The BIRN Ontology Task Forse (OTF) has made a lot of progress on biomedical imaging ontology in general.

NITRC will 'insert' the tool and resrouces specific needs into this framework.

The first public release of the BIRNLex product is here:

OBO Annotation properties:
http://www.nbirn.net/birnlex/1.0/OBO_ann...
BIRNLex Annotation properties:
http://www.nbirn.net/birnlex/1.0/BIRNLex...
BIRNLex-OBO Upper Biomedical Ontology:
http://www.nbirn.net/birnlex/1.0/BIRNLex...
BIRNLex Organismal Anatomy:
http://www.nbirn.net/birnlex/1.0/BIRNLex...
BIRNLex Organismal Anatomy:
http://www.nbirn.net/birnlex/1.0/BIRNLex...

Hi David,

Please note the following in regards to the structure, content, and intended use of this collection of BIRN Ontology OWL files:

1) BIRNLex support page
We'll be trying to keep the following page current with the latest info on the current and pending releases of BIRNLex

http://purl.org/nbirn/birnlex/support/

2) BIRNLex-Main.owl
The overall BIRNLex ontology which unites this collection of modules in the appropriate relationships can be obtained by viewing the BIRNLex-Main.owl OWL file. The production version of this Main file will be available at the following Persistent URL:

http://purl.org/nbirn/birnlex/

(Soon this will be mirrored at http://purl.org/birn/birnlex/)

3) BIRNLex modules:
It is intended for those who only wish to re-use a specific semantic domain within BIRNLex - e.g., neuroanatomy - they can just import that module - e.g.:
http://purl.org/birn/birnlex/BIRNLex-Ana...

This is not currently enabled (currently you must include the file version in the path to get to the specific files - e.g.: http://purl.org/nbirn/birnlex/1.2.3/BIRN...), but as soon as this latest version (v1.2.3) is released, accessing the current production version of a given module will be possible using the generic URL given above (the one lacking the version).

The current collection of modules are:
OBO Annotation Properties:
OBO_annotation_properties.owl
BIRNLex Annotation Properties:
BIRNLex_annotation_properties.owl
OBO Foundry Core (BFO + OBO-RO + PATO):
obo-foundry-core-full-import.owl
OBO Upper Bio Ontology (OBO UBO):
BIRNLex-OBO-UBO.owl
BIRNLex Organismal Taxonomy:
BIRNLex-OrganismalTaxonomy.owl
BIRNLex Anatomy (primarily neuroanatomy):
BIRNLex-Anatomy.owl
BIRNLex Cognition & Behavior:
BIRNLex-CogBehavior.owl
BIRNLex Investigation (experiment provenance):
BIRNLex-Investigation.owl

These modules are brought together via cascasding owl:imports - e.g., obo-foundry-core imports OBO_annotation_properties.owl; OBO-UBO imports obo-foundry-core-full-import.owl; BIRNLex-Organism Taxonomy.owl imports OBO-UBO, etc.. BIRNLex-Main.owl mere imports BIRNLex-Investigation.owl and thereby gets all the other required modules. This also implies there is a hierarchical set of module dependencies that anyone intending to use one of the module should understand (and can easily view by opening any module - or BIRNLex-Main in Protege or SWOOP).

4) OBO vs. BIRNLex
The artifacts with OBO in their name are essentially placeholders for modules we hope will eventually be supplied by the larger Open Bioontology community, but are not yet available from them. Files with BIRNLex in their name contain domains more specifically required to semantically integrate the neuroscience data BIRN is currently handling across all the testbeds.

5) BIRNLex-Investigation & OBI
The BIRNLex Investigation OWL file is built on top of the Ontology of Biomedical Investigation (OBI)_ - a major community ontology development dedicated to providing the semantic entities required to representation experimental provenance across the broad swarth of experimentation (basic and clinical) thoughout the biomedical research community. Since OBI is still a work-in-progress, there is a lot in BIRNLex-Investigation that may ultimately get absorbed by OBI, but we need it NOW, so we've put it into our own OWL file. This will ultimately include a means to generically describe studies-experiments-assays in a manner that is commensurate both with the approach adopted by the gene expression community in the MAGE and FuGE XML export/exchange schemas, as well as that adopted by BIRN's own XML-Based Clinical Experiment Data Exchange Schema (XCEDE - http://www.nbirn.net/downloads/xcede/ind...).

BTW - all this info will ultimately be posted on our BIRNLex support page - and explained in much more detail in our upcoming publications on BIRNLex.

Cheers,
Bill

Bill Bug
Lab. of Bioimaging and Anatomical Informatics
Drexel U. College of Medicine
BIRN, Ontology Task Force and Mouse BIRN