421:
440:) and a local numeric identifier within the ontology. The choice of a numerical ID was made in order to improve maintenance and evolution of the resources. In order to participate in OBO Foundry, ontologies have to be orthogonal and the concepts it models must be unique within OBO, so each concept has a single
273:
As a community effort, standard common mappings have been created for lossless roundtrip transformations between Open
Biomedical Ontologies (OBO) format and OWL. The research contains methodical examination of each of the constructs of OBO and a layer cake for OBO, similar to the Semantic Web stack.
202:
The OBO Foundry is open to participations of any interested individuals. Ontologies that intend to be officially part of the OBO Foundry have to adhere to the OBO principles and pass a series of reviews done by the members, when "the
Foundry coordinators serve as analogs of journal editors". There
159:
Consortium, a part of the OBO Foundry. This has led to the development of certain proposed principles of good practice in ontology development, which are now being put into practice within the framework of the Open
Biomedical Ontologies consortium through its OBO Foundry initiative. OBO ontologies
352:. One of the goals of the integration of OBO Foundry to Wikidata has been to lower the barriers for non-ontologists to contribute to and use ontologies. Wikidata is arguably easier to understand and use than the traditional ontology models (which require a high degree of specific expertise).
456:
Ontologies evolve in time, refining concepts and descriptions according to advances in the knowledge of their specific domains. In order to ensure that new versions are updated, but tools that use older version of the ontologies are still function, OBO enforces a system of
1493:
Waagmeester, Andra; Stupp, Gregory; Burgstaller-Muehlbacher, Sebastian; Good, Benjamin M; Griffith, Malachi; Griffith, Obi L; Hanspers, Kristina; Hermjakob, Henning; Hudson, Toby S; Hybiske, Kevin; Keating, Sarah M (2020-03-17). Rodgers, Peter; Mungall, Chris (eds.).
540:
The ontologies should be useful for multiple different people, and ontology developers should document the evidence of use. This criterion is important for the review process. Examples of use include linking to terms by other ontologies, use in
447:
Despite the ideal of uniqueness of terms and interoperability, in practice, this is difficult to enforce, leading to the occurrence of term duplication. Furthermore, some ontologies do not reuse terms or even reuse terms inappropriately.
1197:
Diehl, Alexander D.; Meehan, Terrence F.; Bradford, Yvonne M.; Brush, Matthew H.; Dahdul, Wasila M.; Dougall, David S.; He, Yongqun; Osumi-Sutherland, David; Ruttenberg, Alan; Sarntivijai, Sirarat; Van Slyke, Ceri E. (2016-07-04).
598:. The OBO Foundry defines scientific consensus as "multiple publications by independent labs over a year come to the same conclusion, and there is no or limited (<10%) dissenting opinions published in the same time frame."
290:, FMAO), by mergers of previously existing ontologies (ex: the Cell Ontology, CL, formed from different dedicated ontologies, and related parts on GO and FMAO) and by development of new ontologies based on its principles.
586:, which allows labels in different systems. The naming system in OBO is based on a series of surveys at cataloguing naming conventions of current ontologies, as well as discover issues relating to these conventions.
1376:
Smith, Barry; Ashburner, Michael; Rosse, Cornelius; Bard, Jonathan; Bug, William; Ceusters, Werner; Goldberg, Louis J; Eilbeck, Karen; Ireland, Amelia; Mungall, Christopher J; Leontis, Neocles (November 2007).
573:
Naming conventions for OBO ontologies aim at making primary labels unambiguous and unique inside the ontology (and preferably, inside OBO). Labels and synonyms should be written in
English, avoiding the use of
234:
management of ontologies in a Protégé- and OWL-compatible format, the OBO Foundry has developed the tool ROBOT (ROBOT is an OBO Tool). ROBOT aggregates functions for routine tasks in ontology development, is
1602:
Schriml, Lynn M.; Mitraka, Elvira; Munro, James; Tauber, Becky; Schor, Mike; Nickle, Lance; Felix, Victor; Jeng, Linda; Bearer, Cynthia; Lichenstein, Richard; Bisordi, Katharine (2019-01-08).
2250:
Schober, Daniel; Smith, Barry; Lewis, Suzanna E; Kusnierczyk, Waclaw; Lomax, Jane; Mungall, Chris; Taylor, Chris F; Rocca-Serra, Philippe; Sansone, Susanna-Assunta (2009).
144:
The
Foundry initiative aims at improving the integration of data in the life sciences. One approach to integration is the annotation of data from different sources using
1684:
516:
between different biomedical concepts. It describes rigorously relations like "part_of", "located_in" and "preceded_by" that are reused by many OBO Foundry ontologies.
895:
1114:
Golbreich, Christine; Horridge, Matthew; Horrocks, Ian; Motik, Boris; Shearer, Rob (2007), "OBO and OWL: Leveraging
Semantic Web Technologies for the Life Sciences",
2079:
Smith, Barry; Ceusters, Werner; Klagges, Bert; Köhler, Jacob; Kumar, Anand; Lomax, Jane; Mungall, Chris; Neuhaus, Fabian; Rector, Alan L; Rosse, Cornelius (2005).
485:
way. That means that beside the alphanumeric identification for each item, they should be described in natural language by logical affirmations following the
214:
has been proposed as a step to standardize candidate ontologies. This integration would make it easier to develop software to automatically check candidates.
180:) for use across biological and medical domains. A subset of the original OBO ontologies has started the OBO Foundry, which leads the OBO efforts since 2007.
2399:
Web-based tool to display relationships between biological objects annotated to an ontology in the form of a tree, based on their annotation similarity. On
1683:
Jacobsen, Annika; Waagmeester, Andra; Kaliyaperumal, Rajaram; Stupp, Gregory S.; M. Schriml, Lynn; Thompson, Mark; I. Su, Andrew; Roos, Marco (2018-12-04).
340:
knowledge graph. This has led to the integration of OBO structured ontologies to data from other, non-OBO databases . For example, the integration of the
222:
The OBO Foundry community is also dedicated to developing tools to facilitate creating and maintaining ontologies. Most ontology developers in OBO use the
856:
833:
2427:
191:
161:
1553:
Turki, Houcemeddine; Shafee, Thomas; Hadj Taieb, Mohamed Ali; Ben
Aouicha, Mohamed; Vrandečić, Denny; Das, Diptanshu; Hamdi, Helmi (2019-11-01).
2386:
633:
314:
1141:
258:. There are also plugins for OBO-Edit which facilitate the development of ontologies, such as the semi-automatic ontology generator DOG4DAG.
2437:
622:
648:
529:
509:
325:
173:
149:
114:
102:
1055:
Tirmizi, Syed; Aitken, Stuart; Moreira, Dilvan A; Mungall, Chris; Sequeda, Juan; Shah, Nigam H; Miranker, Daniel P (2011).
2351:
294:
287:
400:. In practice, that means that ontologies that are part of the OBO foundry need to describe items unsing the formats OWL/
124:. It does so by offering a structured reference for terms of different research fields and their interconnections (ex: a
437:
461:, with each ontology version receiving a unique identifier, either in the format of a date or a numbering system, and
441:
405:
109:. The OBO Foundry establishes a set of principles for ontology development for creating a suite of interoperable
2432:
565:
The ontologies should have one person responsible for the ontology who mediates interaction with the community.
172:
The Open
Biological and Biomedical Ontologies (OBO; formerly Open Biomedical Ontologies) is an effort to create
2357:
889:
612:
255:
223:
266:
The OBO file format is a biology-oriented language for building ontologies. It is based on the principles of
2442:
2396:
1758:
Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, et al. (2016-01-01).
607:
2365:
341:
231:
63:
482:
420:
401:
267:
227:
177:
145:
106:
2405:
557:
The ontologies should be developed in a way that allows collaborations with other OBO Foundry members.
428:
Terms should be unique in the OBO space, meaning that each item has a unique ontology prefix (such as
1436:"The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio"
1119:
595:
501:. This ensures that different ontologies can integrated seamlessly, which is specially important for
240:
236:
110:
2031:
1118:, Lecture Notes in Computer Science, vol. 4825, Springer Berlin Heidelberg, pp. 169–182,
513:
194:(NCBIO) and a central element of the NCBO's BioPortal. It is an initiative led by the OBO Foundry.
2226:
2202:
2007:
486:
458:
324:
The number of ontologies in OBO has grown to the order of hundreds, and they are gathered in the
120:
The OBO Foundry effort makes it easier to integrate biomedical results and carry out analysis in
1434:
Van Slyke, Ceri E.; Bradford, Yvonne M.; Westerfield, Monte; Haendel, Melissa A. (2014-02-25).
155:
The formalization of concepts in the biomedical domain is especially known via the work of the
2291:
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2112:
1965:
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1221:
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1034:
983:
942:
814:
777:
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617:
502:
498:
310:
293:
The original set of ontologies also included the
Zebrafish Anatomical Ontology (a part of the
251:
67:
2178:
1379:"The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration"
685:"The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration"
152:, which support logical reasoning over the data annotated using the terms in the vocabulary.
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318:
302:
2309:
2130:
1983:
733:
397:
17:
2055:
1200:"The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability"
380:). The openness of the ontologies has enabled, for example, the import of terms from the
282:
The initial set of OBO Foundry ontologies was composed by mature ontologies (such as the
1685:"Wikidata as an intuitive resource towards semantic data modeling in data FAIRification"
1123:
239:, and can be used either via the command line or as a library for any language on the
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2251:
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1002:
937:
910:
772:
737:
709:
684:
683:
Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al. (November 2007).
638:
473:
The ontologies should have a clearly specified scope (the domain it intends to cover).
306:
121:
1807:
1350:
1317:
1293:
1258:
424:
Mapping from OBO IDs to OBO Unified
Resource Identifiers (URIs), unique for each item.
203:
are ontologies that follow OBO principles but are not officially part of OBO, such as
2421:
2154:
433:
381:
372:
The ontologies are openly available and have to be released under either the license
360:
Summary of OBO Foundry Principles for development of an OBO-compatible life sciences
283:
247:
188:
184:
156:
59:
1831:
1734:
1604:"Human Disease Ontology 2018 update: classification, content and workflow expansion"
1174:
1157:
1019:
978:
961:
1696:
909:
Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA (July 2019).
627:
542:
1158:"ONTO-PERL: An API for supporting the development and analysis of bio-ontologies"
1132:
2400:
1926:"Evolution of biomedical ontologies and mappings: Overview of recent approaches"
884:. Proceedings of the International Conference on Biomedical Ontology (CEUR 993).
349:
129:
1942:
1891:
1775:
1571:
1554:
1216:
1073:
927:
643:
579:
575:
546:
336:
A number of different OBO Foundry ontologies have also been integrated to the
2411:
2382:
Ontology browser for most of the Open Biological Ontologies at BRENDA website
2381:
2277:
2268:
2252:"Survey-based naming conventions for use in OBO Foundry ontology development"
1951:
1627:
1580:
1521:
1461:
1402:
1341:
1284:
1225:
1082:
818:
763:
524:
OBO ontologies need to be thoroughly documented. Frequently this is done via
2097:
1275:
834:"Developing a reagent application ontology within the OBO foundry framework"
754:
373:
345:
211:
133:
125:
2295:
2116:
1969:
1910:
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1645:
1588:
1539:
1479:
1452:
1420:
1359:
1302:
1243:
1183:
1100:
1038:
987:
946:
864:. Proceedings of the International Conference on Biomedical Ontology. Graz.
832:
Brush MH, Vasilevsky N, Torniai C, Johnson T, Shaffer C, Haendel M (2011).
809:
796:
781:
718:
1619:
2391:
876:
583:
462:
385:
361:
337:
2372:
MIBBI (Minimum Information for Biological and Biomedical Investigations)
1512:
1862:. CEURS Proceedings: International Conference on Biomedical Ontologies.
1156:
Antezana, E.; Egana, M.; De Baets, B.; Kuiper, M.; Mironov, V. (2008).
653:
444:(URI). New ontologies have, then, to reuse work done in other efforts.
409:
204:
183:
The creation of OBO in 2001 was largely inspired by the efforts of the
1333:
207:'s Reagent Application Ontology. and the Animals in Context Ontology.
525:
1555:"Wikidata: A large-scale collaborative ontological medical database"
1394:
700:
878:
Applying Rigidity to Standardizing OBO Foundry Candidate Ontologies
481:
The ontologies should have textual definitions for each item, in a
113:
in the biomedical domain. Currently, there are more than a hundred
2376:
658:
429:
419:
298:
1318:"eVOC: A Controlled Vocabulary for Unifying Gene Expression Data"
1257:
Bard, Jonathan; Rhee, Seung Y.; Ashburner, Michael (2005-01-14).
582:. OBO lacks a mechanism for multilingual support, in contrast to
2371:
2346:
797:"Multiple Ontologies for Integrating Complex Phenotype Datasets"
2341:
1760:"Wikidata as a semantic framework for the Gene Wiki initiative"
795:
Shimoyama, Mary; Dwinell, Melinda; Jacob, Howard (2009-08-05).
732:
Mungall, Christopher J; Gkoutos, Georgios V; Smith, Cynthia L;
164:, where they form a central component of the NCBO's BioPortal.
377:
960:
Day-Richter J, Harris MA, Haendel M, Lewis S (August 2007).
594:
The ontologies should be updated with regards to changes in
497:
The ontologies should use relations between items from the
738:"Integrating phenotype ontologies across multiple species"
384:(one of the ontologies that follow OBO Principles) to the
148:. Ideally, such controlled vocabularies take the form of
78:
2336:
1858:
Courtot M, Mungall C, Brinkman RR, Ruttenberg A (2010).
344:
to Wikidata has enabled its link to the description of
1496:"Wikidata as a knowledge graph for the life sciences"
493:
Standardized relations and the Relation Ontology (RO)
1659:
1057:"Mapping between the OBO and OWL ontology languages"
1003:"Semi-automated ontology generation within OBO-Edit"
73:
53:
43:
35:
1930:Computational and Structural Biotechnology Journal
1924:GroĂź, Anika; Pruski, CĂ©dric; Rahm, Erhard (2016).
911:"ROBOT: A Tool for Automating Ontology Workflows"
115:ontologies that follow the OBO Foundry principles
1875:"How orthogonal are the OBO Foundry ontologies?"
396:The ontologies have to be available in a common
187:project. OBO forms part of the resources of the
875:Seyed, Patrice, and Stuart C. Shapiro. (2011).
736:; Lewis, Suzanna E; Ashburner, Michael (2010).
528:repositories for each specific ontologies (see
2408:by University of Austin, Texas. On archive.org
2155:"Documented Plurality of Users (principle 9)"
1860:Building the OBO Foundry-One Policy at a Time
962:"OBO-Edit--an ontology editor for biologists"
489:in a way that is unique within the ontology.
230:(OWL) for building ontologies. To facilitate
8:
2179:"Commitment To Collaboration (principle 10)"
894:: CS1 maint: multiple names: authors list (
101:is a group of people who build and maintain
30:
1873:Ghazvinian A, Noy NF, Musen MA (May 2011).
858:Development the Animals in Context ontology
29:
2387:PubOnto: OBO-based literature search tool
2285:
2267:
2106:
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1959:
1941:
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1890:
1783:
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1511:
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1349:
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1233:
1215:
1173:
1131:
1090:
1072:
1028:
1018:
977:
936:
926:
808:
771:
753:
708:
168:Open Biological and Biomedical Ontologies
91:Open Biological and Biomedical Ontologies
246:Other tool related to the OBO effort is
670:
192:National Center for Biomedical Ontology
162:National Center for Biomedical Ontology
887:
634:Ontology for Biomedical Investigations
315:Ontology for Biomedical Investigations
27:Collaborative development organization
1853:
1851:
1371:
1369:
1050:
1048:
412:syntax to maximize interoperability.
7:
2081:"Relations in biomedical ontologies"
1832:"URI/Identifier Space (principle 3)"
1001:Wächter T, Schroeder M (June 2010).
678:
676:
674:
2352:First set of OBO Foundry ontologies
2227:"Naming Conventions (principle 12)"
2203:"Locus of Authority (principle 11)"
2032:"Textual Definitions (principle 6)"
160:form part of the resources of the
39:Improvent of biomedical ontologies
25:
1559:Journal of Biomedical Informatics
508:The Relation Ontology (RO) is an
2412:Relation ontology on OBO Foundry
623:Generic Model Organism Databases
549:or other research applications.
2377:Ontology Lookup Service website
1879:Journal of Biomedical Semantics
1440:Journal of Biomedical Semantics
1204:Journal of Biomedical Semantics
1061:Journal of Biomedical Semantics
210:An integration into OBO of the
2428:Ontology (information science)
1697:10.6084/m9.figshare.7415282.v2
649:List of OBO Foundry ontologies
530:List of OBO Foundry ontologies
326:list of OBO Foundry ontologies
212:OntoClean's theory of rigidity
1:
2131:"Documentation (principle 8)"
1808:"Common Format (principle 2)"
1175:10.1093/bioinformatics/btn042
1020:10.1093/bioinformatics/btq188
979:10.1093/bioinformatics/btm112
295:Zebrafish Information Network
288:Foundational Model of Anatomy
132:and its related phenotype in
2366:slide-deck about OBO Foundry
2310:"Maintenance (principle 16)"
1259:"An ontology for cell types"
1133:10.1007/978-3-540-76298-0_13
376:or under the public domain (
442:Uniform Resource Identifier
268:Web Ontology Language (OWL)
2459:
1984:"Versioning (principle 4)"
1943:10.1016/j.csbj.2016.08.002
553:Openness to collaborations
512:designed to represent the
18:Open Biomedical Ontologies
2056:"Relations (principle 7)"
1892:10.1186/2041-1480-2-s2-s2
1572:10.1016/j.jbi.2019.103292
1217:10.1186/s13326-016-0088-7
1074:10.1186/2041-1480-2-s1-s3
928:10.1186/s12859-019-3002-3
838:CEUR Workshop Proceedings
250:, an ontology editor and
2362:course on bio-ontologies
2269:10.1186/1471-2105-10-125
1316:Kelso, J. (2003-05-12).
628:Functional Genomics Data
613:Gene Ontology Consortium
477:Have textual definitions
332:OBO Foundry and Wikidata
256:Gene Ontology Consortium
226:ontology editor and the
2098:10.1186/gb-2005-6-5-r46
1776:10.1093/database/baw015
1276:10.1186/gb-2005-6-2-r21
755:10.1186/gb-2010-11-1-r2
608:Ontology Lookup Service
499:Relations Ontology (RO)
198:Rules for participation
178:controlled vocabularies
146:controlled vocabularies
2438:Medical classification
1608:Nucleic Acids Research
1453:10.1186/2041-1480-5-12
855:Santamaria SL (2012).
810:10.1038/npre.2009.3554
425:
342:Human Disease Ontology
278:OBO Foundry Ontologies
2008:"Scope (principle 5)"
423:
228:Web Ontology Language
1735:"Open (principle 1)"
1383:Nature Biotechnology
689:Nature Biotechnology
596:scientific consensus
241:Java Virtual Machine
111:reference ontologies
1620:10.1093/nar/gky1032
1513:10.7554/eLife.52614
1124:2007LNCS.4825..169G
262:The OBO file format
32:
2256:BMC Bioinformatics
915:BMC Bioinformatics
734:Haendel, Melissa A
569:Naming conventions
561:Locus of authority
536:Plurality of users
487:Aristotelian logic
459:versioning systems
426:
348:from the resource
2406:Morphster Project
1614:(D1): D955–D962.
1389:(11): 1251–1255.
1334:10.1101/gr.985203
1143:978-3-540-76297-3
801:Nature Precedings
618:Sequence Ontology
545:projects, use in
503:logical inference
311:Sequence Ontology
87:
86:
68:Michael Ashburner
16:(Redirected from
2450:
2433:Health standards
2347:NCBO's BioPortal
2324:
2323:
2321:
2320:
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2300:
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2289:
2271:
2247:
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2240:
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2022:
2021:
2019:
2018:
2004:
1998:
1997:
1995:
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1980:
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1963:
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1664:www.wikidata.org
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1414:
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1328:(6): 1222–1230.
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1247:
1237:
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1116:The Semantic Web
1111:
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1094:
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1052:
1043:
1042:
1032:
1022:
998:
992:
991:
981:
972:(16): 2198–200.
957:
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829:
823:
822:
812:
792:
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729:
723:
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712:
680:
319:Protein Ontology
303:Disease Ontology
83:
80:
33:
21:
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576:underscores
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130:mouse model
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