Releases/2015-03-17

= Ontology for Biomedical Investigations Release 2015-03-17 =

Date of Release: 2015-03-17

Subversion Revision: 3975

Access

 * This version in OWL format: http://purl.obolibrary.org/obo/obi/2015-03-17/obi.owl
 * This release directory in Subversion: https://sourceforge.net/p/obi/code/HEAD/tree/releases/2015-03-17/
 * 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 3975 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,

There are 27 new classes, see docs/newIDs.tab for details:


 * OBI_0002021 NextSeq 500
 * OBI_0002022 HiSeq 1000
 * OBI_0002023 Human Genome U133 Plus 2.0 tiling array
 * OBI_0002024 SOLiD 4 System
 * OBI_0002025 Human Exon 1.0 ST tilling array
 * OBI_0002026 Human Genome U133 tiling array
 * OBI_0002027 Genome Analyzer IIe
 * OBI_0002028 SAGE ditag library preparation
 * OBI_0002029 serial analysis of gene expression
 * OBI_0002030 genotyping by tiling array
 * OBI_0002031 genotyping by SNP array
 * OBI_0002032 parallel analysis of RNA structure
 * OBI_0002033 translation-associated transcript leader sequencing
 * OBI_0002034 transcript leader sequencing
 * OBI_0002035 peptide mass fingerprinting
 * OBI_0002036 array based nucleic acid structure mapping assay
 * OBI_0002037 micrococcal nuclease digestion followed by tiling array assay
 * OBI_0002038 ribosomal profiling by sequencing assay
 * OBI_0002039 assay for transposase-accessible chromatin using sequencing
 * OBI_0002040 chromatin isolation by RNA purification sequencing assay
 * OBI_0002041 self-transcribing active regulatory region sequencing assay
 * OBI_0002042 carbon-copy chromosome conformation capture assay followed by sequencing assay
 * OBI_0002043 individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay
 * OBI_0002044 RNA Bind-n-Seq assay
 * OBI_0002045 poly(A)-site sequencing assay
 * OBI_0002046 surface plasmon resonance sensor chip
 * OBI_0002047 enzyme-linked antibody

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 