Releases/2011-12-13

= Release notes for OBI 2011-12-13 Release =

Date of release: 2012-01-27

Access:  This version: http://purl.obolibrary.org/obo/obi/2011-12-13/obi.owl  Latest Version: http://purl.obolibrary.org/obo/obi.owl  Browse: http://purl.obolibrary.org/obo/obi/browse  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:
 * 100 newly added classes

A total of 100 new classes (excluding the terms imported from external resources) were added to OBI in this release. Most are types of binding assays and related terms such as binding measurement data required by the IEDB group. The current release contains all terms necessary to represent peptide:MHC binding experiments by the IEDB group, but the inferred term hierarchy is not final. Several terms related to represent services requested by the eagle-i group were also added in this release.

The newly added OBI classes are listed on http://obi.svn.sourceforge.net/viewvc/obi/releases/2011-12-13/merged/newClasses.html

https://obi.svn.sourceforge.net/svnroot/obi/releases/2012-01-18/doc/BFO-RO-terms.xls
 * Import BFO 2.0 (unofficial version) which URI is: http://purl.obolibrary.org/obo/bfo.owl. This version contains OBO_REL relations and URI changed to official format which is http://purl.obolibrary.org/obo/BFO_XXXXXXX. The mapped old BFO ids -> new BFO ids are listed in the file:

The changes that had to be made in OBI to switch over to the new versions does not substantially effect the meaning of OBI terms. Much of what is new in BFO 2/RO 2 is leaving stuff out that was not used by OBI. we do not expect the changes in the official release of BFO 2 that impact the OBI classes in the release.

The current BFO changes that effect OBI are the 'BFO: function' is subclass of 'BFO: disposition' rather than sibling class now.

URIs of all terms imported from OBO foundry ontologies have been updated in new format, such as http://purl.obolibrary.org/obo/CL_XXXXXXX rather than http/purl.org/obo/owl/CL#CL_XXXXXXX for CL ontology.

The same version BFO was used in the new OBO to OWL conversion. So having OBI use these URIs are better integration with other OBO foundry ontologies, which now have resolvable URIs too. (see http://www.ontobee.org/).


 * Replaced species specific anatomical terms with cross species ones which are in either CARO or UBERON


 * fix the issues of terms with 'uncurated' status, provide required metadata to five terms with 'uncurated' status and deprecated the other three.

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

 * Imported unofficial BFO 2.0, the labels of object properties appending with @en need to be fixed. The domain and range of some object properties have not been defined yet.


 * Without release version of IAO transited in BFO 2.0, the development version of IAO is merged to the current OBI release.


 * This release is available only in OWL format. There is no official OBO Format version at present: OBI cannot be loaded nor viewed in OBO-Edit and is not available from the Ontology Lookup Service at EBI.

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 1910 Imported Classes 1591 OBI Properties 38 Imported Properties 104

Imported Classes Breakdown:

NCBITAXON 1170 IAO        109 GO         102 CHEBI       53 PATO        49 BFO         27 CL          19 UBERON      19 PR          15 UO          11 CARO         5 SO           3 OGMS         3 ENVO         2 VO           2 HP           1 GAZ          1

Release note authors:


 * Jie Zheng
 * Bjoern Peters