Why we need the OBO Core Michael Ashburner, Suzanna Lewis and Barry Smith

DO Accident to powered aircraft, other and unspecified, injuring occupant of military aircraft, any rank Other accidental submersion or drowning in water transport accident injuring occupant of other watercraft – crew

DO Fall on stairs or ladders in water transport injuring occupant of small boat, unpowered Railway accident involving collision with rolling stock and injuring pedal cyclist Non-traffic accident involving motor-driven snow vehicle injuring pedestrian

DO Fitting and adjustment of wheelchair

Disease Ontology Fitting and adjustment of wheelchair is_a disease

Goal of the OBO Core project To introduce some of the features of scientific peer review into biomedical ontology development

Some OBO ontologies are of high quality Some not How to avoid poisoning of the wells?

Further arguments Some OBO ontologies are already designated as OBO Core ontologies; The community wanted it – so we need to publish the criteria Several groups within the Center want to do this Several new groups without the Center want us to do this (preNCIT, FuGO,...) It is entirely voluntary

NCI Thesaurus net.com/index.php/search/show/ =“Review of NCI Thesaurus and Development of Plan to Achieve OBO Compliance”

Further arguments The idea is part of what we agreed to do in the BISTI proposal: “We will take steps to forge a common set of principles (best practices) and a common methodology for those active in ontology building in the life sciences” Core 6 needs an explicit statement of methodology and criteria in order to do its work

Further arguments It is an exciting and original alternative to the wiki/democracy/schemaweb based approaches à la CBioC It will provide a small reward for those doing good work in science-based ontology It will provide a step towards the day when interoperability through controlled vocabularies can be enforced through agreements with biological research groups, clinical guidelines bodies, and scientific journals

Further arguments No objections have been made to the actual criteria proposed, except... Orthogonality: ontology groups who choose to be part of the OBO Core thereby commit themselves to collaborating to resolve disagreements which arise where their respective domains overlap (They commit themselves to conceiving ontology as a science, not as a hobby)

How to achieve orthogonality 1.Good ontologies (FMA) can incorporate alternative views or partitions of the same domain (regional partition, structural partition...) 2.Some ontologies (NCIT) will be Application Ontologies, which commit to maintaining compatibility with Reference Ontologies covering overlapping domains

Some OBO ontologies are of high quality Some are not Compare a scientific journal which publishes both high-quality peer-reviewed articles, and some other stuff,... but does not distinguish between them

OBO CORE EVALUATION CRITERIA internal/images/2/21/OBO-criteria-v7.doc

The ontologies are developed in collaboration with other OBO core ontologies. When disagreements arise the rationale for these disagreements should be documented, and efforts will be undertaken, for example, within the framework of the Center’s Dissemination Workshops, in order to resolve these disagreements. The ontology is open and available to be used by all The ontology is in, or can be instantiated in, a common shared syntax. See: The ontology possesses a unique identifier space. The ontology provider has procedures for identifying distinct successive versions. The ontology is well-documented. The ontology has a plurality of independent users. The ontology has clearly specified and clearly delineated content. The ontology includes textual definitions for all terms. The ontology uses relations which are unambiguously defined following the pattern of definitions laid down in the OBO Relation Ontology.OBO Relation Ontology

OBO Relation Ontology Foundationalis_a part_of Spatiallocated_in contained_in adjacent_to Temporaltransformation_of derives_from preceded_by Participationhas_participant has_agent

How to use the OBO Relation Ontology Tell curators to keep in mind that when they make e.g. an A is_a B assertion in an ontology, they need to remember that this is a statement about As to the effect that each A is a B.

OBO CORE EVALUATION CRITERIA Further criteria will be added over time in order to bring about a gradual improvement in the quality of ontologies included in the OBO core.

Reference Ontology vs. Application Ontology A reference ontology is analogous to a scientific theory; it seeks to optimize descriptive or representational adequacy to its subject matter to the maximal degree that is compatible with the constraints of computational usefulness. An application ontology is comparable to an engineering artifact such as a software tool. It is constructed for specific practical purposes.

Reference Ontology vs. Application Ontology Application ontologies often built afresh for each new task; commonly introducing not only idiosyncrasies of format or logic, but also simplifications or distortions of their subject- matters. To solve this problem OBO Core proposes a methodology according to which application ontology development shoud take place always against the background of a formally robust reference ontology framework