1 The OBO Foundry

2 A prospective standard designed to guarantee interoperability of ontologies from the very start (contrast to: post hoc mapping) established March initial candidate OBO ontologies – focused primarily on 1. basic science domains of natural objects 2. investigation domains (of equipment and other artifacts)

3 OntologyScopeURLCustodians Cell Ontology (CL) cell types from prokaryotes to mammals obo.sourceforge.net/cgi- bin/detail.cgi?cell Jonathan Bard, Michael Ashburner, Oliver Hofman Chemical Entities of Bio- logical Interest (ChEBI) molecular entitiesebi.ac.uk/chebi Paula Dematos, Rafael Alcantara Common Anatomy Refer- ence Ontology (CARO) anatomical structures in human and model organisms (under development) Melissa Haendel, Terry Hayamizu, Cornelius Rosse, David Sutherland, Foundational Model of Anatomy (FMA) structure of the human body fma.biostr.washington. edu JLV Mejino Jr., Cornelius Rosse Functional Genomics Investigation Ontology (FuGO) design, protocol, data instrumentation, and analysis fugo.sf.netFuGO Working Group Gene Ontology (GO) cellular components, molecular functions, biological processes Ontology Consortium Phenotypic Quality Ontology (PaTO) qualities of anatomical structures obo.sourceforge.net/cgi -bin/ detail.cgi? attribute_and_value Michael Ashburner, Suzanna Lewis, Georgios Gkoutos Protein Ontology (PrO) protein types and modifications (under development)Protein Ontology Consortium Relation Ontology (RO) relationsobo.sf.net/relationshipBarry Smith, Chris Mungall RNA Ontology (RnaO) three-dimensional RNA structures (under development)RNA Ontology Consortium Sequence Ontology (SO) properties and features of nucleic sequences song.sf.netKaren Eilbeck

4 RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy?) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Organism-Level Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Cellular Process (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Annotations plus ontologies yield an ever-growing computer-interpretable map of biological reality.

5 RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy?) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Building out from the original GO

6 Natural  Disease Ontology (DO)  Drug Ontology (DrO)  Environment Ontology (EnvO)  Systems Biology Ontology (SBO)  Upper Biomedical Ontology (OBO UBO) Artifactual  Clinical Trial Ontology (CTO)  Biomedical Imaging Ontology (BIO)  (Upper-Level) Investigation Ontology (IO)  Unit Ontology (UO) Under consideration:

7 RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism NCBI Taxonomy? Anatomica l Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Compone nt (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Pathological Investigation

8 Ontology Functional Genomic Investigation Ontology Clinical Trial Ontology Imaging Ontology Unit Ontology

9 CRITERIA  The ontology is OPEN and available to be used by all.  The ontology is in, or can be instantiated in, a COMMON FORMAL LANGUAGE.  The developers of the ontology agree in advance to COLLABORATE with developers of other OBO Foundry ontology where domains overlap. CRITERIA The OBO Foundry

10 CRITERIA  UPDATE: The developers of each ontology commit to its maintenance in light of scientific advance, and to soliciting community feedback for its improvement.  ORTHOGONALITY: They commit to working with other Foundry members to ensure that, for any particular domain, there is community convergence on a single controlled vocabulary. The OBO Foundry

11 for science if we annotate a database or body of literature or images with one high-quality biomedical ontology, we should be able to add annotations from a second such ontology without conflicts orthogonality of ontologies implies additivity of annotations The OBO Foundry

12 CRITERIA  IDENTIFIERS: The ontology possesses a unique identifier space within OBO.  VERSIONING: The ontology provider has procedures for identifying distinct successive versions to ensure BACKWARDS COMPATIBITY with annotation resources already in common use  The ontology includes TEXTUAL DEFINITIONS and where possible equivalent formal definitions of its terms. CRITERIA

13  CLEARLY BOUNDED: The ontology has a clearly specified and clearly delineated content.  DOCUMENTATION: The ontology is well- documented.  USERS: The ontology has a plurality of independent users. CRITERIA The OBO Foundry

14  COMMON ARCHITECTURE: The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.* * Smith et al., Genome Biology 2005, 6:R46 CRITERIA The OBO Foundry

15 Foundational is_a part_of Spatial located_in contained_in adjacent_to Temporal transformation_of derives_from preceded_by Participation has_participant has_agent OBO Relation Ontology The OBO Foundry

16 Further criteria will be added over time in light of lessons learned in order to bring about a gradual improvement in the quality of Foundry ontologies ALL FOUNDRY ONTOLOGIES WILL BE SUBJECT TO CONSTANT UPDATE IN LIGHT OF SCIENTIFIC ADVANCE IT WILL GET HARDER The OBO Foundry

17 But not everyone needs to join The Foundry is not seeking to serve as a check on flexibility or creativity ALL FOUNDRY ONTOLOGIES WILL ENCOURAGE COMMUNITY CRITICISM, CORRECTION AND EXTENSION WITH NEW TERMS IT WILL GET HARDER The OBO Foundry

18 Single inheritance All terms in ontology are singular nouns Term-by-term versioning Uniform naming conventions Independence of ontology from computational idiom PROPOSED NEW CRITERIA The OBO Foundry

19  to introduce some of the features of SCIENTIFIC PEER REVIEW into biomedical ontology development  CREDIT for high quality ontology development work  KUDOS for early adopters of high quality ontologies / terminologies e.g. in reporting clinical trial results GOALS The OBO Foundry

20  to providing a FRAMEWORK OF RULES to counteract the current policy of ad hoc creation of new annotation schemas by each clinical research group by  REUSABILITY: if data-schemas are formulated using a single well-integrated framework ontology system in widespread use, then this data will be to this degree itself become more widely accessible and usable GOALS The OBO Foundry

21  to serve as BENCHMARK FOR IMPROVEMENTS in discipline-focused terminology resources  once a system of interoperable reference ontologies is there, it will make sense to calibrate existing terminologies in its terms in order to achieve more robust alignment and greater domain coverage  exploit the avenue of EVIDENCE-BASED MEDICINE (NIH CLINICAL RESEARCH NETWORKS) to foster their use by clinicians GOALS The OBO Foundry

22 June 2006: establishment of MICheck: reflects growing need for prescriptive checklists specifying the key information to include when reporting experimental results (concerning methods, data, analyses and results). MICheck The OBO Foundry

23  MICheck: ‘a common resource for minimum information checklists’ analogous to OBO / NCBO BioPortal  MICheck Foundry: will create ‘a suite of self- consistent, clearly bounded, orthogonal, integrable checklist modules’ * * Taylor CF, et al. Nature Biotech, in press MICheck Foundry The OBO Foundry

24 From OBO to OBD: Open Biomedical Data OBD is part of NCBO BioPortal: houses data annotated using ontologies –open to all –with a flexible ontology-based schema

25 OBD Foundry The OBD Foundry –data annotated using OBO Foundry ontologies –emphasis on coordination especially with NCBO Driving Biological Projects linking genes to disease via model organism mutant phenotypes high-quality clinical trial data additivity of annotations implies additivity of data