Ontology of Biomedical Investigation -- OBI
Contact e-mail: obi-coord # lists.sourceforge.net
Application
General purpose and services to the end user
The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and medical experiments and investigations. This includes a set of 'universal' terms, that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. This ontology will support the consistent annotation of biomedical investigations, regardless of the particular field of study. The ontology will model the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This project was formerly called the Functional Genomics Investigation Ontology (FuGO) project.
Functionality examples
When constructed, generally to support coding (eg, consistency checks), annotation, relational and generalized querying or associative knowledge browsing of biomedical investigation data. Ensuring minimal requirements for journal submission? Standardisation of terminologies,…etc Some of the functionalities required by applications utilizing OBI will be similar to the ones described here: a) Search for class codes according to query terms or definitions, b) browse for class codes according to a taxonomic hierarchy of classes, c) display to the user result sets of queries, and concept details including all the terms by which a concept is referred as well as definitions and other attributes
Application architecture
Applications that utilize OBI (below) have not yet been constructed.
Additional references
N/A
Vocabularies
Titles of Vocabularies
Ontology for Biomedical Investigations (OBI). The Upper Level ontology that this work extends from is the Basic Formal Ontology (BFO).
General characteristics (size, coverage) of the vocabularies
OBI is built following OBO Foundry best practices and uses BFO as it's Upper Level ontology. The ontology currently has 200 terms, but is early in development and will increase in size. The scope of this ontology is generally described above and there are ~15 communities participating in this development effort. See http://obi.sourceforge.net/community/index.php for a updated listing.
OBI is currently under construction. Its scope is limited to biological investigation terminology, with references/mappings to terminologies covering specific domains, as necessary. Already present in the development version are references to the the BFO top-level ontology. Of interest to us are other vocabularies/terminologies such as SKOS that provide a set of standardized names for specific annotations that we are interested in, to include names for properties that hold terms, definitions, curatorial status, editor notes, scope notes and others. We would be interested in referring to an external resource for these entities rather than creating our own properties. One issue that arises in re-utilizing SKOS is that some relations are already defined (e.g. skos:narrower) and it’s not clear how to avoid clashes where these types of relations might conflict with OWL’s built-in relations.
Structure of the Vocabulary
The ontology is built using OWL. The Upper Level ontology that this work extends from is the Basic Formal Ontology (BFO). Classes and properties as defined in OWL. Terms and definitions are included as annotations of classes and properties. Relationships other than “is_a” will be expressed as object properties, or by another mechanism if the relationship is not definitional (definitional in the OWL Description Logic sense). The relationships used will extend from the Relationship Ontology (RO). The is_a subsumption relation as in OWL (rdfs:subClassOf) is the primary relationship used. Other relations are under discussion and will later be added as owl object properties once the taxonomy is more robust and the ultimate application is more clear...
There are duplications with Protégé metadata tags, the Dublin Core and the existing terms in SKOS. It would be nice to include SKOS as a default import for Protégé. Our ontological effort would need administrative/ontology editing, as well as terminological metadata descriptors.
Here is a list of metadata properties and definitions used in OBI: http://obi.sourceforge.net/ontologyInformation/MinimalMetadata.html This list was compiled from RU_metadata.owl, the BirnLex metadata requirements and the metadata annotations provided by the NCIT (all of which can be found on the OBI-Wiki at https://www.cbil.upenn.edu/fugowiki/index.php/RepresentationalUnitMetadataTable). This minimal subset of metadata properties was agreed upon, and had its definitions finalized by the OBI metadata subgroup. The added cardinalities are still under discussion, as is the implementation and in some cases the domain of the metadata properties.
Language(s) in which the vocabulary is provided
English, with plans to include other languages utilizing the xml:lang attribute.
Machine-readable representation of the vocabulary
http://svn.sourceforge.net/viewvc/obi/ontology/trunk/OBI.owl
Software applications used to create and/or maintain the vocabulary, features lacking for the case
Protege-OWL.
Standards and guidelines considered during the design and construction of the vocabulary
OBO Foundry principles (http://obofoundry.org/) and the Protégé tutorials. One possible area that may be seen as divergence tackles the general practice within the Protégé tutorials. We is the use ofan an alphanumeric identifier for the term versus using the human readable term name. The reason for this was to remove semantics from the unique identifier for the term.render the identifier unique and ease term obsoletion and versioning.
Management of changes
The terminology is stored in OWL-DL. The main storage of the ontology is theThe owl files are stored in Sourceforge SVN repositories. Individual communities may have there own preferred database storage and perhaps should answer individually?
Additional references
The current list of information that we would like to capture as metadata for representational units is listed at: https://www.cbil.upenn.edu/obiwiki/index.php/RuMetadataRefinedRefined