classification http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000592 obsolete Likelihood method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000595 obsolete Linear modelling http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000596 obsolete lma http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000597 obsolete Local-pooled-error http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000598 obsolete log file http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000600 obsolete logicFS dataset http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000602 obsolete Logit-t algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000614 obsolete 'MAS5' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000615 obsolete mas5 format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000618 obsolete M-estimation regression http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000620 obsolete Meta data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000624 obsolete_Microarray data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000626 obsolete mrnet algorithm http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000627 obsolete Multinomial probit regression with Gaussian Process priors http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000628 obsolete Multiple testing http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000629 obsolete Multivariate t mixture models http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000631 obsolete Negative binomial distribution http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000633 obsolete Neural networks models http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000634 obsolete_newick http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000640 obsolete OMICS data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000644 obsolete pair file http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000655 obsolete pedigree data file http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000664 obsolete Position weight matrix (PWM ) http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000670 obsolete qPCR data http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000673 obsolete Quantile normalization http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000674 obsolete Quantile regression techniques http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000680 obsolete Rank-invariant set normalization http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000681 obsolete Rank product non-parametric method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000682 obsolete .raw files http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000684 obsolete rda http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000695 obsolete Sim method http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000708 obsolete sproc http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000709 obsolete sqlite http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000713 obsolete Statistical tests http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000715 obsolete 't-test' http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000722 obsolete Two-stage measurement error model http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/efo/swo/SWO_0000724 obsolete data visualization http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/data/SWO_3000005 obsolete_XML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/data/SWO_3000037 obsolete_SBML http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/data/SWO_3000040 obsolete_OBO flat file format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/data/SWO_3000041 obsolete_text file format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/data/SWO_3000045 obsolete_MAGE tab format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://www.ebi.ac.uk/swo/data/SWO_3000048 obsolete_PSI-MI format http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/NCBITaxon_33154 Opisthokonta http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_33208 Metazoa http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_545286 data cleaning algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM_361570 data processing algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_573276 data selection algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM_361570 data processing algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_776185 data integration algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM_361570 data processing algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM-KDD_806059 data construction algorithm http://kt.ijs.si/panovp/OntoDM#OntoDM_361570 data processing algorithm http://edamontology.org/format_1910 newick http://edamontology.org/format_2330 Textual format http://edamontology.org/format_1929 FASTA format http://edamontology.org/format_2330 Textual format http://edamontology.org/format_2305 GFF http://edamontology.org/format_2330 Textual format http://edamontology.org/format_3003 BED format http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/data/SWO_3000043 plain text file format http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/data/SWO_3000056 BioPAX Manchester OWL Syntax format http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/SWO_0000363 Rnw http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/SWO_0000378 SBMLR format http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/SWO_0000381 SDF format http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/SWO_0000409 R data frame http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/SWO_0000615 mas5 format http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/SWO_0000684 rda http://edamontology.org/format_2330 Textual format http://www.ebi.ac.uk/swo/SWO_1100126 GEO Matrix Series format http://edamontology.org/format_2330 Textual format http://edamontology.org/format_3161 MAGE-ML http://edamontology.org/format_2332 XML http://edamontology.org/format_1478 PDBML http://edamontology.org/format_2332 XML http://www.ebi.ac.uk/swo/SWO_0000249 KGML http://edamontology.org/format_2332 XML http://www.ebi.ac.uk/swo/SWO_0000570 gxl format http://edamontology.org/format_2332 XML http://www.ebi.ac.uk/swo/SWO_1100014 ARR http://edamontology.org/format_2332 XML http://www.ebi.ac.uk/swo/SWO_0000596 lma http://edamontology.org/format_2333 binary format http://www.ebi.ac.uk/swo/SWO_0000010 WordStar http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000019 STARLIMS http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000026 software with image input http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000028 ontology engineering software http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000029 Microsoft developed software http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000031 Smultron http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000050 Ensembl http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000060 MUSCLE http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000064 TCoffee http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_9000076 software suite http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_9000077 Adobe Acrobat Reader http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_9000079 BioJava http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_9000081 BioPerl http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_9000091 Eclipse http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_9000093 Endnote http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000034 Agilent Technologies Software http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000167 GMS http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000228 ICS-501 (version 2.3) Image Capture System http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000237 ImageReader http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000275 MAVI Pro http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000420 scanning software http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000428 Spot quantification http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_1100006 AIDA http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_1100022 Affymetrix Software http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_1100079 MAGE-TAB inputting software http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_1100115 matlab software http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_1100127 software before Microsoft 2007 http://www.ebi.ac.uk/swo/SWO_0000001 software http://www.ebi.ac.uk/swo/SWO_0000016 MATLAB 7 http://www.ebi.ac.uk/swo/SWO_0000005 MATLAB http://www.ebi.ac.uk/swo/SWO_0000017 MATLAB 6 http://www.ebi.ac.uk/swo/SWO_0000005 MATLAB http://www.ebi.ac.uk/swo/SWO_0000018 MATLAB 7.12 http://www.ebi.ac.uk/swo/SWO_0000005 MATLAB http://www.ebi.ac.uk/swo/SWO_0000020 Unix http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_0000022 Linux http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_9000072 Microsoft Windows http://www.ebi.ac.uk/swo/SWO_0000029 Microsoft developed software http://www.ebi.ac.uk/swo/SWO_0000023 Microsoft Word 2001 http://www.ebi.ac.uk/swo/SWO_0000025 Microsoft Word http://www.ebi.ac.uk/swo/SWO_0000009 Kakadu http://www.ebi.ac.uk/swo/SWO_0000026 software with image input http://www.ebi.ac.uk/swo/SWO_0000006 Protege 4 http://www.ebi.ac.uk/swo/SWO_0000028 ontology engineering software http://www.ebi.ac.uk/swo/SWO_0000025 Microsoft Word http://www.ebi.ac.uk/swo/SWO_0000029 Microsoft developed software http://www.ebi.ac.uk/swo/SWO_9000070 Microsoft Excel http://www.ebi.ac.uk/swo/SWO_0000029 Microsoft developed software http://www.ebi.ac.uk/swo/SWO_0000062 MUSCLE 3.8.31 http://www.ebi.ac.uk/swo/SWO_0000063 Drive5 MUSCLE http://www.ebi.ac.uk/swo/SWO_0000137 NONMEM http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_9000083 DNDC http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_9000089 DROID http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_9000090 Dropbox http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_9000092 EMBOSS package http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_9000094 Grimoires http://www.ebi.ac.uk/swo/SWO_0000030 software with command line interface http://www.ebi.ac.uk/swo/SWO_0000053 ClustalW http://www.ebi.ac.uk/swo/SWO_0000051 Clustal http://www.ebi.ac.uk/swo/SWO_0000054 ClustalX http://www.ebi.ac.uk/swo/SWO_0000051 Clustal http://www.ebi.ac.uk/swo/SWO_0000058 EBI Clustal W2 Web Tool http://www.ebi.ac.uk/swo/SWO_0000051 Clustal http://www.ebi.ac.uk/swo/SWO_0000059 EBI Clustal Omega Web Tool http://www.ebi.ac.uk/swo/SWO_0000051 Clustal http://www.ebi.ac.uk/swo/SWO_0000055 Clustal Omega 1.1 http://www.ebi.ac.uk/swo/SWO_0000052 Clustal Omega http://www.ebi.ac.uk/swo/SWO_0000056 ClustalW 2.1 http://www.ebi.ac.uk/swo/SWO_0000053 ClustalW http://www.ebi.ac.uk/swo/SWO_0000057 ClustalX 2.1 http://www.ebi.ac.uk/swo/SWO_0000054 ClustalX http://www.ebi.ac.uk/swo/SWO_0000061 EBI Muscle Web Tool http://www.ebi.ac.uk/swo/SWO_0000060 MUSCLE http://www.ebi.ac.uk/swo/SWO_0000063 Drive5 MUSCLE http://www.ebi.ac.uk/swo/SWO_0000060 MUSCLE http://www.ebi.ac.uk/swo/SWO_0000074 Q 4.2 http://www.ebi.ac.uk/swo/SWO_0000073 Q http://www.ebi.ac.uk/swo/SWO_0000076 SPSS 20.0 http://www.ebi.ac.uk/swo/SWO_0000075 SPSS http://www.ebi.ac.uk/swo/SWO_0000078 SAM 3.5 http://www.ebi.ac.uk/swo/SWO_0000077 Sequence Alignment and Modeling System http://www.ebi.ac.uk/swo/SWO_0000080 Cytoscape 2.8 http://www.ebi.ac.uk/swo/SWO_0000079 Cytoscape http://www.ebi.ac.uk/swo/SWO_0000015 Microsoft Excel 2002 http://www.ebi.ac.uk/swo/SWO_9000070 Microsoft Excel http://www.ebi.ac.uk/swo/SWO_9000071 Microsoft Excel for Windows 2010 http://www.ebi.ac.uk/swo/SWO_9000070 Microsoft Excel http://www.ebi.ac.uk/swo/SWO_9000073 Windows Vista http://www.ebi.ac.uk/swo/SWO_9000072 Microsoft Windows http://www.ebi.ac.uk/swo/SWO_9000074 Windows XP http://www.ebi.ac.uk/swo/SWO_9000072 Microsoft Windows http://www.ebi.ac.uk/swo/SWO_9000075 Microsoft Office 2001 http://www.ebi.ac.uk/swo/SWO_9000076 software suite http://www.ebi.ac.uk/swo/objective/SWO_7000003 multiple sequence alignment http://www.ebi.ac.uk/swo/objective/SWO_7000002 sequence alignment http://www.ebi.ac.uk/swo/objective/SWO_7000004 pairwise sequence alignment http://www.ebi.ac.uk/swo/objective/SWO_7000002 sequence alignment http://www.ebi.ac.uk/swo/license/SWO_1000056 Artistic License http://www.ebi.ac.uk/swo/SWO_0000002 software license http://www.ebi.ac.uk/swo/license/SWO_1000069 GNU AGPL http://www.ebi.ac.uk/swo/SWO_0000002 software license http://www.ebi.ac.uk/swo/license/SWO_1000095 Open Data Commons http://www.ebi.ac.uk/swo/SWO_0000002 software license http://www.ebi.ac.uk/swo/license/SWO_1000002 Proprietary commercial software license http://www.ebi.ac.uk/swo/SWO_0000002 software license http://www.ebi.ac.uk/swo/license/SWO_1000008 Open source software license http://www.ebi.ac.uk/swo/SWO_0000002 software license http://www.ebi.ac.uk/swo/license/SWO_1000009 License without restrictions on derivatives http://www.ebi.ac.uk/swo/SWO_0000002 software license http://www.ebi.ac.uk/swo/data/SWO_3000055 BioPAX RDF/XML format http://www.ebi.ac.uk/swo/data/SWO_3000007 RDF-XML http://www.ebi.ac.uk/swo/data/SWO_3000031 WordStar format http://www.ebi.ac.uk/swo/data/SWO_3000030 word processing document format http://www.ebi.ac.uk/swo/data/SWO_3000004 Matlab .m file http://www.ebi.ac.uk/swo/data/SWO_3000033 programming language format http://www.ebi.ac.uk/swo/SWO_0000682 .raw files http://www.ebi.ac.uk/swo/data/SWO_3000042 ASCII format http://www.ebi.ac.uk/swo/data/SWO_3000042 ASCII format http://www.ebi.ac.uk/swo/data/SWO_3000043 plain text file format http://www.ebi.ac.uk/swo/SWO_0000493 cdt http://www.ebi.ac.uk/swo/data/SWO_3000046 tab delimited file format http://www.ebi.ac.uk/swo/SWO_0000569 gtr http://www.ebi.ac.uk/swo/data/SWO_3000046 tab delimited file format http://www.ebi.ac.uk/swo/SWO_0000687 .rma format http://www.ebi.ac.uk/swo/data/SWO_3000079 audio format http://www.ebi.ac.uk/swo/SWO_0000045 Array_vision_(Interfocus) http://www.ebi.ac.uk/swo/SWO_0000042 ArrayVision http://www.ebi.ac.uk/swo/SWO_1100028 ArrayVision 6.0 (Imaging Research Inc.) http://www.ebi.ac.uk/swo/SWO_0000042 ArrayVision http://www.ebi.ac.uk/swo/SWO_0000177 GenePix 3.0.6 http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix http://www.ebi.ac.uk/swo/SWO_0000178 GenePix 4.1 http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix http://www.ebi.ac.uk/swo/SWO_0000180 GenePix 5.0.1 http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro http://www.ebi.ac.uk/swo/SWO_0000176 Gene Pix http://www.ebi.ac.uk/swo/SWO_0000183 GenePix Pro 3 http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro http://www.ebi.ac.uk/swo/SWO_0000184 GenePix Pro 5.0 http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro http://www.ebi.ac.uk/swo/SWO_0000185 GenePix Pro 6.0 http://www.ebi.ac.uk/swo/SWO_0000182 GenePix Pro http://www.ebi.ac.uk/swo/SWO_0000047 Axon GenePix Pro 3 http://www.ebi.ac.uk/swo/SWO_0000187 GenePix Pro [Axon Instruments] http://www.ebi.ac.uk/swo/SWO_0000186 GenePix Pro 6 [Axon Instruments] http://www.ebi.ac.uk/swo/SWO_0000187 GenePix Pro [Axon Instruments] http://www.ebi.ac.uk/swo/SWO_0000194 GeneSpringGX http://www.ebi.ac.uk/swo/SWO_0000193 GeneSpring http://www.ebi.ac.uk/swo/SWO_0000234 ImaGene4.1 software http://www.ebi.ac.uk/swo/SWO_0000238 ImaGene http://www.ebi.ac.uk/swo/SWO_0000235 ImaGene 3.0 http://www.ebi.ac.uk/swo/SWO_0000238 ImaGene http://www.ebi.ac.uk/swo/SWO_0000239 Imagene v4.0 http://www.ebi.ac.uk/swo/SWO_0000238 ImaGene http://www.ebi.ac.uk/swo/SWO_0000297 MicroArraySuite 4.0 http://www.ebi.ac.uk/swo/SWO_0000271 MIcroarray Analysis Suite http://www.ebi.ac.uk/swo/SWO_0000327 Probe Cell Analysis http://www.ebi.ac.uk/swo/SWO_0000272 MicroArraySuite 5.0 http://www.ebi.ac.uk/swo/SWO_1100017 Absolute Expression Analysis http://www.ebi.ac.uk/swo/SWO_0000272 MicroArraySuite 5.0 http://www.ebi.ac.uk/swo/SWO_1100016 Absolute Expression Analysis http://www.ebi.ac.uk/swo/SWO_0000297 MicroArraySuite 4.0 http://www.ebi.ac.uk/swo/SWO_0000330 QuantArray, PackaardBiochip technologies http://www.ebi.ac.uk/swo/SWO_0000329 QuantArray scanner software http://www.ebi.ac.uk/swo/SWO_0000331 QuantArray version 2 http://www.ebi.ac.uk/swo/SWO_0000329 QuantArray scanner software http://www.ebi.ac.uk/swo/SWO_0000344 RMAExpress 2.0 http://www.ebi.ac.uk/swo/SWO_0000343 RMAExpress http://www.ebi.ac.uk/swo/SWO_0000345 RMAExpress quantification http://www.ebi.ac.uk/swo/SWO_0000343 RMAExpress http://www.ebi.ac.uk/swo/SWO_0000475 arrayWoRx 2.0 http://www.ebi.ac.uk/swo/SWO_0000476 arrayWoRx http://www.ebi.ac.uk/swo/SWO_1100020 Affymetrix GCOS v1.2 http://www.ebi.ac.uk/swo/SWO_1100021 Affymetrix GeneChip Operating Software http://www.ebi.ac.uk/swo/SWO_1100071 Feature Extraction Software http://www.ebi.ac.uk/swo/SWO_1100021 Affymetrix GeneChip Operating Software http://www.ebi.ac.uk/swo/SWO_1100066 ChipSkipper V0.99 http://www.ebi.ac.uk/swo/SWO_1100065 ChipSkipper http://www.ebi.ac.uk/swo/SWO_0000718 tkWidgets http://www.ebi.ac.uk/swo/SWO_1100075 R software http://www.ebi.ac.uk/swo/SWO_9000078 Annotare http://www.ebi.ac.uk/swo/SWO_1100079 MAGE-TAB inputting software http://www.ebi.ac.uk/swo/SWO_1100024 Agilent Feature Extraction 5.1.1 http://www.ebi.ac.uk/swo/SWO_1100104 Agilent Feature Extraction Software http://www.ebi.ac.uk/swo/SWO_1100025 Agilent Feature Extraction software version 7.1 http://www.ebi.ac.uk/swo/SWO_1100104 Agilent Feature Extraction Software http://www.ebi.ac.uk/swo/SWO_1100026 Agilent Feature Extraction software version 7.5 http://www.ebi.ac.uk/swo/SWO_1100104 Agilent Feature Extraction Software http://www.ebi.ac.uk/swo/SWO_1100027 Agilent Feature Extraction software version A.5.1.1 http://www.ebi.ac.uk/swo/SWO_1100104 Agilent Feature Extraction Software http://www.ontodm.com/OntoDM-core/OntoDM_530819 ensemble algorithm http://www.ontodm.com/OntoDM-core/OntoDM_000038 data mining algorithm http://www.ontodm.com/OntoDM-core/OntoDM_731692 single generalization algorithm http://www.ontodm.com/OntoDM-core/OntoDM_000038 data mining algorithm http://www.ebi.ac.uk/swo/objective/SWO_7000002 sequence alignment http://www.ontodm.com/OntoDM-core/OntoDM_000092 pattern discovery task http://www.ontodm.com/OntoDM-core/OntoDM_000087 probability distribution estimation task http://www.ontodm.com/OntoDM-core/OntoDM_000098 data mining task http://www.ontodm.com/OntoDM-core/OntoDM_000092 pattern discovery task http://www.ontodm.com/OntoDM-core/OntoDM_000098 data mining task http://www.ontodm.com/OntoDM-core/OntoDM_000235 predictive modeling task http://www.ontodm.com/OntoDM-core/OntoDM_000098 data mining task http://www.ontodm.com/OntoDM-core/OntoDM_000264 clustering task http://www.ontodm.com/OntoDM-core/OntoDM_000098 data mining task http://www.ontodm.com/OntoDM-core/OntoDM_000253 probability distribution estimation algorithm http://www.ontodm.com/OntoDM-core/OntoDM_731692 single generalization algorithm http://purl.obolibrary.org/obo/GO_0003674 molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. http://purl.obolibrary.org/obo/GO_0008150 biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. http://purl.obolibrary.org/obo/BFO_0000001 entity http://www.geneontology.org/formats/oboInOwl#ObsoleteClass Obsolete Class http://purl.obolibrary.org/obo/RO_0002234 has output http://purl.obolibrary.org/obo/RO_0000057 has participant produces p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. http://purl.obolibrary.org/obo/RO_0000052 characteristic of http://purl.obolibrary.org/obo/RO_0002314 characteristic of part of inheres_in a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. http://purl.obolibrary.org/obo/RO_0000079 function of http://purl.obolibrary.org/obo/RO_0000052 characteristic of is function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000080 quality of http://purl.obolibrary.org/obo/RO_0000052 characteristic of quality_of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000085 has function http://purl.obolibrary.org/obo/RO_0000053 has characteristic has_function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000086 has quality http://purl.obolibrary.org/obo/RO_0000053 has characteristic has_quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002350 member of http://purl.obolibrary.org/obo/BFO_0000050 part of member part of is member of is a mereological relation between a item and a collection. http://purl.obolibrary.org/obo/BFO_0000051 has part http://purl.obolibrary.org/obo/RO_0002131 overlaps has_part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/RO_0000087 has_role http://purl.obolibrary.org/obo/RO_0000053 has characteristic has_role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002327 enables http://purl.obolibrary.org/obo/RO_0002215 capable of is executing c enables p iff c is capable of p and c acts to execute p. http://purl.obolibrary.org/obo/RO_0002409 indirectly negatively regulates http://purl.obolibrary.org/obo/RO_0012012 indirectly regulates indirectly inhibits p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. http://purl.obolibrary.org/obo/RO_0002436 molecularly interacts with http://purl.obolibrary.org/obo/RO_0002434 interacts with molecularly binds with An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. http://purl.obolibrary.org/obo/RO_0002449 directly negatively regulates activity of http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of directly inhibits The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. http://purl.obolibrary.org/obo/BFO_0000062 preceded by http://purl.obolibrary.org/obo/RO_0002086 ends after preceded_by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/RO_0000081 role of http://purl.obolibrary.org/obo/RO_0000052 characteristic of role_of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/BFO_0000050 part of http://purl.obolibrary.org/obo/RO_0002131 overlaps part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/RO_0002233 has input http://purl.obolibrary.org/obo/RO_0000057 has participant consumes p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. http://purl.obolibrary.org/obo/RO_0002314 characteristic of part of http://purl.obolibrary.org/obo/RO_0002502 depends on inheres in part of q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. http://purl.obolibrary.org/obo/RO_0002215 capable of http://purl.obolibrary.org/obo/RO_0002216 capable of part of has function realized in A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. http://purl.obolibrary.org/obo/RO_0002331 involved in http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of enables part of c involved_in p if and only if c enables some process p', and p' is part of p http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of http://purl.obolibrary.org/obo/RO_0002500 causal agent in process involved in or reguates c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p http://purl.obolibrary.org/obo/RO_0002216 capable of part of http://purl.obolibrary.org/obo/RO_0002500 causal agent in process has function in c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. http://purl.obolibrary.org/obo/RO_0002329 part of structure that is capable of http://purl.obolibrary.org/obo/RO_0002328 functionally related to 0 this relation holds between c and p when c is part of some c', and c' is capable of p. http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes influences (processual) p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. http://purl.obolibrary.org/obo/RO_0002407 indirectly positively regulates http://purl.obolibrary.org/obo/RO_0012012 indirectly regulates indirectly activates p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. http://purl.obolibrary.org/obo/RO_0002450 directly positively regulates activity of http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of directly activates The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. http://purl.obolibrary.org/obo/RO_0002025 has effector activity http://purl.obolibrary.org/obo/RO_0002017 has component activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/RO_0002222 temporally related to x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. http://purl.obolibrary.org/obo/OBI_0000293 has_specified_input http://purl.obolibrary.org/obo/RO_0000057 has participant The inverse property of is_specified_input_of http://purl.obolibrary.org/obo/OBI_0000295 is_specified_input_of http://purl.obolibrary.org/obo/RO_0000056 participates in A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000299 has_specified_output http://purl.obolibrary.org/obo/RO_0000057 has participant The inverse property of is_specified_output_of http://purl.obolibrary.org/obo/OBI_0000312 is_specified_output_of http://purl.obolibrary.org/obo/RO_0000056 participates in A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/RO_0002351 has member http://purl.obolibrary.org/obo/BFO_0000051 has part has member is a mereological relation between a collection and an item. http://purl.obolibrary.org/obo/RO_0002018 has component process http://purl.obolibrary.org/obo/RO_0002180 has component w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. http://purl.obolibrary.org/obo/RO_0019000 regulates characteristic http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. http://purl.obolibrary.org/obo/RO_0019001 positively regulates characteristic http://purl.obolibrary.org/obo/RO_0019000 regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. http://purl.obolibrary.org/obo/RO_0019002 negatively regulates characteristic http://purl.obolibrary.org/obo/RO_0019000 regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. http://purl.obolibrary.org/obo/RO_0002333 enabled by http://purl.obolibrary.org/obo/RO_0002328 functionally related to inverse of enables http://purl.obolibrary.org/obo/RO_0002404 causally downstream of http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within inverse of upstream of http://purl.obolibrary.org/obo/RO_0002412 immediately causally upstream of http://purl.obolibrary.org/obo/RO_0002411 causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. http://purl.obolibrary.org/obo/RO_0002448 directly regulates activity of http://purl.obolibrary.org/obo/RO_0011002 regulates activity of The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. http://purl.obolibrary.org/obo/RO_0002566 causally influences http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). http://purl.obolibrary.org/obo/RO_0002263 acts upstream of http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. http://purl.obolibrary.org/obo/RO_0002304 causally upstream of, positive effect http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. http://purl.obolibrary.org/obo/RO_0002305 causally upstream of, negative effect http://purl.obolibrary.org/obo/RO_0004046 causally upstream of or within, negative effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. http://www.ebi.ac.uk/efo/swo/SWO_0000395 obsolete_is_published_by http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property The relationship between software and a software publisher. http://www.ebi.ac.uk/swo/SWO_0000046 has download location http://www.ebi.ac.uk/swo/SWO_0004006 has website homepage The location from where the software can be downloaded. http://www.ebi.ac.uk/swo/SWO_0000131 directly preceded by http://www.ebi.ac.uk/swo/SWO_0000301 follows Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software. http://www.ebi.ac.uk/swo/SWO_0000132 directly followed by http://www.ebi.ac.uk/swo/SWO_0000300 followed by 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s. http://www.ebi.ac.uk/swo/SWO_0004002 has format specification http://www.ebi.ac.uk/swo/SWO_0000741 is encoded in Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification. http://www.ebi.ac.uk/swo/SWO_9001002 has clause http://purl.obofoundry.org/obo/IAO_0000136 is about Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied. http://www.ebi.ac.uk/swo/has_license has license http://purl.obofoundry.org/obo/IAO_0000136 is about The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license. http://www.ebi.ac.uk/swo/is_license_for is license for http://purl.obofoundry.org/obo/IAO_0000136 is about The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. http://www.ebi.ac.uk/swo/maturity/SWO_9000067 has declared status http://purl.obofoundry.org/obo/IAO_0000136 is about 'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information. http://purl.obolibrary.org/obo/RO_0002131 overlaps http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/RO_0000091 has disposition http://purl.obolibrary.org/obo/RO_0000053 has characteristic a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000092 disposition of http://purl.obolibrary.org/obo/RO_0000052 characteristic of inverse of has disposition http://purl.obolibrary.org/obo/RO_0011002 regulates activity of http://purl.obolibrary.org/obo/RO_0002566 causally influences The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. http://purl.obolibrary.org/obo/RO_0002411 causally upstream of http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. http://purl.obolibrary.org/obo/RO_0002211 regulates http://purl.obolibrary.org/obo/RO_0002411 causally upstream of p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. http://purl.obolibrary.org/obo/RO_0002212 negatively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. http://purl.obolibrary.org/obo/RO_0002213 positively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. http://purl.obolibrary.org/obo/RO_0002180 has component http://purl.obolibrary.org/obo/BFO_0000051 has part w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. http://purl.obolibrary.org/obo/RO_0002352 input of http://purl.obolibrary.org/obo/RO_0002328 functionally related to An entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B. http://purl.obolibrary.org/obo/RO_0002353 output of http://purl.obolibrary.org/obo/RO_0002328 functionally related to An entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B. http://purl.obolibrary.org/obo/RO_0002023 directly negatively regulated by http://purl.obolibrary.org/obo/RO_0002022 directly regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. http://purl.obolibrary.org/obo/RO_0002024 directly positively regulated by http://purl.obolibrary.org/obo/RO_0002022 directly regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. http://purl.obolibrary.org/obo/RO_0012011 indirectly causally upstream of http://purl.obolibrary.org/obo/RO_0002411 causally upstream of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. http://purl.obolibrary.org/obo/RO_0012012 indirectly regulates http://purl.obolibrary.org/obo/RO_0012011 indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0002500 causal agent in process c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. http://purl.obolibrary.org/obo/RO_0004031 enables subfunction http://purl.obolibrary.org/obo/RO_0002328 functionally related to Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. http://purl.obolibrary.org/obo/RO_0004034 acts upstream of, positive effect http://purl.obolibrary.org/obo/RO_0004032 acts upstream of or within, positive effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive http://purl.obolibrary.org/obo/RO_0004035 acts upstream of, negative effect http://purl.obolibrary.org/obo/RO_0004033 acts upstream of or within, negative effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative http://purl.obolibrary.org/obo/RO_0002334 regulated by http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within inverse of regulates http://purl.obolibrary.org/obo/RO_0002335 negatively regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by inverse of negatively regulates http://purl.obolibrary.org/obo/RO_0002336 positively regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by inverse of positively regulates http://purl.obolibrary.org/obo/RO_0002427 causally downstream of or within http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes inverse of causally upstream of or within http://purl.obolibrary.org/obo/RO_0002500 causal agent in process http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process A relationship between a material entity and a process where the material entity has some causal role that influences the process http://purl.obolibrary.org/obo/RO_0002501 causal relation between processes http://purl.obolibrary.org/obo/RO_0002410 causally related to p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. http://purl.obolibrary.org/obo/RO_0002584 has part structure that is capable of http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p http://purl.obolibrary.org/obo/RO_0002595 causal relation between material entity and a process http://purl.obolibrary.org/obo/RO_0002410 causally related to A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. http://purl.obolibrary.org/obo/RO_0002596 capable of regulating http://purl.obolibrary.org/obo/RO_0002500 causal agent in process Holds between c and p if and only if c is capable of some activity a, and a regulates p. http://purl.obolibrary.org/obo/RO_0002597 capable of negatively regulating http://purl.obolibrary.org/obo/RO_0002596 capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. http://purl.obolibrary.org/obo/RO_0002598 capable of positively regulating http://purl.obolibrary.org/obo/RO_0002596 capable of regulating Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. http://purl.obolibrary.org/obo/RO_0002608 process has causal agent http://purl.obolibrary.org/obo/RO_0002410 causally related to Inverse of 'causal agent in process' http://purl.obolibrary.org/obo/RO_0002015 has positive regulatory component activity http://purl.obolibrary.org/obo/RO_0002013 has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. http://purl.obolibrary.org/obo/RO_0002013 has regulatory component activity http://purl.obolibrary.org/obo/RO_0002017 has component activity A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. http://purl.obolibrary.org/obo/RO_0002014 has negative regulatory component activity http://purl.obolibrary.org/obo/RO_0002013 has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. http://www.ebi.ac.uk/swo/SWO_0000741 is encoded in http://purl.obofoundry.org/obo/IAO_0000136 is about Is encoded in is an "is about" relationship which describes the type of encoding used for the referenced class. http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of http://purl.obolibrary.org/obo/RO_0002431 involved in or involved in regulation of c involved in regulation of p if c is involved in some p' and p' regulates some p http://purl.obolibrary.org/obo/RO_0002429 involved in positive regulation of http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p http://purl.obolibrary.org/obo/RO_0002430 involved in negative regulation of http://purl.obolibrary.org/obo/RO_0002428 involved in regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p http://purl.obolibrary.org/obo/RO_0002578 directly regulates http://purl.obolibrary.org/obo/RO_0002211 regulates p directly regulates q iff p is immediately causally upstream of q and p regulates q. http://purl.obolibrary.org/obo/RO_0002629 directly positively regulates http://purl.obolibrary.org/obo/RO_0002578 directly regulates p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. http://purl.obolibrary.org/obo/RO_0002630 directly negatively regulates http://purl.obolibrary.org/obo/RO_0002578 directly regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded by starts_at_end_of http://purl.obolibrary.org/obo/RO_0002090 immediately precedes http://purl.obolibrary.org/obo/BFO_0000063 precedes meets http://purl.obolibrary.org/obo/RO_0002447 phosphorylates http://purl.obolibrary.org/obo/RO_0002436 molecularly interacts with An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. http://purl.obolibrary.org/obo/RO_0002405 immediately causally downstream of http://purl.obolibrary.org/obo/RO_0002404 causally downstream of http://purl.obolibrary.org/obo/RO_0002017 has component activity http://purl.obolibrary.org/obo/RO_0002018 has component process http://purl.obolibrary.org/obo/RO_0002559 causally influenced by http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities http://purl.obolibrary.org/obo/RO_0002563 interaction relation helper property http://purl.obolibrary.org/obo/RO_0002464 helper property (not for use in curation) http://purl.obolibrary.org/obo/RO_0002564 molecular interaction relation helper property http://purl.obolibrary.org/obo/RO_0002563 interaction relation helper property http://purl.obolibrary.org/obo/RO_0002481 is kinase activity http://purl.obolibrary.org/obo/RO_0002564 molecular interaction relation helper property http://www.ebi.ac.uk/efo/swo/SWO_0000394 obsolete is developed by http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://www.ebi.ac.uk/efo/swo/SWO_0000739 has legal status http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://www.ebi.ac.uk/swo/SWO_0004003 obsolete_is developed by http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://www.ebi.ac.uk/swo/SWO_9000058 obsolete_is specified output of http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://www.ebi.ac.uk/swo/organization/SWO_9000059 obsolete_has_participant http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://www.ebi.ac.uk/efo/reason_for_obsolescence obsolete reason_for_obsolescence http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://www.ebi.ac.uk/efo/swo/SWO_0000740 obsolete implements http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://www.ebi.ac.uk/efo/swo/SWO_0000741 obsolete is encoded in http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property http://purl.obolibrary.org/obo/RO_0002086 ends after http://purl.obolibrary.org/obo/RO_0002222 temporally related to http://purl.obolibrary.org/obo/RO_0004033 acts upstream of or within, negative effect http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0004032 acts upstream of or within, positive effect http://purl.obolibrary.org/obo/RO_0002264 acts upstream of or within http://purl.obolibrary.org/obo/RO_0002022 directly regulated by http://purl.obolibrary.org/obo/RO_0002334 regulated by http://purl.obolibrary.org/obo/RO_0002506 causal relation between entities http://purl.obolibrary.org/obo/RO_0002410 causally related to http://purl.obolibrary.org/obo/RO_0004046 causally upstream of or within, negative effect http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/RO_0004047 causally upstream of or within, positive effect http://purl.obolibrary.org/obo/RO_0002418 causally upstream of or within http://purl.obolibrary.org/obo/OBI_0000304 is manufactured by has_manufacturer c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. http://purl.obolibrary.org/obo/RO_0000053 has characteristic is bearer of Inverse of characteristic_of http://purl.obolibrary.org/obo/RO_0000056 participates in participates_in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000057 has participant has_participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. http://www.ebi.ac.uk/swo/SWO_0000394 is developed by The relationship between a software and software developer. http://www.ebi.ac.uk/swo/SWO_0000740 implements implements is the relationship between software and an algorithm that is defined for use within that software when executed. http://purl.obolibrary.org/obo/IAO_0000136 is about A (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/OBI_0000417 achieves_planned_objective This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. http://purl.obolibrary.org/obo/OBI_0000833 objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. http://purl.obolibrary.org/obo/RO_0000058 is concretized as A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. http://purl.obolibrary.org/obo/RO_0000059 concretizes A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/RO_0017001 device utilizes material X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. http://purl.obolibrary.org/obo/RO_0002434 interacts with A relationship that holds between two entities in which the processes executed by the two entities are causally connected. http://www.ebi.ac.uk/swo/SWO_0000043 has documentation Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class. http://www.ebi.ac.uk/swo/SWO_0000081 is version of 'is version of' provides a link between a 'version name' and the entity with that version. http://www.ebi.ac.uk/swo/SWO_0000082 uses software This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package, and 'uses platform' relationship should be used to describe which operating system(s) a particular piece of software can use. http://www.ebi.ac.uk/swo/SWO_0000085 is implemented by is implemented by is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed. http://www.ebi.ac.uk/swo/SWO_0000086 has specified data input The relationship between input data which is permitted to a piece of software. http://www.ebi.ac.uk/swo/SWO_0000087 has specified data output The relationship between a piece of software and the data that it is possible to output. http://www.ebi.ac.uk/swo/SWO_0000088 is specified data input of The relationship between a data and the software which can possibly take this data as input. http://www.ebi.ac.uk/swo/SWO_0000089 is specified data output of The relationship between a data and the software which can possibly produce this data as output. http://www.ebi.ac.uk/swo/SWO_0000150 uses platform 'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example. http://www.ebi.ac.uk/swo/SWO_0004000 has version relationship between an entity and a version name or number http://www.ebi.ac.uk/swo/SWO_0004001 has interface Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy. http://www.ebi.ac.uk/swo/SWO_0004004 is published by 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list. http://www.ebi.ac.uk/swo/SWO_0004006 has website homepage The URL of the homepage for the resource this property is associated with. http://www.ebi.ac.uk/swo/SWO_0004007 obsolete object property Stores those object properties which are no longer appropriate for use within SWO. http://www.ebi.ac.uk/swo/SWO_0040005 is executed in is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, http://www.ebi.ac.uk/swo/data/SWO_3000054 is alternative format of With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data. http://www.ebi.ac.uk/swo/license/SWO_1000048 is compatible license of 'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program. http://purl.obofoundry.org/obo/IAO_0000136 is about 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign. http://purl.obolibrary.org/obo/RO_0002323 mereotopologically related to A mereological relationship or a topological relationship http://purl.obolibrary.org/obo/RO_0002328 functionally related to A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. http://www.obofoundry.org/ro/ro.owl#part_of part of For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) http://purl.obolibrary.org/obo/RO_0002410 causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. http://purl.obolibrary.org/obo/BFO_0000054 realized in realized_in http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/RO_0002464 helper property (not for use in curation) http://www.ebi.ac.uk/swo/SWO_0000157 is software for http://www.ebi.ac.uk/swo/maturity/SWO_9000068 has release date http://www.ebi.ac.uk/swo/maturity/SWO_9000070 has support URL http://purl.obolibrary.org/obo/RO_0002222 temporally related to http://www.ebi.ac.uk/swo/SWO_0000300 followed by http://www.ebi.ac.uk/swo/SWO_0000301 follows http://purl.obolibrary.org/obo/RO_0002502 depends on http://www.obofoundry.org/ro/ro.owl#has_part has_part