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OBO Foundry


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OBO Foundry presentation delivered at Clinical Trial Ontology Meeting, Bethesda, 2007

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OBO Foundry

  1. 1. The OBO Foundry Chris Mungall Lawrence Berkeley Laboratory NCBO GO Consortium May 2007
  2. 2. The Open Biomedical Ontologies (OBO) Foundry <ul><li>A collection of orthogonal reference ontologies in the biological/biomedical domain </li></ul><ul><li>Each is committed to an agreed upon set of principles governing best practices in ontology development </li></ul>
  3. 3. Outline <ul><li>Motivation </li></ul><ul><li>History/Background </li></ul><ul><li>Organisation and dependencies </li></ul><ul><li>Foundry Principles </li></ul><ul><li>Results </li></ul>
  4. 4. (NCBO)
  5. 5. Why is the OBO Foundry necessary? <ul><li>For the sharing, integration and analysis of biological and biomedical data </li></ul><ul><ul><li>Common standards are required </li></ul></ul><ul><ul><li>Ontologies must be interoperable and logically well-formed </li></ul></ul><ul><ul><li>Ontologies should be developed collaboratively </li></ul></ul>
  6. 6. Origins of OBO: The Gene Ontology (GO) <ul><li>3 ontologies intended primarily for the annotation of genes and gene products across a spectrum of organisms </li></ul><ul><ul><li>Molecular function </li></ul></ul><ul><ul><li>Biological process </li></ul></ul><ul><ul><li>Cellular component </li></ul></ul><ul><li>These ontologies are organised as a collection of related terms, constituting nodes in a graph </li></ul>
  7. 7. Annotation and GO <ul><li>187,000 genes and gene products have high quality annotations to GO terms </li></ul><ul><ul><li>2.6m including automated predictions </li></ul></ul><ul><ul><li>63,000 publications curated </li></ul></ul><ul><li>Variety of analysis tools </li></ul><ul><ul><li> </li></ul></ul><ul><li>Annotation of primary and literature data is one use of OBO Foundry ontologies </li></ul>
  8. 8. GO and the need for OBO <ul><li>GO terms implicitly reference kinds of entities outwith the scope of GO </li></ul><ul><ul><li>Cysteine biosynthesis </li></ul></ul><ul><ul><li>Neural crest cell migration </li></ul></ul><ul><ul><li>Cardiac muscle morphogenesis </li></ul></ul><ul><ul><li>Regulation of vascular permeability </li></ul></ul><ul><li>OBO was born from the need to create cross products wth GO </li></ul><ul><ul><li>Also coincided with growth in model organism anatomy ontologies </li></ul></ul>ChEBI Cell Anatomy quality
  9. 9. Organisation of the OBO Foundry <ul><li>Ontologies should be orthogonal </li></ul><ul><ul><li>Minimise overlap </li></ul></ul><ul><ul><li>Each distinct entity type (universal) should only be represented once </li></ul></ul><ul><li>We can partition the OBO Foundry rationally to help organise and coordinate the ontologies </li></ul>
  10. 10. Partitions <ul><li>Type of entity </li></ul><ul><ul><li>Relationship to time </li></ul></ul><ul><ul><ul><li>Continuant </li></ul></ul></ul><ul><ul><ul><li>Occurrent </li></ul></ul></ul><ul><ul><li>Dependent or independent </li></ul></ul><ul><li>Granularity </li></ul><ul><ul><li>Molecular </li></ul></ul><ul><ul><li>Cellular </li></ul></ul><ul><ul><li>Organismal </li></ul></ul><ul><ul><li>Multi-organismal </li></ul></ul><ul><li>Generality </li></ul><ul><ul><li>Upper domain ontology </li></ul></ul><ul><ul><li>Core biology </li></ul></ul><ul><ul><li>Species specific </li></ul></ul><ul><li>Occurrence </li></ul><ul><ul><li>Canonical </li></ul></ul><ul><ul><li>Variant </li></ul></ul><ul><ul><li>Pathological </li></ul></ul><ul><ul><li>Experimental </li></ul></ul>
  11. 12. Connecting the Foundry: The OBO Relation Ontology <ul><li>Standardized set of formally defined relations between types and/or instances </li></ul><ul><ul><li>is_a </li></ul></ul><ul><ul><li>part_of </li></ul></ul><ul><ul><li>has_participant </li></ul></ul><ul><ul><li>… </li></ul></ul><ul><li>For use within and across OBO ontologies </li></ul><ul><ul><ul><li> </li></ul></ul></ul><ul><ul><li>Molecules and cells participate in cellular processes </li></ul></ul><ul><ul><li>Cellular components are parts of cells which are parts of larger anatomical entities </li></ul></ul><ul><ul><li>Phenotypic qualities inhere in anatomical entities </li></ul></ul>
  12. 13. OBO Foundry Principles <ul><li>Open </li></ul><ul><li>Well-defined exchange format </li></ul><ul><ul><ul><li>E.g. OBO or OWL </li></ul></ul></ul><ul><li>Unique ID-Space </li></ul><ul><li>Ontology Life-cycle / versioning </li></ul><ul><li>Clearly specified and delineated content </li></ul><ul><li>Definitions </li></ul><ul><li>Use relations according to the standards of the OBO Relation Ontology </li></ul><ul><li>Well documented </li></ul><ul><li>Plurality of users </li></ul><ul><li>Collaborative development </li></ul>
  13. 14. Results <ul><li>Phenotype Annotation </li></ul><ul><li>Ontology for Biomedical Investigations (OBI) </li></ul><ul><li>GO cross-products </li></ul><ul><li>Anatomy Ontologies </li></ul><ul><li>Semantic Web Health Care and Life Sciences (HCLS) interest group </li></ul>
  14. 15. Genotype-Phenotype Annotation <ul><li>NCBO Driving Biological Project </li></ul><ul><ul><li>Deep genotype-phenotype association curation of disease genes and genotypes </li></ul></ul><ul><ul><ul><li>Human, Fruitfly, Zebrafish </li></ul></ul></ul><ul><li>Methodology: Flexible post-coordination of phenotype descriptions using Foundry ontologies </li></ul><ul><ul><li>Based on ‘PATO’ ontology of qualities </li></ul></ul><ul><ul><li>E.g. </li></ul></ul><ul><ul><ul><li>Shortened length of dendrite of columnar neuron </li></ul></ul></ul>
  15. 16. OBI: Ontology for Biomedical Investigations <ul><li>An integrated ontology for experiments and investigations </li></ul><ul><li>Reuses terms from OBO Foundry ontologies in a modular way </li></ul><ul><li>Classes representing experimental artefacts, roles, hypotheses, variables etc </li></ul><ul><li>Adherence to upper ontology (BFO) </li></ul>
  16. 17. Results: GO cross-products <ul><li>Ongoing work: </li></ul><ul><ul><li>Processes and functions with chemical entities as participants </li></ul></ul><ul><ul><ul><li>E.g. cysteine biosynthesis </li></ul></ul></ul><ul><ul><li>Processes defined in terms of types of cell </li></ul></ul><ul><ul><ul><li>E.g. neural crest cell migration </li></ul></ul></ul><ul><li>Mutual feedback </li></ul>
  17. 18. Anatomy Ontologies <ul><li>Common Anatomy Reference Ontology </li></ul><ul><ul><li>Ontologies of gross anatomy have been developed using divergent methodologies </li></ul></ul><ul><ul><li>CARO was developed after an NCBO sponsored meeting on anatomy ontologies </li></ul></ul><ul><ul><ul><li>Ontology based on structure of the FMA </li></ul></ul></ul><ul><ul><li>Common framework and upper-level terms for taxon-specific anatomical ontologies </li></ul></ul><ul><li>Cell ontology </li></ul><ul><ul><li>Merge of EVOC and initial OBO Cell ontology </li></ul></ul>
  18. 19. Finding out more and participating <ul><li> </li></ul><ul><li> </li></ul><ul><li>[email_address] </li></ul>
  19. 20. Acknowledgements NCBO/Berkeley Nicole Washington Mark Gibson John Day-Richter Suzanna Lewis NCBO/Stanford Nigam Shah Daniel Rubin Archana Verbakam Lynn Murphy Michael J Montague Mark Musen Ontologies Amelia Ireland Jane Lomax Jen Clark Midori Harris David Hill Karen Eilbeck Seth Carbon Judith Blake & GO NCBO/Buffalo Fabian Neuhaus Werner Ceusters Louis Goldberg Barry Smith NCBO/Eugene Melissa Haendel Monte Westerfield NCBO/Cambridge Michael Ashburner George Gkoutos NCBO/Victoria Chris Callender Margaret-Anne Storey NCBO/Mayo James Buntrock Chris Chute NIH Peter Good Carol Bean David Sutherland Oliver Hofmann Sue Rhee Johnathan Bard Lindsay Cowell Erik Segerdell Alan Rector Cynthia Smith Jannan Eppig Rex Chisholm Pascale Gaudet Paula de Matos Rafael Alcantra Kirill Degtyarenko Pankaj Jaiswal Onard Mejino Cornelius Rosse William Bug Alan Ruttenberg Trish Whetzel Jennifer Fostel & OBI Consortium NCBO/UCSF Simona Carini Ida Sim Nation Heart, Lung and Blood Institute
  20. 21. <ul><li>Karen Eilbeck </li></ul><ul><li> </li></ul><ul><li>properties and features of </li></ul><ul><li>nucleic sequences </li></ul><ul><li>Sequence Ontology </li></ul><ul><li>(SO) </li></ul><ul><li>RNA Ontology Consortium </li></ul><ul><li>(under development) </li></ul><ul><li>three-dimensional RNA </li></ul><ul><li>structures </li></ul><ul><li>RNA Ontology </li></ul><ul><li>(RnaO) </li></ul><ul><li>Barry Smith, Chris Mungall </li></ul><ul><li> </li></ul><ul><li>relations </li></ul><ul><li>Relation Ontology (RO) </li></ul><ul><li>Protein Ontology Consortium </li></ul><ul><li>(under development) </li></ul><ul><li>protein types and </li></ul><ul><li>modifications </li></ul><ul><li>Protein Ontology </li></ul><ul><li>(PrO) </li></ul><ul><li>Michael Ashburner, Suzanna </li></ul><ul><li>Lewis, Georgios Gkoutos </li></ul><ul><li> </li></ul><ul><li>-bin/ detail.cgi? </li></ul><ul><li>attribute_and_value </li></ul><ul><li>qualities of biomedical entities </li></ul><ul><li>Phenotypic Quality </li></ul><ul><li>Ontology </li></ul><ul><li>(PaTO) </li></ul><ul><li>Gene Ontology Consortium </li></ul><ul><li> </li></ul><ul><li>cellular components, </li></ul><ul><li>molecular functions, </li></ul><ul><li>biological processes </li></ul><ul><li>Gene Ontology </li></ul><ul><li>(GO) </li></ul><ul><li>FuGO Working Group </li></ul><ul><li> </li></ul><ul><li>design, protocol, data </li></ul><ul><li>instrumentation, and analysis </li></ul><ul><li>Functional Genomics </li></ul><ul><li>Investigation Ontology </li></ul><ul><li>(FuGO) </li></ul><ul><li>JLV Mejino Jr., </li></ul><ul><li>Cornelius Rosse </li></ul><ul><li>fma.biostr.washington. </li></ul><ul><li>edu </li></ul><ul><li>structure of the human body </li></ul><ul><li>Foundational Model of Anatomy (FMA) </li></ul><ul><li>Melissa Haendel, Terry </li></ul><ul><li>Hayamizu, Cornelius Rosse, </li></ul><ul><li>David Sutherland, </li></ul><ul><li>(under development) </li></ul><ul><li>anatomical structures in </li></ul><ul><li>human and model organisms </li></ul><ul><li>Common Anatomy Refer- </li></ul><ul><li>ence Ontology (CARO) </li></ul><ul><li>Paula Dematos, </li></ul><ul><li>Rafael Alcantara </li></ul><ul><li> </li></ul><ul><li>molecular entities </li></ul><ul><li>Chemical Entities (ChEBI) </li></ul><ul><li>Jonathan Bard, Michael </li></ul><ul><li>Ashburner, Oliver Hofman </li></ul><ul><li> </li></ul><ul><li>bin/detail.cgi?cell </li></ul><ul><li>cell types from prokaryotes </li></ul><ul><li>to mammals </li></ul><ul><li>Cell Ontology </li></ul><ul><li>(CL) </li></ul><ul><li>Custodians </li></ul><ul><li>URL </li></ul><ul><li>Scope </li></ul><ul><li>Ontology </li></ul>