Ontology of Biomedical Investigation--OBI
Contact e-mail: William.Bug # DrexelMed.edu
Application
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"^^http://www.w3.org/2001/XMLSchema#date obo_annot:modifiedDate "2006-10-08"^^http://www.w3.org/2001/XMLSchema#date 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"^^http://www.w3.org/2001/XMLSchema#date
obo_annot:modifiedDate "2006-09-28"^^http://www.w3.org/2001/XMLSchema#date
skos:prefLabel Medium_spiny_neuron
Application architecture
The following is a subset of tools either extant or in the offing:
a) online curation: we are moving to an RDF backend that will enable us to curate the BIRNLex ontology+lexicon via the web
b) annotation: we have applications designed to support domain experts annotating neuroimaging data.
c) query/mediation: the BIRN mediator is design to federate the 60+ resident laboratory data repositories. Site databases register with the mediator by mapping the relevant elements from their resident data model into the mediator's global model.
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
N/A
Vocabularies
Titles of Vocabularies
The following are the collection of terminologies and ontologies we are linking into BIRNLex: Neuronames, Brainmap.org classification schemes, RadLex, Gene Ontology, Reactome, OBI, PATO, Subcellular Anatomy Ontology (CCDB - http://ccdb.ucsd.edu/), MeSH
General characteristics of the vocabularies
Neuronames: brain anatomy (~750 classes and 1000s of associated lexical variants) Brainmap.org 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"^^http://www.w3.org/2001/XMLSchema#date
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"^^http://www.w3.org/2001/XMLSchema#date
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"^^http://www.w3.org/2001/XMLSchema#date
obo_annot:modifiedDate "2006-09-28"^^http://www.w3.org/2001/XMLSchema#date
obo_annot:synonym prosencephalon
skos:prefLabel Forebrain
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
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 (www.gridsphere.org).