Releases/2011-04-20

= Release notes for OBI 2011-04-20 Release =

Date of release: 2011-05-10

Access:  This version: http://purl.obolibrary.org/obo/obi/2011-04-20/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 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 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.

A total of 293 new classes and 18 new instances (excluding the terms imported from external resources) were added into this release, including
 * A list of terms related to the MGED ontology, most are subclasses of study design and their related assays
 * A list of assay terms required by IEDB group (around 100 terms) and influenza group
 * A total of 18 terms were added as instances of manufacturer, provided by influenza group

The newly added OBI classes are listed on - http://obi.svn.sourceforge.net/viewvc/obi/releases/2011-04-20/merged/newClasses.html

Most of commonly used MGED ontology (MO) terms in annotation of functional genomics experiments are available in this release. The FGED community can switch from Mged Ontology (MO) to OBI.

Design template of 'service' is remodeled as: service is_a 'planned process' and ((realizes some 'service consumer role') and (realizes some 'service provider role')) service has_part some 'planned process'

Eagle-i group will add specific service terms follow this template in the near future.

Some known issues are fixed.

For all the details of the difference of this release from the previous one, please check the files under http://obi.svn.sourceforge.net/svnroot/obi/releases/2011-04-20/merged/

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

 * 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.

- activation - binding complex 3D structure determination assay - general scalar measurement datum - identification - questionaire - reagent application function - scalar score from composite inputs - specimen labeling function
 * 8 classes are created as uncurated status. They are very likely to be changed before next release. We recommend that they not be used yet.

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
 * 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)
 * 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
- OBI Classes 1764 Imported Classes OBI Individuals Imported Individuals OBI Properties Imported Properties

Imported Classes Breakdown:

IAO        112 NCBITAXON 1170 BFO         39 GO          95 PATO        49 CHEBI       53 CL          19 FMA         12 PR          15 UO           9 CARO         3 ENVO         2 VO           2 BIRNLEX      1 SO           3 HP           1 UBERON       4 OGMS         3 GAZ          1

Release note authors:


 * Alan Ruttenberg
 * Jie Zheng