From noy at stanford.edu  Tue Feb  2 20:47:00 2010
From: noy at stanford.edu (Natasha Noy)
Date: Tue, 2 Feb 2010 17:47:00 -0800
Subject: [Gramene] [bioportal-announce] Upcoming BioPortal 2.3 release: NOTE
	changes in the Annotator service and Hierarchy services
Message-ID: <E762F0E9-36A2-477D-B336-6BC2ED6D4D0D@stanford.edu>

Dear NCBO Users,

We are planning a BioPortal 2.3 release tomorrow, February 3d, 2010.  
These release includes some changes to the Annotator Service and  
Hierarchy Services. Specifically, there are changes in the content the  
services access, the way UMLS terminologies are addressed, and minor  
changes in the Annotator service XML output. Please, see the release  
notes below for the details.

If these upcoming changes present a serious problem for you, please  
let us know at support at bioontology.org as soon as possible.

Natasha

BioPortal 2.3

New features:
BioPortal will process SKOS labels for preferred names and synonyms
Ontologies used by Annotator & Hierarchy services will now be updated  
on a regular basis (around every week).
The filtering of annotation by semantic types is available only for  
the ontologies which provide that information
The Annotator scoring function has changed a bit.
Users can now exclude the annotations created with synonym terms.
Users can now exclude the annotations less than a certain length.
There is a change in the XML returned by the Annotator service. The  
<sematicTypeBean> information is presented differently. The Get all  
terms REST service is also affected.
Please refer to http://www.bioontology.org/wiki/index.php/Annotator_User_Guide 
  for details on Annotator enhancements

New way to address UMLS ontologies:

We have harmonized the ontologies in the Annotator and BioPortal. The  
full list is available at: http://rest.bioontology.org/obs/ontologies.  
This change has implications when using the Annotator with UMLS  
ontologies.
Currently, BioPortal (and, therefore, Annotator and Hierarchy  
services) can use 16 ontologies from UMLS. We will add UMLS ontologies  
to BioPortal on demand. Please send email to support at bioontology.org  
to request a specific UMLS ontology to be added to BioPortal.
UMLS SAB is no longer valid as ontologyId. Please refer to http://bioportal.bioontology.org/ontologies/?filter=UMLS 
  to map your SAB to the corresponding ontology version id.
UMLS CUIs are no longer valid as conceptId. You can look up the  
conceptId corresponding to a CUI by using the NCBO search interface (http://bioportal.bioontology.org/search 
): type in the CUI and check "Include attributes in search". You can  
also use the search REST service (http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_services 
) to search for the concept by CUI.  We are working on a new concept  
service that will accept CUI as conceptId in the near future.
Known issues:
ISA closure in the Annotator and Hierarchy services do not work  
properly for NCIT and Galen. This will be fixed in an upcoming release.
Some mappings present in BioPortal are not yet available for use with  
the Annotator.

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