Fyi ... (01)
---------- Forwarded message ----------
From: Trish Whetzel <plwhetzel@xxxxxxxxx>
Date: Wed, Oct 28, 2009 at 11:27 PM
Subject: [ontolog-forum] BioPortal 2.2 Release
To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx> (02)
The BioPortal team is pleased to announce the release of BioPortal 2.2
(http://bioportal.bioontology.org/). Release notes and known issues
are listed below. (03)
New Features (04)
Ontology Views (05)
Views in BioPortal are subsets or other derivatives of ontologies in
the repository that you can share with the community. You can upload
views for any ontology, and review them, add notes, create mappings,
and use REST Web services to access them programmatically.
A view can also serve as a mechanism to define value sets, which are
quite useful in combination with the BioPortal ontology-term selection
widget.
View generation and storage in BioPortal is the result of
collaboration with Dr. Jim Brinkley’s group at the University of
Washington. (06)
NCBO Resource Index (07)
We have initiated automated indexing of the contents of public
databases using ontology terms. The indexing is done using the same
workflow that drives the previously released Annotator web service.
Currently we index the following public databases: Array Express,
Biositemaps, caNanoLab, Conserved Domain Database, ClinicalTrials.gov,
DrugBank, Gene Expression Omnibus, Online Mendelian Inheritance in
Man, PharmGKB, Reactome, ResearchCrossroads (Grant funding database),
Stanford Microarray Database, UniProt KB, and WikiPathways. The
resulting annotations are accessible for browsing via the Resources
tab corresponding to any ontology concept. The annotations can also be
accessed programmatically:
http://www.bioontology.org/wiki/index.php/Resource_Index.
If you have recommendations on additional publicly accessible
resources to index, let us know at support@xxxxxxxxxxxxxxxx (08)
Search filter for Ontology Groups and Categories (09)
You can now limit your search to ontologies from a certain group
(e.g., OBO Foundry, caBIG) or ontologies in a certain category (e.g.,
anatomy). (010)
New REST Web Services (011)
Services to access ontologies and ontology versions (012)
List all Categories
List all Groups
Download by virtual ontology identifier (013)
Services to access ontology views and ontology view versions (014)
List all Views of all Ontologies (lists the latest version)
List all versions for a given View (015)
Concept services (016)
Get all concepts (017)
Search service – parameter added to enable search within an ontology branch
Service to access the NCBO Resource Index (018)
See http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
for the full list of BioPortal REST Web services. (019)
New Data: (020)
Mapping data generated by the LOOM algorithm are now in BioPortal
(close to 1 million new lexical-based mappings). See
http://www.bioontology.org/wiki/index.php/LOOM for more details about
this tool.
Selected UMLS ontologies are now available in BioPortal. Email
support@xxxxxxxxxxxxxxx to request loading of additional UMLS
ontologies. (021)
Known Issues: (022)
The tree navigation shows ‘Too many children’ in cases where the
number of siblings is greater than 500. (023)
Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel@xxxxxxxxxxxx
http://www.bioontology.org (024)
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