Releases/2012-07-01

= Release notes for OBI 2012-07-01 Release =

Date of release: 2012-07-01

Access:  This version: OWL format - http://purl.obolibrary.org/obo/obi/2012-07-01/obi.owl  This version: OBO format - http://purl.obolibrary.org/obo/obi/2012-07-01/obi.obo  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  IEDB View Latest Version: http://purl.obolibrary.org/obo/obi/obi_IEDBview.owl

 Tracker: http://purl.obolibrary.org/obo/obi/tracker  Please see the Tutorials for instructions on downloading and viewing. http://obi-ontology.org/page/Tutorials  Previous release notes 

About this ontology
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.

New to this OBI release
There are more changes since the last release than can be compactly described here. Users with questions are directed to the OBI users list.

Here are the highlight:

- types of binding assays and related terms such as binding measurement data required by the IEDB group - types of assays related to ECO
 * A total of 105 new classes (excluding the terms imported from external resources) were added to OBI in this release containing:

The newly added OBI classes are listed on http://obi.svn.sourceforge.net/viewvc/obi/releases/2012-07-01/docs/newClasses.html

Obsolete classes in OBI
The obsoletion policy is described on the OBI wiki - http://obi-ontology.org/page/OBIDeprecationPolicy

OBI enforces a strict deprecation policy: OBI Identifiers in this release are stable and will be maintained in new versions.

Known issues
We have used the following version of IAO: http://information-artifact-ontology.googlecode.com/svn/releases/2012-01-05/merged/iao-all.owl and the following version of BFO2: http://bfo.googlecode.com/svn/releases/owl-ruttenberg-2010-05-25/ruttenberg-bfo2.owl
 * Without release version of IAO transited in BFO 2.0 (alan version, not official release version), the development version of IAO and BFO is merged to the current OBI release.


 * device classes which are part of their parent classes

- subclasses of 'chromatography device' All parts of the device, like 'detector lamp', 'syringe filter', etc. are defined as its subclasses. So, they inheres all the functions inheres_in "chromatography device".

- subclasses of 'chromatography instrument' has same issue as 'chromatography device'

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.


 * Information Artifact Ontology (IAO)
 * NCBI Taxonomy (NCBITAXON)
 * Basic Formal Ontology (BFO)
 * Gene Ontology (GO)
 * Phenotypic Quality Ontology (PATO)
 * Chemical Entities of Biological Interest (ChEBI)
 * Cell Type Ontology (CL)
 * Protein Ontology (PR)
 * Unit Ontology (UO)
 * Common Anatomy Reference Ontology (CARO)
 * Environment Ontology (ENVO)
 * Vaccine Ontology (VO)
 * Sequence Ontology (SO)
 * Human Phenotype Ontology (HPO)
 * Uber anatomy ontology (UBERON)
 * Ontology for General Medical Science (OGMS)
 * Gazetteer (GAZ)

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 (need to update)
- OBI Classes 2042 Imported Classes 1649 OBI Properties 40 Imported Properties 120

Imported Classes Breakdown:

NCBITaxon 1170 GO        129 IAO       125 CHEBI     54 PATO      49 BFO       27 UBERON    20 CL        19 PR        15 UO        11 CARO      5 OGMS      4 ENVO      3 SO        3 VO        2 HP        1 GAZ       1

Release note authors:


 * Carlo Torniai
 * Jie Zheng