Releases/2009-11-06

= Release notes for OBI 2009-11-06 Release Candidate 1.0 (RC1.0) =

Date of release: 06 November 2009

Access:  This version: http://purl.obolibrary.org/obo/obi/2009-11-06/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

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 importes 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 terms 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 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 here: http://obi-ontology.org/page/Tutorials

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

How to contact us
Send mail with questions about 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 is 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 at 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 mail to obi-users@googlegroups.com if this is problematic.

New to OBI release candidate 1.0
OBI RC.10 is a pre-1.0 version which has had all _ prefix placeholder classes removed, and mandatory meta data annotation properties have been cleaned.

All classes have text definitions.

Terms used by IEDB (Immune Epitope Database) contained in the ONTIE ontology have been merged into OBI - http://ontology.iedb.org/ and assigned OBI identifiers.

Typographical errors in rdfs labels, definitions and notes have been cleaned.

Uninformative editor notes have been removed; where editor notes remain, these contain information OBI developers believe to be useful for users.

Collective review has resulted in parts of OBI being refactored. This process is ongoing and future OBI releases will be supplied with a summary of changes across versions.

'Conferred qualities' (i.e. 'qualities' resulting from a process, such as ligated, activated, labeled...) have been removed where these were previously generated by OBI in an attempt to support text mining applications. There are still such 'conferred qualities' imported from PATO (e.g., diluted). This will be resolved in future releases in collaboration with the source ontology.

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

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

Known issues

 * OBI RC1.0 supports the OBI manuscript to be submitted to Nature Biotechnology (http://obi.svn.sourceforge.net/viewvc/obi/trunk/docs/papers/release/manuscript.doc). OBI is a work in progress and is expected to evolve. We have a strict deprecation policy which has been adhered to for RC1.0 and which will be used in future. (See http://obi-ontology.org/page/OBIDeprecationPolicy )


 * RC1.0 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.


 * Conferred qualities have been removed to a separate file where these were generated by OBI. There are still conferred qualities imported from PATO, e.g., diluted. This will be resolved in future releases with the source ontology and the OBO foundry.

Please sign up to the obi-users mailing list to get details of new releases and links to versioned release notes.

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. Proceedings of the International Conference on Biomedical Ontologies (ICBO) http://icbo.buffalo.edu/) is below.


 * Information Artifact Ontology (IAO)
 * NCBI Taxonomy
 * Basic Formal Ontology (BFO)
 * Gene Ontology (GO)
 * Phenotypic Quality Ontology (PATO)
 * Chemical Entities of Biological Interest ChHEBI
 * Cell Type Ontology (CL)
 * Foundational Model of Anatomy (FMA)
 * Protein Ontology (PRO)
 * Unit Ontology (UO)
 * Common Anatomy Reference Ontology (CARO)
 * Environment Ontology (ENVO)
 * Vaccine Ontology (VO)
 * Neuroscience Information Framework Ontologies and Terminologies (NIFSTD)
 * Sequence Ontology (SO)
 * Human Phenotype Ontology (HPO)

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		1180 Imported Classes	1447 OBI Individuals		 59 Imported Individuals	 17 OBI Properties		 31 Imported Properties	 62

Imported Classes Breakdown:

IAO		 91 NCBITaxon	1165 BFO		 39 GO		 68 PATO		 23 CHEBI		 20 CL		 18 FMA		  5 PRO		  4 UO		  4 CARO		  3 ENVO		  2 VO		  2 Birnlex		  1 SO		  1 HP		  1

Imported Individuals Breakdown: -- IAO		 17

Imported Properties Breakdown: -- IAO		  31 RO		  24 RO proposed	   7

Release note authors: Helen Parkinson, Melanie Courtot, Alan Ruttenberg