Peter, (01)
Thank you for the kind words. (02)
And to answer your question -- no, there is no change to the
installation process. (03)
Best regards, (04)
Natasha (05)
On Oct 29, 2009, at 8:08 AM, Peter Yim wrote: (06)
> Natasha, Misha, Mark and All on the NCBO-BioPortal Team,
>
> Congratulations on the new (BioPortal v2.2) release, which we were so
> excited to hear about at the OOR luncheon from Mark yesterday.
>
> Natasha ... for the installation of the OOR-sandbox (on
> <oor-01f.cim3.net> ... which will be renamed <oor-01.cim3.net>
> eventually) please let us know if we should be expecting an update to
> the installation instructions, or, if we are ok doing it according to
> the last set (for v2.1d) you provided.
>
> Thanks & regards. =ppy
> --
>
>
> ---------- 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>
>
>
> 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.
>
> New Features
>
> Ontology Views
>
> 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.
>
> NCBO Resource Index
>
> 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
>
> Search filter for Ontology Groups and Categories
>
> 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).
>
> New REST Web Services
>
> Services to access ontologies and ontology versions
>
> List all Categories
> List all Groups
> Download by virtual ontology identifier
>
> Services to access ontology views and ontology view versions
>
> List all Views of all Ontologies (lists the latest version)
> List all versions for a given View
>
> Concept services
>
> Get all concepts
>
> Search service – parameter added to enable search within an ontology
> branch
> Service to access the NCBO Resource Index
>
> See http://www.bioontology.org/wiki/index.php/BioPortal_REST_services
> for the full list of BioPortal REST Web services.
>
>
>
> New Data:
>
> 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.
>
>
>
> Known Issues:
>
> The tree navigation shows ‘Too many children’ in cases where the
> number of siblings is greater than 500.
>
>
>
>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel@xxxxxxxxxxxx
> http://www.bioontology.org
>
>
> _______________________________________________
> bioportal-announce mailing list
> bioportal-announce@xxxxxxxxxxxxxxxxxx
> https://mailman.stanford.edu/mailman/listinfo/bioportal-announce
>
>
>
>
>
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