Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module subset ontology An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. http://purl.obolibrary.org/obo/IAO_0000648 zone improvement plan code http://purl.obolibrary.org/obo/IAO_0000646 postal code ZIP code A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. http://purl.obolibrary.org/obo/IAO_0000580 looking up a centrally registered identifier http://purl.obolibrary.org/obo/OBI_0000011 planned process looking up a CRID A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol 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_0000132 lot number http://purl.obolibrary.org/obo/IAO_0000028 symbol batch number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. 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/IAO_0000300 textual entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity text A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. http://purl.obolibrary.org/obo/IAO_0000311 publication http://purl.obolibrary.org/obo/IAO_0000310 document published document A document that is the output of a publishing process. http://purl.obolibrary.org/obo/IAO_0000312 publication about an investigation http://purl.obolibrary.org/obo/IAO_0000311 publication scientific publication A publication that is about an investigation http://purl.obolibrary.org/obo/IAO_0000315 abstract http://purl.obolibrary.org/obo/IAO_0000314 document part precis A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. http://purl.obolibrary.org/obo/IAO_0000316 introduction to a publication about an investigation http://purl.obolibrary.org/obo/IAO_0000314 document part overview A part of a publication about an investigation that is about the objective specification (why the investigation is being done) http://purl.obolibrary.org/obo/IAO_0000317 methods section http://purl.obolibrary.org/obo/IAO_0000314 document part experimental methods A part of a publication about an investigation that is about the study design of the investigation http://purl.obolibrary.org/obo/IAO_0000318 results section http://purl.obolibrary.org/obo/IAO_0000314 document part results A part of a publication about an investigation that is about a study design execution http://purl.obolibrary.org/obo/IAO_0000319 discussion section of a publication about an investigation http://purl.obolibrary.org/obo/IAO_0000314 document part discussions A part of a publication about an investigation that is about the study interpretation of the investigation http://purl.obolibrary.org/obo/IAO_0000320 references section http://purl.obolibrary.org/obo/IAO_0000314 document part reference list A part of a document that has citations as parts http://purl.obolibrary.org/obo/IAO_0000323 author contributions section http://purl.obolibrary.org/obo/IAO_0000314 document part contributorship A part of a publication that is about the specific contributions of each author http://purl.obolibrary.org/obo/IAO_0000324 acknowledgements section http://purl.obolibrary.org/obo/IAO_0000314 document part acknowledgment Part of a publication that is about the contributions of people or institutions other than the authors. http://purl.obolibrary.org/obo/IAO_0000325 footnote http://purl.obolibrary.org/obo/IAO_0000314 document part footnotes A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. http://purl.obolibrary.org/obo/IAO_0000326 supplementary material to a document http://purl.obolibrary.org/obo/IAO_0000314 document part supplementary materials A part of a document that is segregated from the rest of the document due to its size http://purl.obolibrary.org/obo/IAO_0000573 line graph http://purl.obolibrary.org/obo/IAO_0000038 graph line chart A line graph is a type of graph created by connecting a series of data points together with a line. http://purl.obolibrary.org/obo/IAO_0000574 assigning a centrally registered identifier http://purl.obolibrary.org/obo/OBI_0000011 planned process assigning a CRID A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity http://purl.obolibrary.org/obo/IAO_0000575 associating information with a centrally registered identifier in its registry http://purl.obolibrary.org/obo/OBI_0000011 planned process associating information with a CRID in the CRID registry A planned process in which a CRID registry associates an information content entity with a CRID symbol http://purl.obolibrary.org/obo/IAO_0000577 centrally registered identifier symbol http://purl.obolibrary.org/obo/IAO_0000028 symbol CRID symbol A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/IAO_0000578 centrally registered identifier http://purl.obolibrary.org/obo/IAO_0020000 identifier CRID An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs. http://purl.obolibrary.org/obo/IAO_0000579 centrally registered identifier registry http://purl.obolibrary.org/obo/IAO_0020020 code set CRID registry A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. http://purl.obolibrary.org/obo/IAO_0000584 time sampled measurement data set http://purl.obolibrary.org/obo/IAO_0000100 data set experimental time series A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. 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_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/IAO_0020000 identifier http://purl.obolibrary.org/obo/IAO_0000030 information content entity proper name An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. http://purl.obolibrary.org/obo/IAO_0020010 identifier creating process http://purl.obolibrary.org/obo/OBI_0000011 planned process naming A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. 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_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_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/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_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. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact. http://www.ebi.ac.uk/swo/license/SWO_1000046 GNU GPL v3 http://www.ebi.ac.uk/swo/license/SWO_1000004 GNU GPL GNU General Public License Version 3 The GNU GPL v3 is the latest version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. 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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/license/SWO_1000006 Academic Free License version 3 http://www.ebi.ac.uk/swo/SWO_0000002 software license 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/SWO_0000002 software license 2-clause BSD License This is the original BSD license with the advertising clause and another clause removed. 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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/IAO_0000707 graphical abstract http://purl.obolibrary.org/obo/IAO_0000315 abstract visual abstract An abstract that is pictorial summary of the main findings described in the document. http://purl.obolibrary.org/obo/IAO_0000606 abbreviations section http://purl.obolibrary.org/obo/IAO_0000314 document part nonstandard abbreviations and acronyms A part of a document where abbreviations and their long-forms used within the document are listed. http://purl.obolibrary.org/obo/IAO_0000607 author information section http://purl.obolibrary.org/obo/IAO_0000314 document part contributor information A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. http://purl.obolibrary.org/obo/IAO_0000609 author summary section http://purl.obolibrary.org/obo/IAO_0000314 document part synopsis A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. http://purl.obolibrary.org/obo/IAO_0000611 availability section http://purl.obolibrary.org/obo/IAO_0000314 document part data sharing statement A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. http://purl.obolibrary.org/obo/IAO_0000613 case report section http://purl.obolibrary.org/obo/IAO_0000314 document part case report A part of a document about the medical history of a specific patient as it relates to the topic of the document. http://purl.obolibrary.org/obo/IAO_0000615 conclusion section http://purl.obolibrary.org/obo/IAO_0000314 document part summary A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. http://purl.obolibrary.org/obo/IAO_0000616 conflict of interest section http://purl.obolibrary.org/obo/IAO_0000314 document part authors' disclosures of potential conflicts of interest A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. http://purl.obolibrary.org/obo/IAO_0000618 consent section http://purl.obolibrary.org/obo/IAO_0000314 document part consent A part of a document about the consent process that was used to enroll patients in a study. http://purl.obolibrary.org/obo/IAO_0000620 ethical approval section http://purl.obolibrary.org/obo/IAO_0000314 document part ethics statement A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. http://purl.obolibrary.org/obo/IAO_0000622 figures section http://purl.obolibrary.org/obo/IAO_0000314 document part figures A part of a document that contains one or more figures. http://purl.obolibrary.org/obo/IAO_0000623 funding source declaration section http://purl.obolibrary.org/obo/IAO_0000314 document part study funding A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. http://purl.obolibrary.org/obo/IAO_0000625 future directions section http://purl.obolibrary.org/obo/IAO_0000314 document part outlook A part of a document detailing extensions of the described work that may be implemented at some future point in time. http://purl.obolibrary.org/obo/IAO_0000627 genome announcement section http://purl.obolibrary.org/obo/IAO_0000314 document part genome announcement A document part announcing the publication of a novel draft genome sequence. http://purl.obolibrary.org/obo/IAO_0000630 keywords section http://purl.obolibrary.org/obo/IAO_0000314 document part keywords A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. http://purl.obolibrary.org/obo/IAO_0000631 study limitations section http://purl.obolibrary.org/obo/IAO_0000314 document part study limitations A part of a document about biases or short comings related to the study design and execution. http://purl.obolibrary.org/obo/IAO_0000633 materials section http://purl.obolibrary.org/obo/IAO_0000314 document part materials A part of a document about the materials required to reproduce the content of the document. http://purl.obolibrary.org/obo/IAO_0000634 notes section http://purl.obolibrary.org/obo/IAO_0000314 document part notes A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. http://purl.obolibrary.org/obo/IAO_0000637 pre-publication history section http://purl.obolibrary.org/obo/IAO_0000314 document part pre-publication history A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. http://purl.obolibrary.org/obo/IAO_0000639 related work section http://purl.obolibrary.org/obo/IAO_0000314 document part related work A part of a document about work in other publications that is relevant to the content of the document. http://purl.obolibrary.org/obo/IAO_0000641 requirements section http://purl.obolibrary.org/obo/IAO_0000314 document part requirements A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. http://purl.obolibrary.org/obo/IAO_0000644 statistical analysis section http://purl.obolibrary.org/obo/IAO_0000314 document part statistical analysis A part of the document used to describe the statistical methodologies employed in the work presented in the document. http://purl.obolibrary.org/obo/IAO_0000645 tables section http://purl.obolibrary.org/obo/IAO_0000314 document part tables A part of a document that contains one or more tables. http://purl.obolibrary.org/obo/IAO_0000650 database extract, transform, and load process http://purl.obolibrary.org/obo/OBI_0000011 planned process ETL A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. http://purl.obolibrary.org/obo/IAO_8000002 editors ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module source ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. http://purl.obolibrary.org/obo/IAO_8000005 import ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module import file A subset ontology module that is intended to be imported from another ontology. http://purl.obolibrary.org/obo/IAO_8000009 single layer subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module ribbon subset A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. http://purl.obolibrary.org/obo/IAO_8000010 exclusion subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module antislim A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. http://purl.obolibrary.org/obo/IAO_8000011 external import ontology module http://purl.obolibrary.org/obo/IAO_8000005 import ontology module external import An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. http://purl.obolibrary.org/obo/IAO_8000012 species subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module taxon subset A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. 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://purl.obolibrary.org/obo/IAO_0020020 code set http://purl.obolibrary.org/obo/IAO_0000030 information content entity code map An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. http://purl.obolibrary.org/obo/MCRO_0000012 False Positive Rate Information Section http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section This content describes the information pertaining to the model's false postive rate. "A false positive error, or false positive, is a result that indicates a given condition exists when it does not. For example, a pregnancy test which indicates a woman is pregnant when she is not, or the conviction of an innocent person. A false positive error is a type I error where the test is checking a single condition, and wrongly gives an affirmative (positive) decision." http://purl.obolibrary.org/obo/MCRO_0000020 Model Card Graphic http://purl.obolibrary.org/obo/IAO_0000038 graph a graph content specifically for a model card report http://purl.obolibrary.org/obo/MCRO_0000033 Risk Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Content information relating to potential uncertainity about utilizing the model http://purl.obolibrary.org/obo/MCRO_0000001 Model Card Report http://purl.obolibrary.org/obo/IAO_0000088 report The Model Card (MC) is the document designed for transparent reporting of AI model provenance, usage, and ethics-informed evaluation. A report that details characteristics of machine learning model to supplement its release to the public. http://purl.obolibrary.org/obo/MCRO_0000036 Trade-off Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Content involving known trade-offs for the use of the model. Trade offs might include performance or technical or ethical. "This section should list additional concerns that were not covered in the previous sections. For example, did the results suggest any further testing? Were there any relevant groups that were not represented in the evaluation dataset? Are there additional recommendations for model use? What are the ideal characteristics of an evaluation dataset for this model?" http://purl.obolibrary.org/obo/MCRO_0000022 Model Parameter Section http://purl.obolibrary.org/obo/IAO_0000314 document part Section summarizing the content relating to the parameters for the development of the model. http://purl.obolibrary.org/obo/MCRO_0000032 Reference Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part information for any references related to the machine learning model (research papers, website, etc.) 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/IAO_0000646 postal code http://purl.obolibrary.org/obo/IAO_0020000 identifier An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. http://purl.obolibrary.org/obo/IAO_0000647 Postal delivery route http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. http://purl.obolibrary.org/obo/PATO_0000051 morphology http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. http://purl.obolibrary.org/obo/PATO_0001018 physical quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. http://purl.obolibrary.org/obo/PATO_0001241 physical object quality http://purl.obolibrary.org/obo/BFO_0000019 quality A quality which inheres in a continuant. 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 specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) 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_0000035 process boundary http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) 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/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) http://purl.obolibrary.org/obo/BFO_0000144 process profile http://purl.obolibrary.org/obo/BFO_0000015 process b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) http://purl.obolibrary.org/obo/BFO_0000145 relational quality http://purl.obolibrary.org/obo/BFO_0000019 quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) http://purl.obolibrary.org/obo/IAO_0000001 conditional specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A directive information entity that specifies what should happen if the trigger condition is fulfilled. 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_0000006 narrative object http://purl.obolibrary.org/obo/IAO_0000030 information content entity A narrative object is an information content entity that is a set of propositions. 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_0000013 journal article http://purl.obolibrary.org/obo/IAO_0000311 publication A report that is published in a journal. http://purl.obolibrary.org/obo/IAO_0000015 information carrier http://purl.obolibrary.org/obo/BFO_0000019 quality A quality of an information bearer that imparts the information content http://purl.obolibrary.org/obo/IAO_0000017 model number http://purl.obolibrary.org/obo/IAO_0000028 symbol A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. 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_0000029 numeral http://purl.obolibrary.org/obo/IAO_0000028 symbol A symbol that denotes a number. 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_0000031 integer numeral http://purl.obolibrary.org/obo/IAO_0000029 numeral A numeral that denotes an integer http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 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_0000055 rule http://purl.obolibrary.org/obo/IAO_0000001 conditional specification A rule is an executable which guides, defines, restricts actions. http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000104 plan specification An algorithm is a set of instructions for performing a paticular calculation. http://purl.obolibrary.org/obo/IAO_0000065 software interpreter http://purl.obolibrary.org/obo/IAO_0000064 algorithm A software interpreter is a software application that executes some specified input software. 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_0000079 density plot http://purl.obolibrary.org/obo/IAO_0000038 graph A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. http://purl.obolibrary.org/obo/IAO_0000088 report http://purl.obolibrary.org/obo/IAO_0000310 document A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). 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 The syntax by which data is specified which renders it valid for a given format. 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_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000027 data item A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. http://purl.obolibrary.org/obo/IAO_0000129 version name http://purl.obolibrary.org/obo/IAO_0000030 information content entity 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_0000131 serial number http://purl.obolibrary.org/obo/IAO_0000028 symbol A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. http://purl.obolibrary.org/obo/IAO_0000140 setting datum http://purl.obolibrary.org/obo/IAO_0000027 data item A settings datum is a datum that denotes some configuration of an instrument. http://purl.obolibrary.org/obo/IAO_0000144 conclusion textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 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_0000181 Venn diagram http://purl.obolibrary.org/obo/IAO_0000038 graph A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. 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_0000185 photograph http://purl.obolibrary.org/obo/IAO_0000101 image A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. http://purl.obolibrary.org/obo/IAO_0000186 photographic print http://purl.obolibrary.org/obo/IAO_0000178 material information bearer A photographic print is a material entity upon which a photograph generically depends. 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_0000301 citation http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity intended to identify a particular publication. http://purl.obolibrary.org/obo/IAO_0000302 author identification http://purl.obolibrary.org/obo/IAO_0000590 written name A textual entity intended to identify a particular author http://purl.obolibrary.org/obo/IAO_0000303 institutional identification http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity intended to identify a particular institution http://purl.obolibrary.org/obo/IAO_0000304 caption http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that describes a figure http://purl.obolibrary.org/obo/IAO_0000305 document title http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that names a document http://purl.obolibrary.org/obo/IAO_0000306 table http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions http://purl.obolibrary.org/obo/IAO_0000307 table of abbreviations http://purl.obolibrary.org/obo/IAO_0000306 table A table where the constituent texts are abbreviations and their expansions 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_0000313 patent http://purl.obolibrary.org/obo/IAO_0000310 document A document that has been accepted by a patent authority http://purl.obolibrary.org/obo/IAO_0000314 document part http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is part of a document. http://purl.obolibrary.org/obo/IAO_0000321 author list http://purl.obolibrary.org/obo/IAO_0000314 document part A part of a document that enumerates the authors of the document http://purl.obolibrary.org/obo/IAO_0000322 institution list http://purl.obolibrary.org/obo/IAO_0000314 document part A part of a document that has parts that are institution identifications associated with the authors of the document http://purl.obolibrary.org/obo/IAO_0000327 table of contents http://purl.obolibrary.org/obo/IAO_0000306 table A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). http://purl.obolibrary.org/obo/IAO_0000328 table of figures http://purl.obolibrary.org/obo/IAO_0000306 table A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). http://purl.obolibrary.org/obo/IAO_0000329 running title http://purl.obolibrary.org/obo/IAO_0000305 document title A shorter version of a document title http://purl.obolibrary.org/obo/IAO_0000330 copyright section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that describes legal restrictions on making or distributing copies of the document http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000027 data item A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude http://purl.obolibrary.org/obo/IAO_0000401 one dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000402 two dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000403 three dimensional cartesian spatial coordinate datum http://purl.obolibrary.org/obo/IAO_0000400 cartesian spatial coordinate datum A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region http://purl.obolibrary.org/obo/IAO_0000408 length measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measurement of length quality 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/IAO_0000414 mass measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measurement of mass quality http://purl.obolibrary.org/obo/IAO_0000415 hypothesis textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses an assertion that is intended to be tested. http://purl.obolibrary.org/obo/IAO_0000416 time measurement datum http://purl.obolibrary.org/obo/IAO_0000032 scalar measurement datum A scalar measurement datum that is the result of measuring a temporal interval http://purl.obolibrary.org/obo/IAO_0000422 postal address http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that is used as directive to deliver something to a person, or organization http://purl.obolibrary.org/obo/IAO_0000442 author role http://purl.obolibrary.org/obo/BFO_0000023 role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. http://purl.obolibrary.org/obo/IAO_0000443 data item extraction from journal article http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing http://purl.obolibrary.org/obo/IAO_0000572 documenting http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which a document is created or added to by including the specified input in it. http://purl.obolibrary.org/obo/IAO_0000590 written name http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that denotes a particular in reality. http://purl.obolibrary.org/obo/IAO_0000591 software method http://purl.obolibrary.org/obo/IAO_0000010 software A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. http://purl.obolibrary.org/obo/IAO_0000592 software module http://purl.obolibrary.org/obo/IAO_0000010 software A software module is software composed of a collection of software methods. http://purl.obolibrary.org/obo/IAO_0000593 software library http://purl.obolibrary.org/obo/IAO_0000010 software A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. http://purl.obolibrary.org/obo/IAO_0000594 software application http://purl.obolibrary.org/obo/IAO_0000010 software A software application is software that can be directly executed by some processing unit. http://purl.obolibrary.org/obo/IAO_0000595 software script http://purl.obolibrary.org/obo/IAO_0000010 software A software script is software whose instructions can be executed using a software interpreter. 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_0000066 investigation http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). 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_0000471 study design execution http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that carries out a study design http://purl.obolibrary.org/obo/OBI_0500000 study design http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. http://purl.obolibrary.org/obo/PATO_0000122 length http://purl.obolibrary.org/obo/PATO_0000051 morphology A 1-D extent quality which is equal to the distance between two points. http://purl.obolibrary.org/obo/PATO_0000125 mass http://purl.obolibrary.org/obo/PATO_0001018 physical quality A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. http://purl.obolibrary.org/obo/APOLLO_SV_00000032 count http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that is the output of counting. http://purl.obolibrary.org/obo/IAO_0020015 personal name http://purl.obolibrary.org/obo/IAO_0020000 identifier An identifier referring to an individual entity that is ascribed personhood by the user of the identifier. http://purl.obolibrary.org/obo/MCRO_0000002 Accuracy Information Section http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section Section content in this section should describe information in "how close or far off a given set of measurements (observations or readings) are to their true value" http://purl.obolibrary.org/obo/MCRO_0000005 Consideration Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part This section pertains to "Factors" of the model card report by Mitchell et al., 2019. The considerations section includes qualitative information about your model, including some analysis of its risks and limitations. As such, this section usually requires careful consideration, and conversations with many relevant stakeholders, including other model developers, dataset producers, and downstream users likely to interact with your model, or be affected by its outputs. http://purl.obolibrary.org/obo/MCRO_0000010 False Discovery Rate Information Section http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section The section describes information about the false discovery rate of the machine learning model. "The false discovery rate (FDR) is a method of conceptualizing the rate of type I errors in null hypothesis testing when conducting multiple comparisons. FDR-controlling procedures are designed to control the FDR, which is the expected proportion of "discoveries" (rejected null hypotheses) that are false (incorrect rejections of the null)". quivalently, the FDR is the expected ratio of the number of false positive classifications (false discoveries) to the total number of positive classifications (rejections of the null). The total number of rejections of the null include both the number of false positives (FP) and true positives (TP). Simply put, FDR = FP / (FP + TP). FDR-controlling procedures provide less stringent control of Type I errors compared to familywise error rate (FWER) controlling procedures (such as the Bonferroni correction), which control the probability of at least one Type I error. Thus, FDR-controlling procedures have greater power, at the cost of increased numbers of Type I errors." http://purl.obolibrary.org/obo/MCRO_0000024 Output Format Information Section http://purl.obolibrary.org/obo/MCRO_0000013 Format Information Section This secton content serves to describe the outputted data's format for the machine learning model. http://purl.obolibrary.org/obo/MCRO_0000006 Dataset Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Information about the data that was used to develop the model http://purl.obolibrary.org/obo/MCRO_0000030 Primary Intended User Information Section http://purl.obolibrary.org/obo/MCRO_0000039 User Information Section This section describes the primary intended user for the machine learning model. "For example, was the model developed for entertainment purposes, for hobbyists, or enterprise solutions? This helps users gain insight into how robust the model may be to different kinds of inputs." http://purl.obolibrary.org/obo/APOLLO_SV_00000033 counting http://purl.obolibrary.org/obo/OBI_0000011 planned process The planned process of finding the number of elements in a finite set of objects. 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/swo/SWO_0000001 software http://purl.obolibrary.org/obo/IAO_0000030 information content entity 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_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_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_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_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 role http://purl.obolibrary.org/obo/BFO_0000023 role 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_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. 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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. 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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/SWO_0000002 software license 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://purl.obolibrary.org/obo/IAO_0020001 grapheme http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity that is a fundamental unit in a written language. http://purl.obolibrary.org/obo/MCRO_0000026 Percision-Recall Curve Information Section http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section This section is for the description of the precision and recall information of the machine learning model's performance. http://purl.obolibrary.org/obo/MCRO_0000034 Sensitive Data Information Section http://purl.obolibrary.org/obo/MCRO_0000006 Dataset Information Section Information relating to sensitive datasets that contain info like personal information that was used to develop the machine learning model http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Section content here summarizing the information about the metrics (precision, recall, f1 score, etc.) that measured the performance of the model. One can report the values and portion of the data (slice). http://purl.obolibrary.org/obo/MCRO_0000016 License Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Section for information about the licensing for the machine learning model. http://purl.obolibrary.org/obo/MCRO_0000007 Ethical Consideration Section http://purl.obolibrary.org/obo/MCRO_0000033 Risk Information Section Content information that is a type of risk information that is specific to ethical consideration if using the model. 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_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/IAO_0000444 publishing process http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. http://purl.obolibrary.org/obo/IAO_0000445 document in preparation for publication http://purl.obolibrary.org/obo/IAO_0000310 document A document that is in preparation for submission to be published. http://purl.obolibrary.org/obo/IAO_0000701 descriptive data section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made. http://purl.obolibrary.org/obo/IAO_0000702 additional results section http://purl.obolibrary.org/obo/IAO_0000318 results section A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.) http://purl.obolibrary.org/obo/IAO_0000703 research participants section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.). http://purl.obolibrary.org/obo/IAO_0000704 measurement methods section http://purl.obolibrary.org/obo/IAO_0000317 methods section A methods section that describes details of data assessment methods (data measurement). http://purl.obolibrary.org/obo/IAO_0000705 research settings section http://purl.obolibrary.org/obo/IAO_0000314 document part A document part that describes the physical/social/cultural conditions around a research trial. http://purl.obolibrary.org/obo/IAO_0000706 study bias section http://purl.obolibrary.org/obo/IAO_0000631 study limitations section A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others. http://purl.obolibrary.org/obo/MCRO_0000017 Limitation Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Content section relating to the technical limits of the machine learning model (e.g. trained on ungeneralized data). http://purl.obolibrary.org/obo/IAO_0000605 abbreviation textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity listing abbreviations and their expansions that are used in a document. http://purl.obolibrary.org/obo/IAO_0000608 author information textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. http://purl.obolibrary.org/obo/IAO_0000610 author summary textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). http://purl.obolibrary.org/obo/IAO_0000612 availability textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. http://purl.obolibrary.org/obo/IAO_0000614 case report textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. http://purl.obolibrary.org/obo/IAO_0000617 conflict of interest textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. http://purl.obolibrary.org/obo/IAO_0000619 consent textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that documents the consenting process used to enroll patients in a study. http://purl.obolibrary.org/obo/IAO_0000621 ethical approval textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that documents the ethical approval of some study design. http://purl.obolibrary.org/obo/IAO_0000624 funding source declaration textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity documenting the source of funding that supported some study. http://purl.obolibrary.org/obo/IAO_0000626 future directions textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. http://purl.obolibrary.org/obo/IAO_0000628 genome announcement textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that describes the generation and public release of a novel, draft genome sequence. http://purl.obolibrary.org/obo/IAO_0000629 keyword textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity listing keywords indicating the major theme(s) of a document. http://purl.obolibrary.org/obo/IAO_0000632 study limitations textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity addressing a shortcoming or bias of a study design or execution. http://purl.obolibrary.org/obo/IAO_0000635 patients section http://purl.obolibrary.org/obo/IAO_0000314 document part A part of a document about the patients that participated in a study. http://purl.obolibrary.org/obo/IAO_0000636 patients textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity expressing information regarding the patients used in a study. http://purl.obolibrary.org/obo/IAO_0000638 pre-publication history textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. http://purl.obolibrary.org/obo/IAO_0000640 related work textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. http://purl.obolibrary.org/obo/IAO_0000642 requirements textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that expresses the requirements necessary to use a resource, e.g. software. http://purl.obolibrary.org/obo/IAO_0000643 statistical analysis textual entity http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity documenting statistical analysis tools and techniques employed. http://purl.obolibrary.org/obo/IAO_8000001 base ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. http://purl.obolibrary.org/obo/IAO_8000003 main release ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. http://purl.obolibrary.org/obo/IAO_8000004 bridge ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. http://purl.obolibrary.org/obo/IAO_8000007 curation subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. http://purl.obolibrary.org/obo/IAO_8000008 analysis subset ontology module http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module An ontology module that is intended for usage in analysis or discovery applications. http://purl.obolibrary.org/obo/IAO_8000013 reasoned ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. http://purl.obolibrary.org/obo/IAO_8000014 generated ontology module http://purl.obolibrary.org/obo/IAO_8000000 ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. http://purl.obolibrary.org/obo/IAO_8000015 template generated ontology module http://purl.obolibrary.org/obo/IAO_8000014 generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. http://purl.obolibrary.org/obo/IAO_8000018 obo basic subset ontology module http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports http://purl.obolibrary.org/obo/MCRO_0000028 Personally Identifiable Data Information Section http://purl.obolibrary.org/obo/MCRO_0000034 Sensitive Data Information Section personally identifiable information as "any information about an individual maintained by an agency, including (1) any information that can be used to distinguish or trace an individual's identity, such as name, social security number, date and place of birth, mother's maiden name, or biometric records; and (2) any other information that is linked or linkable to an individual, such as medical, educational, financial, and employment information." The section should specificially describe information about the personally identifiable datasets. http://purl.obolibrary.org/obo/MCRO_0000038 Use Case Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part The content here involves information about intential uses of the model. "This section should allow readers to quickly grasp what the model should and should not be used for, and why it was created. It can also help frame the statistical analysis presented in the rest of the card, including a short description of the user(s), use-case(s), and context(s) for which the model was originally developed." http://purl.obolibrary.org/obo/MCRO_0000025 Owner Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Section for the information about the individuals involved in the development of the machine learning model. This includes contact information, the names of the individuals, etc. http://purl.obolibrary.org/obo/MCRO_0000008 Evaluation Data Information Section http://purl.obolibrary.org/obo/MCRO_0000006 Dataset Information Section The section is devoted in describing the evaluation dataset. "Evaluation datasets should include datasets that are publicly available for third-party use. These could be existing datasets or new ones provided alongside the model card analyses to enable further benchmarking... the evaluation datasets should not only be representative of the model’s typical use cases but also anticipated test scenarios and challenging cases." Details on the dataset(s) used for the quantitative analyses in the card. - Datasets - Motivation - Preprocessing" (Mitchell et al., 2019) http://purl.obolibrary.org/obo/MCRO_0000015 Input Format Information Section http://purl.obolibrary.org/obo/MCRO_0000013 Format Information Section This secton content serves to describe the inputed data's format for the machine learning model. http://purl.obolibrary.org/obo/MCRO_0000013 Format Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part This content summarizes the input and output data format for the model. http://purl.obolibrary.org/obo/MCRO_0000021 Model Detail Section http://purl.obolibrary.org/obo/IAO_0000314 document part Basic information about the model that includes licensing information, owner information, the architecture of the model (algorthim employed), references (cited papers), and versioning information. http://purl.obolibrary.org/obo/MCRO_0000035 Synthetic Evaluation Data Information Section http://purl.obolibrary.org/obo/MCRO_0000008 Evaluation Data Information Section The section is devoted in descrbing the synthetic evaluation datasets used for a machine learning model. Synthetic evaluation datasets are a type of evaluation dataset. "It is often difficult to find datasets that represent populations outside of the initial domain used in training. In some of these situations, synthetically generated datasets may provide representation for use cases that would otherwise go unevaluated" (Mitchell et al., 2019). This section should described the aforementioned. http://purl.obolibrary.org/obo/APOLLO_SV_00000522 source code repository http://purl.obolibrary.org/obo/IAO_0000310 document A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. http://purl.obolibrary.org/obo/APOLLO_SV_00000524 compiling software http://purl.obolibrary.org/obo/APOLLO_SV_00000008 software development A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. 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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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_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.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_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://purl.obolibrary.org/obo/MCRO_0000031 Quantative Analysis Section http://purl.obolibrary.org/obo/IAO_0000314 document part content overview of the quantatitve analysis of the model, specifically the performance of the model http://purl.obolibrary.org/obo/MCRO_0000009 F1-Score Information Section http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section The F1 score is the harmonic mean of the precision and recall. This section describes information relating to the F1 score revealed by the performance of the machine learning model. http://purl.obolibrary.org/obo/MCRO_0000039 User Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Content information pertaining to intended users of the model. This includes individuals that may be impacted as an outcome of the use of the model. http://purl.obolibrary.org/obo/MCRO_0000037 Training Data Information Section http://purl.obolibrary.org/obo/MCRO_0000006 Dataset Information Section The section is for information about the training data used for evaluation of a machine learning model. http://purl.obolibrary.org/obo/MCRO_0000014 Graphic Collection Section http://www.w3.org/2004/02/skos/core#Collection Collection A section describing the set of graphics accompanying the model card's dataset http://purl.obolibrary.org/obo/MCRO_0000040 Version Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part This content section describes any versioning information for the machine learning model. http://purl.obolibrary.org/obo/MCRO_0000019 Model Architecture Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part Content section summarizing the architecture of the model (software used, algortihm, etc.) http://purl.obolibrary.org/obo/MCRO_0000029 Primary Intended Use Case Information Section http://purl.obolibrary.org/obo/MCRO_0000038 Use Case Information Section "This section details whether the model was developed with general or specific tasks in mind (e.g., plant recognition worldwide or in the Pacific Northwest). The use cases may be as broadly or narrowly defined as the developers intend. For example, if the model was built simply to label images, then this task should be indicated as the primary intended use case." http://purl.obolibrary.org/obo/MCRO_0000023 Out of Scope Use Case Section Information http://purl.obolibrary.org/obo/MCRO_0000038 Use Case Information Section "Here, the model card should highlight technology that the model might easily be confused with, or related contexts that users could try to apply the model to. This section may provide an opportunity to recommend a related or similar model that was designed to better meet that particular need, where possible. This section is inspired by warning labels on food and toys, and similar disclaimers presented in electronic datasheets." Content that is a type of use case information but specific to use cases that are out of scope of the intended use case. http://purl.obolibrary.org/obo/MCRO_0000004 Citation Information Section http://purl.obolibrary.org/obo/IAO_0000314 document part information relating to the citation for the targetted model. This is part of the model details component of the model card report http://purl.obolibrary.org/obo/MCRO_0000003 Area Under the Curve Information Section http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section The content describes information pertaining to the area under the ROC curve. http://purl.obolibrary.org/obo/MCRO_0000018 Mitigation Strategy Section http://purl.obolibrary.org/obo/IAO_0000314 document part Content section of the model card that addresses the risk or ethical consideration of the model. http://purl.obolibrary.org/obo/MCRO_0000011 False Ommission Rate Section Information http://purl.obolibrary.org/obo/MCRO_0000027 Performance Metric Information Section This section describes information relating to false ommision rate of the performance of the machine learning model. FOR is the probability that the true value is positive. http://purl.obolibrary.org/obo/BFO_0000148 zero-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region temporal instant. 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/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/SWO_0000002 software license GNU General Public License http://www.ebi.ac.uk/swo/license/SWO_9000086 LPPL http://www.ebi.ac.uk/swo/SWO_0000002 software license 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://purl.obolibrary.org/obo/IAO_8000000 ontology module http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part ontology file 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/IAO_8000017 ontology module subsetted by expressivity http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module http://www.w3.org/ns/prov#End End http://www.w3.org/ns/prov#EntityInfluence EntityInfluence http://www.w3.org/ns/prov#Generation Generation http://www.w3.org/ns/prov#ActivityInfluence ActivityInfluence http://www.w3.org/ns/prov#Invalidation Invalidation http://www.w3.org/ns/prov#ActivityInfluence ActivityInfluence http://www.w3.org/ns/prov#Start Start http://www.w3.org/ns/prov#EntityInfluence EntityInfluence http://www.w3.org/ns/prov#Usage Usage http://www.w3.org/ns/prov#EntityInfluence EntityInfluence http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000011 spatiotemporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000009 two-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000018 zero-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000026 one-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000028 three-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000182 history http://purl.obolibrary.org/obo/BFO_0000015 process 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/BFO_0000024 fiat object part http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000027 object aggregate http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000030 object http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000142 one-dimensional continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000146 two-dimensional continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000147 zero-dimensional continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000140 continuant fiat boundary http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000029 site http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/IAO_0000034 time trigger http://purl.obolibrary.org/obo/IAO_0000001 conditional specification http://purl.obolibrary.org/obo/UO_0000001 length unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000002 mass unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/UO_0000003 time 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://purl.obolibrary.org/obo/IAO_0000429 email address http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/IAO_0000057 contour plot http://purl.obolibrary.org/obo/IAO_0000038 graph 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_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/IAO_0000582 time stamped measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum 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://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_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/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.w3.org/ns/prov#SoftwareAgent SoftwareAgent http://www.w3.org/ns/prov#Agent Agent http://www.w3.org/ns/prov#Organization Organization http://www.w3.org/ns/prov#Agent Agent http://www.w3.org/ns/prov#Person Person http://www.w3.org/ns/prov#Agent Agent http://www.w3.org/ns/prov#Bundle Bundle http://www.w3.org/ns/prov#Entity Entity http://www.w3.org/ns/prov#Collection Collection http://www.w3.org/ns/prov#Entity Entity http://www.w3.org/ns/prov#Plan Plan http://www.w3.org/ns/prov#Entity Entity 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_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.w3.org/2004/02/skos/core#OrderedCollection Ordered Collection http://www.w3.org/2004/02/skos/core#Collection Collection http://www.w3.org/ns/prov#ActivityInfluence ActivityInfluence http://www.w3.org/ns/prov#Influence Influence http://www.w3.org/ns/prov#AgentInfluence AgentInfluence http://www.w3.org/ns/prov#Influence Influence http://www.w3.org/ns/prov#EntityInfluence EntityInfluence http://www.w3.org/ns/prov#Influence Influence http://purl.obolibrary.org/obo/IAO_8000016 taxonomic bridge ontology module http://purl.obolibrary.org/obo/IAO_8000004 bridge ontology module http://purl.obolibrary.org/obo/IAO_8000019 ontology module subsetted by OWL profile http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity http://purl.obolibrary.org/obo/IAO_8000020 EL++ ontology module http://purl.obolibrary.org/obo/IAO_8000019 ontology module subsetted by OWL profile 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://www.w3.org/ns/prov#Communication Communication http://www.w3.org/ns/prov#ActivityInfluence ActivityInfluence http://www.w3.org/ns/prov#Association Association http://www.w3.org/ns/prov#AgentInfluence AgentInfluence http://www.w3.org/ns/prov#Attribution Attribution http://www.w3.org/ns/prov#AgentInfluence AgentInfluence http://www.w3.org/ns/prov#Delegation Delegation http://www.w3.org/ns/prov#AgentInfluence AgentInfluence http://www.w3.org/ns/prov#EmptyCollection EmptyCollection http://www.w3.org/ns/prov#Collection Collection http://www.w3.org/ns/prov#PrimarySource PrimarySource http://www.w3.org/ns/prov#Derivation Derivation http://www.w3.org/ns/prov#Quotation Quotation http://www.w3.org/ns/prov#Derivation Derivation http://www.w3.org/ns/prov#Revision Revision http://www.w3.org/ns/prov#Derivation Derivation http://www.w3.org/ns/prov#Derivation Derivation http://www.w3.org/ns/prov#EntityInfluence EntityInfluence http://purl.obolibrary.org/obo/IAO_0000035 obsolete_study interpretation conclusion A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses http://edamontology.org/format_2549 OBO Flat File 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://purl.obolibrary.org/obo/IAO_0000012 obsolete2_digital entity A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. http://purl.obolibrary.org/obo/IAO_0000019 obsolete2_binary digital entity A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. http://purl.obolibrary.org/obo/IAO_0000024 obsolete_unit of measure a unit of measure is the quality of some material entity compared to which another quality is some multiple of. http://purl.obolibrary.org/obo/IAO_0000047 obsolete2_text based digital entity A text based digital entity is a digital entity that is encoded so that it only contains text characters. http://purl.obolibrary.org/obo/IAO_0000059 obsolete2_report figure A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements http://purl.obolibrary.org/obo/IAO_0000091 obsolete_report element A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). http://purl.obolibrary.org/obo/IAO_0000093 obsolete2_binary executable Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) http://purl.obolibrary.org/obo/IAO_0000097 obsolete_report table A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content http://purl.obolibrary.org/obo/IAO_0000105 obsolete2_digital document A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. http://purl.obolibrary.org/obo/IAO_0000182 obsolete_survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. http://purl.obolibrary.org/obo/IAO_0000576 obsolete_establishing a CRID registry a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. http://www.ebi.ac.uk/swo/data/SWO_3000072 BedGraph 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_3000049 SIF 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/SWO_0000498 cls Categorical (e.g tumor vs normal) class file format http://www.ebi.ac.uk/swo/data/SWO_3000083 .mgf MASCOT generic format http://www.ebi.ac.uk/swo/data/SWO_3000082 .csv Comma-separated value format http://www.ebi.ac.uk/swo/data/SWO_3000084 .mysql MySQL format http://www.ebi.ac.uk/swo/data/SWO_3000085 .sql SQL format http://www.ebi.ac.uk/swo/SWO_0000518 dcf debian control file format http://www.w3.org/ns/prov#Activity Activity http://www.w3.org/ns/prov#InstantaneousEvent InstantaneousEvent http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/IAO_0000008 obsolete_artifact http://purl.obolibrary.org/obo/IAO_0000018 obsolete_material_entity http://purl.obolibrary.org/obo/IAO_0000128 obsolete_identifier http://purl.obolibrary.org/obo/IAO_0000141 obsolete_digital quality http://edamontology.org/format_1910 newick http://edamontology.org/format_1929 FASTA format http://edamontology.org/format_2305 GFF http://edamontology.org/format_3003 BED format http://www.w3.org/ns/prov#Role Role http://www.w3.org/ns/prov#Agent Agent http://www.w3.org/ns/prov#Entity Entity http://www.ebi.ac.uk/swo/data/SWO_3000043 plain text file format http://www.w3.org/2004/02/skos/core#Collection Collection http://www.w3.org/2004/02/skos/core#Concept Concept http://www.w3.org/2004/02/skos/core#ConceptScheme Concept Scheme http://www.w3.org/ns/prov#Influence Influence http://www.ebi.ac.uk/swo/SWO_0000363 Rnw http://www.ebi.ac.uk/swo/SWO_0000378 SBMLR format http://www.ebi.ac.uk/swo/SWO_0000381 SDF format http://www.ebi.ac.uk/swo/SWO_0000409 R data frame http://www.ebi.ac.uk/swo/SWO_0000615 mas5 format http://www.ebi.ac.uk/swo/SWO_0000684 rda http://www.ebi.ac.uk/swo/SWO_1100126 GEO Matrix Series format http://www.w3.org/ns/prov#Location Location 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/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_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/MCRO_0000051 slice http://purl.obolibrary.org/obo/MCRO_0000046 model card text This is data property is specific to Perfomance Metric concepts. It attributes information about the data partition used to experiment on the model. http://purl.obolibrary.org/obo/MCRO_0000050 sensitive data http://purl.obolibrary.org/obo/MCRO_0000046 model card text "A description of any sensitive data that may be present in adataset. Be sure to note PII information such as names, addresses, phone numbers, etc. Preferably, such info should be scrubbed from a dataset if possible. Note that even non-identifying information, such as zip code, age, race, and gender, can be used to identify individuals when aggregated. Please describe any such fields here" Google LLC http://purl.obolibrary.org/obo/IAO_0000142 mentions http://purl.obolibrary.org/obo/IAO_0000136 is about An information artifact IA mentions an entity E exactly when it has a component/part that denotes E http://purl.obolibrary.org/obo/IAO_0000219 denotes http://purl.obolibrary.org/obo/IAO_0000136 is about A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically http://purl.obolibrary.org/obo/IAO_0000221 is quality measurement of http://purl.obolibrary.org/obo/IAO_0000136 is about m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q http://purl.obolibrary.org/obo/IAO_0000413 is duration of http://purl.obolibrary.org/obo/IAO_0000136 is about relates a process to a time-measurement-datum that represents the duration of the process http://purl.obolibrary.org/obo/IAO_0000418 is quality specification of http://purl.obolibrary.org/obo/IAO_0000136 is about A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. http://purl.obolibrary.org/obo/IAO_0000581 has time stamp http://purl.obolibrary.org/obo/BFO_0000051 has part relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken http://purl.obolibrary.org/obo/IAO_0000583 has measurement datum http://purl.obolibrary.org/obo/BFO_0000051 has part relates a time stamped measurement datum to the measurement datum that was measured 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_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/MCRO_0000043 contact text http://purl.obolibrary.org/obo/MCRO_0000046 model card text Data pertaining to the contact information of the model's contact information. This is associated to the Owner Information class of the Model Card Ontology http://purl.obolibrary.org/obo/MCRO_0000045 documentation http://purl.obolibrary.org/obo/MCRO_0000046 model card text Detailed textual information of the model card that is attributed to specific concepts of the Model Card Ontology. This contrasts with the "overview" data property as the "overview" has a summarized version of "documentation" http://purl.obolibrary.org/obo/MCRO_0000044 custom_text http://purl.obolibrary.org/obo/MCRO_0000046 model card text Additional textual information attributed to the licensing information. http://www.ebi.ac.uk/swo/SWO_0000088 is specified data input of http://purl.obolibrary.org/obo/RO_0002352 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 http://purl.obolibrary.org/obo/RO_0002353 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_0000131 directly preceded by http://purl.obolibrary.org/obo/BFO_0000060 preceded by 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://purl.obolibrary.org/obo/BFO_0000063 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/efo/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/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://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/MCRO_0000048 overview http://purl.obolibrary.org/obo/MCRO_0000046 model card text Summary textual information for the concepts of the Model Card Ontology http://purl.obolibrary.org/obo/RO_0002352 input of http://purl.obolibrary.org/obo/RO_0000056 participates in 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_0000056 participates in 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/MCRO_0000047 name text http://purl.obolibrary.org/obo/MCRO_0000046 model card text Name of the owner of the model. This is linked to the Owner Information concept of the Model Card Ontology http://www.ebi.ac.uk/efo/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/MCRO_0000049 performance metric value http://purl.obolibrary.org/obo/MCRO_0000046 model card text general numeric value associated with the Performance Metric concepts http://purl.obolibrary.org/obo/MCRO_0000052 threshold value http://purl.obolibrary.org/obo/MCRO_0000046 model card text This is a value pertaining to a threshold value that is attributed to the Performance Metric concept for the Model Card ontology. http://purl.obolibrary.org/obo/MCRO_0000041 citation text http://purl.obolibrary.org/obo/MCRO_0000046 model card text additional information abou the citation associated with the model http://purl.obolibrary.org/obo/MCRO_0000042 confidence interval value http://purl.obolibrary.org/obo/MCRO_0000046 model card text value of the confidence interval attributed to the Performance Metric concept http://purl.obolibrary.org/obo/RO_0000092 disposition of http://purl.obolibrary.org/obo/RO_0000052 characteristic of http://purl.obolibrary.org/obo/IAO_0000039 has measurement unit label http://purl.obolibrary.org/obo/BFO_0000051 has part http://purl.obolibrary.org/obo/IAO_0000407 has coordinate unit label http://purl.obolibrary.org/obo/BFO_0000051 has part http://www.w3.org/2004/02/skos/core#broadMatch has broader match http://www.w3.org/2004/02/skos/core#mappingRelation is in mapping relation with http://www.w3.org/2004/02/skos/core#broader has broader http://www.w3.org/2004/02/skos/core#broaderTransitive has broader transitive http://www.w3.org/2004/02/skos/core#exactMatch has exact match http://www.w3.org/2004/02/skos/core#closeMatch has close match http://www.w3.org/2004/02/skos/core#topConceptOf is top concept in scheme http://www.w3.org/2004/02/skos/core#inScheme is in scheme http://www.w3.org/2004/02/skos/core#closeMatch has close match http://www.w3.org/2004/02/skos/core#mappingRelation is in mapping relation with http://www.w3.org/2004/02/skos/core#narrowMatch has narrower match http://www.w3.org/2004/02/skos/core#narrower has narrower http://www.w3.org/2004/02/skos/core#relatedMatch has related match http://www.w3.org/2004/02/skos/core#related has related http://www.w3.org/2004/02/skos/core#narrower has narrower http://www.w3.org/2004/02/skos/core#narrowerTransitive has narrower transitive http://www.w3.org/2004/02/skos/core#broaderTransitive has broader transitive http://www.w3.org/2004/02/skos/core#semanticRelation is in semantic relation with http://www.w3.org/2004/02/skos/core#mappingRelation is in mapping relation with http://www.w3.org/2004/02/skos/core#semanticRelation is in semantic relation with http://www.w3.org/2004/02/skos/core#narrowerTransitive has narrower transitive http://www.w3.org/2004/02/skos/core#semanticRelation is in semantic relation with http://www.w3.org/2004/02/skos/core#related has related http://www.w3.org/2004/02/skos/core#semanticRelation is in semantic relation with http://www.w3.org/ns/prov#specializationOf specializationOf http://www.w3.org/ns/prov#alternateOf alternateOf http://www.w3.org/ns/prov#generated generated http://www.w3.org/ns/prov#influenced influenced http://www.w3.org/ns/prov#invalidated invalidated http://www.w3.org/ns/prov#influenced influenced http://www.w3.org/ns/prov#entity entity http://www.w3.org/ns/prov#influencer influencer http://www.w3.org/ns/prov#activity activity http://www.w3.org/ns/prov#influencer influencer http://www.w3.org/ns/prov#agent agent http://www.w3.org/ns/prov#influencer influencer http://www.w3.org/ns/prov#qualifiedAssociation qualifiedAssociation http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedAttribution qualifiedAttribution http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedCommunication qualifiedCommunication http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedDelegation qualifiedDelegation http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedDerivation qualifiedDerivation http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedEnd qualifiedEnd http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedGeneration qualifiedGeneration http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedInvalidation qualifiedInvalidation http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedPrimarySource qualifiedPrimarySource http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedQuotation qualifiedQuotation http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedRevision qualifiedRevision http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedStart qualifiedStart http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#qualifiedUsage qualifiedUsage http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#hadPrimarySource hadPrimarySource http://www.w3.org/ns/prov#wasDerivedFrom wasDerivedFrom http://www.w3.org/ns/prov#wasQuotedFrom wasQuotedFrom http://www.w3.org/ns/prov#wasDerivedFrom wasDerivedFrom http://www.w3.org/ns/prov#wasRevisionOf wasRevisionOf http://www.w3.org/ns/prov#wasDerivedFrom wasDerivedFrom http://www.w3.org/ns/prov#actedOnBehalfOf actedOnBehalfOf http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#hadMember hadMember http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#used used http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasAssociatedWith wasAssociatedWith http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasAttributedTo wasAttributedTo http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasDerivedFrom wasDerivedFrom http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasEndedBy wasEndedBy http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasGeneratedBy wasGeneratedBy http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasInformedBy wasInformedBy http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasInvalidatedBy wasInvalidatedBy http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://www.w3.org/ns/prov#wasStartedBy wasStartedBy http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy http://purl.obolibrary.org/obo/RO_0000052 characteristic 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_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://purl.obolibrary.org/obo/RO_0001000 derives from derives_from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001001 derives into derives_into a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001015 location of location_of a relation between two independent continuants, the location and the target, in which the target is entirely within the location http://purl.obolibrary.org/obo/RO_0002000 2D boundary of is boundary of a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0002002 has 2D boundary has_2D_boundary a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0001025 located in located_in a relation between two independent continuants, the target and the location, in which the target is entirely within the location http://purl.obolibrary.org/obo/BFO_0000051 has part has_part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/BFO_0000050 part of part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/BFO_0000066 occurs in unfolds_in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/MCRO_0000046 model card text Model Card Report Ontology specific data properties that provide attributes to its concepts. http://purl.obolibrary.org/obo/IAO_0000143 mentioned by Inverse of the relation 'mentions' http://purl.obolibrary.org/obo/BFO_0000063 followed by The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'. http://purl.obolibrary.org/obo/BFO_0000067 contains process [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/IAO_0000135 obsolete_specifically denotes c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. 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/IAO_0000417 is quality measured as inverse of the relation of is quality measurement of http://purl.obolibrary.org/obo/IAO_0000419 quality is specified as inverse of the relation of is quality specification of 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://www.ebi.ac.uk/efo/swo/SWO_0000394 is developed by The relationship between a software and software developer. http://www.ebi.ac.uk/efo/swo/SWO_0000395 obsolete_is_published_by The relationship between software and a software publisher. 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_0000046 has download location The location from where the software can be downloaded. 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_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_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/SWO_9001002 has clause 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/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://www.ebi.ac.uk/swo/maturity/SWO_9000067 has declared status '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.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://www.ebi.ac.uk/efo/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_0000235 denoted by inverse of the relation 'denotes' http://purl.obolibrary.org/obo/BFO_0000054 realized in realized_in http://purl.obolibrary.org/obo/BFO_0000060 preceded by http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/IAO_0000004 has measurement value http://purl.obolibrary.org/obo/IAO_0000220 obsolete_materially denotes http://purl.obolibrary.org/obo/IAO_0000222 obsolete_describes http://purl.obolibrary.org/obo/IAO_0000223 obsolete_represents http://purl.obolibrary.org/obo/IAO_0000404 has x coordinate value http://purl.obolibrary.org/obo/IAO_0000405 has z coordinate value http://purl.obolibrary.org/obo/IAO_0000406 has y coordinate value http://purl.obolibrary.org/obo/OBI_0000295 is_specified_input_of http://purl.obolibrary.org/obo/RO_0004096 DEPRECATED inheres in http://purl.obolibrary.org/obo/RO_0004097 DEPRECATED bearer of 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.w3.org/2004/02/skos/core#hasTopConcept has top concept http://www.w3.org/2004/02/skos/core#inScheme is in scheme http://www.w3.org/2004/02/skos/core#member has member http://www.w3.org/2004/02/skos/core#memberList has member list http://www.w3.org/2004/02/skos/core#notation notation http://www.w3.org/2004/02/skos/core#semanticRelation is in semantic relation with http://www.w3.org/ns/prov#hadGeneration hadGeneration http://www.w3.org/ns/prov#hadRole hadRole http://www.w3.org/ns/prov#value value http://www.w3.org/ns/prov#alternateOf alternateOf http://www.w3.org/ns/prov#atLocation atLocation http://www.w3.org/ns/prov#atTime atTime http://www.w3.org/ns/prov#endedAtTime endedAtTime http://www.w3.org/ns/prov#generatedAtTime generatedAtTime http://www.w3.org/ns/prov#hadActivity hadActivity http://www.w3.org/ns/prov#hadPlan hadPlan http://www.w3.org/ns/prov#hadUsage hadUsage http://www.w3.org/ns/prov#influenced influenced http://www.w3.org/ns/prov#influencer influencer http://www.w3.org/ns/prov#invalidatedAtTime invalidatedAtTime http://www.w3.org/ns/prov#qualifiedInfluence qualifiedInfluence http://www.w3.org/ns/prov#startedAtTime startedAtTime http://www.w3.org/ns/prov#wasInfluencedBy wasInfluencedBy