Releases/2014-12-03

= Ontology for Biomedical Investigations Release 2014-12-03 =

Date of Release: 2014-12-03

Subversion Revision: 3955

Access

 * This version in OWL format: http://purl.obolibrary.org/obo/obi/2014-12-03/obi.owl
 * This release directory in Subversion: https://sourceforge.net/p/obi/code/HEAD/tree/releases/2014-12-03/
 * 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 3955 of the new OBI build tools:

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

New in this Release
We have added 19 new terms, see docs/newIDs.tab for details:


 * OBI_0001957 hardware testing design
 * OBI_0001958 systematic review study design
 * OBI_0001959 sequencing library multiplexing
 * OBI_0001960 taxonomic diversity assessment by targeted gene survey
 * OBI_0001961 PCR program
 * OBI_0001962 target gene specification
 * OBI_0001963 target subfragment specification
 * OBI_0001964 decision-theoretic analysis objective
 * OBI_0001965 decision analysis study design
 * OBI_0001966 sequence library deconvolution
 * OBI_0001967 multiplexing sequence identifier
 * OBI_0001968 operational taxonomic unit matrix
 * OBI_0001969 biodiversity assessment objective
 * OBI_0001970 multiplexed sequencing library
 * OBI_0002015 transcription profiling by MPSS assay
 * OBI_0002016 histone modification identification by ChIP-chip assay
 * OBI_0002017 histone modification identification by ChIP-Seq assay
 * OBI_0002018 transcription factor binding site identification by ChIP-chip assay
 * OBI_0002019 transcription factor binding site identification by ChIP-Seq assay

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 nodes. In particular, many of the descendants of "measurement data item" have not yet been revised to use the new "value specification" approach.

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

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 