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/COB_0000035 completely executed 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 entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity data item An information content entity that is intended to be one or more truthful statement(s) 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_0000100 homogenous data collection http://purl.obolibrary.org/obo/IAO_0001000 data collection data set 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_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/COB_0000035 completely executed 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/COB_0000035 completely executed 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 homogenous data collection 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/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/COB_0000035 completely executed 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/COB_0000035 completely executed planned process dataset creation A planned process that has a data set as its specified output. http://purl.obolibrary.org/obo/IAO_0020016 given name http://purl.obolibrary.org/obo/IAO_0020015 personal name first name A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name http://purl.obolibrary.org/obo/IAO_0020017 family name http://purl.obolibrary.org/obo/IAO_0020000 identifier surname An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. http://purl.obolibrary.org/obo/IAO_0000708 ORCID identifier http://purl.obolibrary.org/obo/IAO_0000578 centrally registered identifier Open Researcher and Contributor Identifier A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor. 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/COB_0000035 completely executed 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://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/IAO_0001000 data collection http://purl.obolibrary.org/obo/IAO_0000027 data entity data set A data entity that consists of multiple data entities. http://purl.obolibrary.org/obo/APOLLO_SV_00000008 software development http://purl.obolibrary.org/obo/COB_0000035 completely executed 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 b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) 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 b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) 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 that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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 that is intended to be 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 A generically dependent continuant that is about some thing. 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 A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. http://purl.obolibrary.org/obo/IAO_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 A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file http://purl.obolibrary.org/obo/IAO_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 entity 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 entity 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 number http://purl.obolibrary.org/obo/IAO_0000028 symbol A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. http://purl.obolibrary.org/obo/IAO_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 entity 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 entity 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/COB_0000035 completely executed 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/COB_0000035 completely executed 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_0000066 investigation http://purl.obolibrary.org/obo/COB_0000035 completely executed 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_0000471 study design execution http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process a planned process that carries out a study design http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process A completely executed planned process that produces output data from input data. 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/UO_0000001 length unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the distance between two points. http://purl.obolibrary.org/obo/UO_0000002 mass unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the amount of matter/energy of a physical object. http://purl.obolibrary.org/obo/UO_0000003 time unit http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label A unit which is a standard measure of the dimension in which events occur in sequence. http://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/APOLLO_SV_00000033 counting http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process The planned process of finding the number of elements in a finite set of objects. 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/IAO_0000651 title section http://purl.obolibrary.org/obo/IAO_0000314 document part the section of the document where the title appears http://purl.obolibrary.org/obo/COB_0000082 planned process http://purl.obolibrary.org/obo/BFO_0000015 process A process that is initiated by an agent who intends to carry out a plan to achieve an objective through one or more actions as described in a plan specification. http://purl.obolibrary.org/obo/IAO_0000444 publishing process http://purl.obolibrary.org/obo/COB_0000035 completely executed 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/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/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://purl.obolibrary.org/obo/BFO_0000148 zero-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region temporal instant. http://purl.obolibrary.org/obo/IAO_8000000 ontology module http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part ontology file http://purl.obolibrary.org/obo/IAO_8000017 ontology module subsetted by expressivity http://purl.obolibrary.org/obo/IAO_8000006 subset ontology module 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/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://purl.obolibrary.org/obo/IAO_0000582 time stamped measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/COB_0000035 completely executed planned process http://purl.obolibrary.org/obo/COB_0000082 planned process 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://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://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://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://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/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 completely executed planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/RO_0002351 has member http://purl.obolibrary.org/obo/BFO_0000051 has part has member is a mereological relation between a collection and an item. http://purl.obolibrary.org/obo/RO_0000091 has disposition http://purl.obolibrary.org/obo/RO_0000053 has characteristic a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000092 disposition of http://purl.obolibrary.org/obo/RO_0000052 characteristic of 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://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 a relation between a process and a continuant, in which the continuant is somehow involved 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/IAO_0000143 mentioned by Inverse of the relation 'mentions' 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 or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes. http://purl.obolibrary.org/obo/RO_0000059 concretizes A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/IAO_0000011 is directed towards A relationship between a quality and a portion of reality such that the quality refers to or is cognitively directed towards the portion of reality. 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_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