Releases/2013-10-25

= Ontology for Biomedical Investigations Release 2013-10-25 =

Date of Release: 2013-10-25

Subversion Revision: 3886

Access

 * This version in OWL format: http://purl.obolibrary.org/obo/obi/2013-10-25/obi.owl
 * This release directory in Subversion: https://sourceforge.net/p/obi/code/HEAD/tree/releases/2013-10-25/
 * Latest Version in OWL format: http://purl.obolibrary.org/obo/obi.owl
 * Latest Version in OBO format: http://purl.obolibrary.org/obo/obi/obi.obo
 * Browse Latest Version: http://purl.obolibrary.org/obo/obi/browse
 * All Releases: http://obi-ontology.org/page/Releases
 * Issue Tracker: http://purl.obolibrary.org/obo/obi/tracker

Please see the Tutorials for instructions on downloading and viewing: http://obi-ontology.org/page/Tutorials

Release Files

 * obi.owl: the main OBI file in Web Ontology Language (OWL) XML format
 * obi_core.owl: a version with the OBI Core terms
 * obi_iedb.owl: a version of OBI using IEDB's alternative terms for labels
 * obi_isa.owl: a version of OBI using ISA's alternative terms for labels


 * branches: OBI development files used to build the release
 * external: IAO and BFO files used to build the release
 * docs: reports on the release files, for example:
 * newIDs.tab: a list of terms added since the last release
 * obi.txt: report on term types and source ontologies
 * obi.tsv: a list of all the terms in obi.owl

This release candidate was built using revision 3883 of the new OBI build tools:

http://sourceforge.net/p/obi/code/HEAD/tree/trunk/src/tools/build/

New in this Release
Since the last release we have completed the OBI Core review

http://obi-ontology.org/page/Core_review

A significant part of the Core Review involved changes to the modelling of measurement data using value specifications. This document contains an extended discussion:

https://sourceforge.net/p/obi/code/HEAD/tree/trunk/src/examples/development/data-prototype.pdf?format=raw

Align 'cultured cell' modeling with CL/CLO/REO ontologies [Ref]

In October we switched to a new import system using OntoFox. See the https://svn.code.sf.net/p/obi/code/trunk/src/ontology/branches/OntoFox_inputs and https://svn.code.sf.net/p/obi/code/trunk/src/ontology/branches/OntoFox_outputs directories for details. The most significant difference is a large reduction in the number of terms that we import from NCBI Taxonomy.

A total of 178 classes have been added since last release containing - type of assay terms requested by IEDB and ENCODE project - terms for annotation of metadata standards by all ongoing and future NIAID GSC BRC sequencing projects - terms required by modelling 'cell line cell' and 'cell culture'

See docs/newIDs.tab for a list of new terms.

Known Issues
In the course of preparing OBI Core we have made significant changes to many of OBI's upper-level terms. However we have not yet had time to revise all the children of the changed node. In particular, many of the descendants of "measurement data item" have not yet been revised to use the new "value specification" approach.

OBI used BFO pre-Graz version as top level ontology and imported BFO pre-Graz compatible version of IAO.

If you have any questions, please ask on the developer mailing list at http://groups.google.com/group/obi-developer

External ontology and resource mapping/imports list
The full list of ontologies and external resources from which one or more terms are imported into OBI via the MIREOT process (Courtot et al. 2009 MIREOT: the Minimum Information to Reference an External Ontology Term.)[Ref] is below.
 * Basic Formal Ontology (BFO)
 * Common Anatomy Reference Ontology (CARO)
 * Chemical Entities of Biological Interest (ChEBI)
 * Cell Type Ontology (CL)
 * Cell Line Ontology (CLO)
 * Gazetteer (GAZ)
 * Gene Ontology (GO)
 * Human Phenotype Ontology (HP)
 * Information Artifact Ontology (IAO)
 * NCBI Taxonomy (NCBITAXON)
 * Ontology for General Medical Science (OGMS)
 * Phenotypic Quality Ontology (PATO)
 * Protein Ontology (PR)
 * Reagent Ontology (REO)
 * Sequence Ontology (SO)
 * Uber anatomy ontology (UBERON)
 * Unit Ontology (UO)
 * Vaccine Ontology (VO)

You can request import of additional terms by adding a tracker item at http://purl.obolibrary.org/obo/obi/tracker. Please provide details of the source ontology, term ids and a suggested placement in OBI if possible.

Count of terms in and used by OBI
- OBI Classes 2221 Imported Classes 529 OBI Properties 45 Imported Properties 120

Imported Classes Breakdown:

BFO      27 CARO     5 CHEBI    55 CL       23 CLO      6 GAZ      1 GO       136 HP       1 IAO      125 NCBITaxon 32 OGMS     4 PATO     49 PR       15 REO      2 SO       4 UBERON   20 UO       11 VO       2

About the Ontology for Biomedical Investigations
The Ontology for Biomedical Investigations (OBI) project has developed an integrated ontology for the description of biological and clinical 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 supports the consistent annotation of biomedical investigations, regardless of the particular field of study. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. OBI is being built under the Basic Formal Ontology (BFO) and imports terms from OBO foundry ontologies. OBI also reflects domains specific extensions which were merged into obi.owl. These include terms merged into obi.owl from the Immune Epitope Database Ontology (www.ideb.org) and community suggested terms from many communities.

Aims:


 * Develop an Ontology for Biomedical Investigations in collaboration with groups representing different biological and technological domains involved in Biomedical Investigations
 * Make OBI compatible with other bio-ontologies
 * Develop OBI using an open source approach
 * Create a valuable resource for the biomedical communities to provide a source of terms for consistent annotation of investigations

More details at: http://purl.obolibrary.org/obo/obi

Further reading: You can find the OBI manuscript which this version supports at http://purl.obolibrary.org/obo/obi/repository/trunk/docs/papers/release/Manuscript.doc

Ontology Development
OBI Ontology Development is collaborative, term suggestions and new community representatives are welcome. Single term can be suggested via the OBI tracker http://purl.obolibrary.org/obo/obi/tracker

If you represent a community and/or have many terms to suggest please email OBI Developers  with details. If you would like to see the latest development version please check out the development copy of OBI from sourceforge.

Tutorials on how to do this can be found here: http://obi-ontology.org/page/Tutorials

The OBI wiki can be found at: http://obi-ontology.org

How to Contact Us
Send emails with questions on how to use OBI to obi-users@googlegroups.com. You can sign up for this group, or view the archives, at: http://groups.google.com/group/obi-users

Discussion among OBI developers can be found at obi-devel@lists.sourceforge.net. You can sign up for this group, or view the archives, at: https://lists.sourceforge.net/lists/listinfo/obi-devel or http://groups.google.com/group/obi-developer

OBI term requests, as well as reports of bugs or other issues can be entered in our tracker: http://purl.obolibrary.org/obo/obi/tracker The tracker currently requires you to have or sign up for a sourceforge account. Please send an email to obi-users@googlegroups.com if this is problematic.

Release notes author:
 * James A. Overton
 * Jie Zheng