This is an archive of an inactive wiki and cannot be modified.

Ontology of Biomedical Investigation--OBI

Contact e-mail: William.Bug #


General purpose and services to the end user

BIRNLex is an integrated ontology+lexicon used for various purposes - some end-user/interactive, others back-end/infrastructure - within the the BIRN Project to support semantically-formal data annotation, semantic data integration, and semantically-driven, federated query resolution.

Functionality examples

Here a few examples of BIRNLex class definitions that illustrate the need for lexical support and links to external knowledge sources. Our general design goals have been to use both the Dublin Core MD elements and SKOS where ever possible. Preferably we'd like to use SKOS for all lexical qualities. There are certain annotation properties that should be shared across all biomedical knowledge resources. There are other required elements specific to our needs in BIRN.

Class:                                Anterior_ascending_limb_of_lateral_sulcus
birn_annot:birnlexCurator             Bill Bug
birn_annot:birnlexExternalSource      NeuroNames
birn_annot:bonfireID                  C0262186
birn_annot:curationStatus             raw import
birn_annot:neuronamesID               49
birn_annot:UmlsCui                    C0262186
obo_annot:createdDate                 "2006-10-08"^^
obo_annot:modifiedDate                "2006-10-08"^^
skos:prefLabel                        Anterior_ascending_limb_of_lateral_sulcus
skos:scopeNote                        human-only

Class:                                Medium_spiny_neuron
birn_annot:birnlexCurator             Maryann Martone
birn_annot:birnlexDefinition          The main projection neuron found in caudate nucleus, putamen 
                                      and nucleus accumbens...
birn_annot:bonfireID                  BF_C000100
birn_annot:curationStatus             pending final vetting
dc:source                             Maryann Martone
obo_annot:createdDate                 "2006-07-15"^^
obo_annot:modifiedDate                "2006-09-28"^^
skos:prefLabel                        Medium_spiny_neuron

Application architecture

The following is a subset of tools either extant or in the offing:

In all of these applications, it is critical to have a clear, distinct, and shared representation for the associated lexicon. For instance, when integrated BIRN segmented brain images with those from other projects across the net, use of lexical variants from a variety of public terminilogies and thesauri such as SNOMED and MeSH can provide a powerful means to largely automate semantic integration of like entities - e.g., corresponding brain region, equivalent behavioral assays described using different preferred labels/names. In provided a community shared formalism for representing the associated lexicon, SKOS can greatly simplify this task. If, for instance, the lexical repository (collection of LUIs) contained in UMLS were represented according to SKOS, this would provide an extremely valuable resource to the community of semantically-oriented bioinformatics researchers, as well as a powerful tool to support LSI/NLP when linking to unstructured text.

Additional references



Titles of Vocabularies

The following are the collection of terminologies and ontologies we are linking into BIRNLex: Neuronames, classification schemes, RadLex, Gene Ontology, Reactome, OBI, PATO, Subcellular Anatomy Ontology (CCDB -, MeSH

General characteristics of the vocabularies

Neuronames: brain anatomy (~750 classes and 1000s of associated lexical variants) classification: hierarchies to describe neuroanatomy, subject variables, stimulus conditions, and experimental paradigms associated with functional MRI of the nervous system Subcellular Anatomy Ontology: designed to describe the subcellular entities associated with ultrastructural and histological imaging of neural tissue.

Language(s) in which the vocabulary is provided

We currently are only dealing with English.

Machine-readable representation of the vocabulary

Class:                                 Fear
birn_annot:birnlexCurator              Jessica Turner
birn_annot:birnlexExternalSource       UMLS
birn_annot:bonfireID                   C0015726
birn_annot:curationStatus              uncurated
birn_annot:UmlsCui                     C0015726
obo_annot:createdDate                  "2006-06-01"^^
obo_annot:externallySourcedDefinition  Unpleasant but normal emotional response to genuine external danger or threats; 
                                       compare with ANXIETY and CLINICAL ANXIETY. (CSP)
obo_annot:externallySourcedDefinition  The affective response to an actual current external danger which subsides with 
                                       the elimination of the threatening condition. (MeSH)
obo_annot:modifiedDate                 "2006-10-11"^^
skos:prefLabel                         Fear

Class: Forebrain
birn_annot:birnlexCurator              Allan MacKenzie-Graham
birn_annot:birnlexDefinition           The part of the brain developed from the most rostral 
                                       of the three primary vesicles of the embryonic neural tube and 
                                       consisting of the Diencephalon and Telencephalon.
birn_annot:birnlexExternalSource       NeuroNames
birn_annot:bonfireID                   C0085140
birn_annot:curationStatus              pending final vetting
birn_annot:neuronamesID                8
birn_annot:UmlsCui                     C0085140
obo_annot:createdDate                  "2006-07-15"^^
obo_annot:modifiedDate                 "2006-09-28"^^
obo_annot:synonym                      prosencephalon
skos:prefLabel                         Forebrain

Software applications used to create and/or maintain the vocabulary, features lacking for the case


Standards and guidelines considered during the design and construction of the vocabulary

We have been working close with the NCBO to adopt the OBO Foundry recommendations in the construction of our ontology. Use of SKOS elements has been a big help to us here, so that, for instance, we can create software applications specifically designed to draw on "skos:prefLabel", "obo_annot:synonym", "obo_annot:definition", etc.

Management of changes

Currently we are doing this manually in Protege-OWL, but, as mentioned above, we are moving toward a client-server infrastructure that will created an RDF-based backend store and support both curation of the ontology and annotation using the ontology via Java Portlet-based applications. BIRN has a core infrastructure staff dedicated to use of the GridSphere Java Portlet implementation framework (

Additional references