Ontology for Biomedical Investigations
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OBI Ontology
The Ontology for Biomedical Investigations is designed as a resource for the annotation of biomedical investigations and will provide terms that can be used to annotate the investigation, protocols and instrumentation, material used in the investigation, and the data generated and types of analysis performed on the data. A full description of the purpose of the ontology can be viewed in the Mission Statement. The ontology is being developed as an OBO Foundry ontology and also follows other ontology design best practices. The Design Principles followed are described below.

Ontology Draft
The latest complete version of ontology (.owl) file will always be available from http://purl.obofoundry.org/obo/obi.owl. However, development continues in the OBI Subversion repository.
NOTE: This is a DRAFT VERSION and is subject to many more edits before being able to be used in a production system or as as stable release suitable for extension for other domains without needing further updates.

Ontology Development Status
The main area of focus at the Third OBI workshop (Feb, 2007) was to review the OBI classes extending directly from BFO, resulting in a set of OBI 'core' classes. In addition, a policy for further parallel, development from these 'core' classes was drafted and approved by the OBI Coordinators. The policy, ObiBranches, lists the various branch groups and the responsibilities of those working to curate terms and develop, these branches. During this process, additional terms were identified to propose for inclusion in BFO, such as generically_dependent_continuant (currently represented as a sibling to the BFO continuant subclasses).
A first set of information to capture using annotation properties, as listed on the metadata page was also agreed upon.

A new version of the ontology was generated following the second workshop (July, 2006). The focus of this workshop was to refine the scope of OBI/FuGO in light of other OBO Foundry ontologies, review the current structure of OBI/FuGO and add definitions for terms. It was at this workshop that the name Ontology for Biomedical Investigations (OBI) was proposed in order to better reflect the scope of the project. The presentations and workshop report are available for download from the OBI File Release System in the Package titled Workshops.

Following the first workshop (Feb, 2006), a draft of the ontology was constructed. The focus of the workshop was to identify the top level classes of OBI (then named FuGO) and test the structure with domain specific terms (Proteomics). The presentations and workshop report can be found in the OBI File Release System in the Package titled Workshops. The first version of the ontology contains these top level classes as well as some terms that are specific to Proteomics technology.

To follow or join in the development of OBI, subscribe to the mailing list at: OBI Developers. To propose new terms, go to the OBI Term tracker.

Ontology Design Principles
The OBI developers will generate a document based on the proposed Ontology Best Practice information containing the design principles, naming conventions and ontology metadata that will be used for the development of OBI. An agreed upon minimal list of annotation metadata for representational units has been created.

Development Process

General Outline
The development of OBI has consisted of the presentation of Use Cases from the Community Representatives, the generation of Term Lists from the communities, the development of the top-level of OBI and the addition of the the terms in the community Term Lists into the ontology. Generally speaking, the work within the individual communities is proceeding in a bottom-up fashion while the work within the larger OBI Developers Working Group is proceeding in a top-down fashion. The within-community, bottom-up approach consists of Use Case submission and Term List generation. The top-down approach consists of extending a known upper level ontology to the level where communities can then add terms from the Term Lists. More details on each of these processes can be found below.

Use Cases
In order to gain a better understanding of the Communities involved in the project, Community Representatives are encouraged to submit Use Cases. The Use Case will be presented by the Community Representative during a scheduled Developers Group conference call.
Download Selected Use Cases
  1. Epitopes
  2. Flow Cytometry
  3. Reporting Structure for Biological Investigation (RSBI):   Toxicogenomics  |  Nutrigenomics
  4. PharmGKB - SNP Use Case
  5. Proteomics

Community Term Lists for OBI
Each Community has generated a Term List to indicate a sampling of the terms needed by their community. Proposed terms lists are available for download in the downloads section: TermLists

Top-level Structure of OBI
The top-level structure is an extension of the Basic Formal Ontology (BFO).

To report errors with the site, write to obi-web-support at lists.sourceforge.net

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