Core

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OBI Core is a collection of key terms from OBI and related ontologies. It serves two related purposes:

  1. For OBI users the core provides a starting point for understanding the most important high-level terms and their relations.
  2. For ontology developers the core provides the fundamental organization of OBI, and a structure into which more specific terms can be fitted.

OBI Core consists of two parts:

  1. The "inner core" of 29 terms that belong to OBI and IAO.
  2. The "outer core" of 17 terms that belong to other ontologies.

When these 46 terms are taken together and reasoned over using OWL, the result is a set of approximately 100 terms. We call this the "complete core".

You can download the latest OBI Core OWL file from http://purl.obolibrary.org/obo/obi/obi_core.owl.

(See also: status of the term review process and a list of OBI core terms in 2008.)

The Inner Core

The inner core contains terms from OBI and IAO -- the Information Artifact Ontology. Historically, IAO was created as a branch of OBI, and the two remain closely connected. Any detailed model of a biomedical investigation using OBI will involve the majority of the terms on this list. (See below for more on the criteria for inclusion.)

  1. analyte assay
  2. assay
  3. centrally registered identifier (CRID) registry
  4. centrally registered identifier (CRID) symbol
  5. conclusion based on data
  6. data item
  7. data transformation
  8. device
  9. documenting
  10. human subject enrollment
  11. information acquisition
  12. information content entity
  13. investigation
  14. investigation agent role
  15. material acquisition
  16. material information bearer
  17. measure function
  18. measurement datum
  19. planning
  20. protocol
  21. specimen
  22. specimen collection
  23. study design
  24. study design controlled variable
  25. study design dependent variable
  26. study design execution
  27. study design independent variable
  28. study subject role
  29. testable hypothesis

The Outer Core

The outer core consists of terms that fall outside OBI and IAO scope, but are nevertheless important and common when modelling biomedical investigations with OBI. These terms serve the educational purpose of the core by showing how OBI connects to other widely-used ontologies.

  1. biological_process from the Gene Ontology (GO)
  2. cellular_component from the Gene Ontology (GO)
  3. molecular_function from the Gene Ontology (GO)
  4. cell from the Cell Ontology (CL)
  5. environmental material from the Environment Ontology (EnVO)
  6. geographical location from Gazetteer (GAZ)
  7. gross anatomical part from the Common Anatomy Reference Ontology (CARO)
  8. Homo sapiens from the National Center for Biotechnology Information Taxonomy (NCBITaxon)
  9. measurement unit label, included to connect to the Ontology of Units of Measurement (UO)
  10. molecular entity from Chemical Entities of Biological Interest (ChEBI)
  11. organism, included to connect to the National Center for Biotechnology Information Taxonomy (NCBITaxon)
  12. organization, which we expect to connect to work by eagle-i and VIVO
  13. population, which we expect to connect to the Population and Community Ontology (PCO)
  14. quality from the Basic Formal Ontology (BFO), included to connect to the Phenotypic Quality Ontology (PATO)
  15. disease course from the Ontology for General Medical Science (OGMS)
  16. reagent from the Reagent Ontology (ReO)
  17. cell line cell from the Cell Line Ontology (CLO)

The Complete Core

The complete core is automatically generated by taking the union of the inner core and outer core, and then forming a logically closed ontology using an OWL reasoner. The result includes many upper-level terms from the Basic Formal Ontology (BFO).

The complete core contains approximately 100 terms at present. Understanding these 100 terms will provide an excellent overview of OBI.

OBI will provide an OWL file containing the complete core for use in Protegé and other ontology tools.

Criteria for Inclusion in OBI Core

OBI Core serves educational and organizational goals. We have selected the core terms because they are:

  1. important for modelling a large majority of biomedical investigations with OBI
  2. are ready for widespread use

While meeting these two criteria, we also aim to keep the complete core fairly small.

Terms may be added to or removed from OBI Core from time to time on the basis of these criteria. Proposals for changes to OBI Core can be made to the OBI Developers mailing list.

Inner Core versus Complete Core

The complete core is generated automatically from the inner and outer cores. We could make the inner core smaller by removing certain mid-level terms that would automatically be included in the complete core anyway. For instance, we could leave a child (e.g. "document") in the inner core while removing its parent (e.g. "information content entity") from the inner core, since the parent would automatically be included in the complete core.

The criterion of importance applies here. When both the parent and the child are important for modelling biomedical investigations with OBI, both have been included in the inner core. In order to model a large majority of biomedical investigations with OBI both "document" and "information content entity" will be involved, and so both are included in the inner core. This serves both the educational and organizational goals of the core.

Inner Core versus Outer Core

Every term in the inner core falls within OBI or IAO scope. All of them belong to the OBI or IAO namespaces. The terms in the outer core fall outside of OBI/IAO scope, and therefore most of them belong to different ontologies with different namespaces.

However there are some terms in the outer core that belong to the OBI or IAO namespaces. This has been done when the term was included in OBI or IAO in order to make a connection to another ontology. For instance, "measurement unit label" is an IAO term, but all of its children belong to the Ontology of Units of Measurement (UO).

The term "organism" is an edge case. It is outside of OBI scope and was designed primarily to connect to NCBITaxon (see the editor notes for the term), however some of its children are OBI terms.

Representation of Biomedical Investigation Using OBI Core

Representation of biomedical investigation using 28 inner core and some of outer core terms


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