BioPortal 2.0.1 (Label 1005) Release Notes

Author: Misha Dorf 9/19/2008

We have completed a production release of the latest version of BioPortal 2.0 (labeled “1005”), designed to address numerous critical issues as well as implement a number of server optimizations, UI fixes, and performance enhancements. Here is the list of resolved issues and new features:

Bugs Fixes

Bug #703: Very large XML path to root document for TAO:0000578

Bug #541: BP should have the NCIT version that is available on the NCICB site and *not* pull it from OBO foundry

Bug #472: "Lost your password" doesn't work

Bug #531: URLs for BioPortal concepts

Bug #465: Uploaded ontology doesn't show up in list

Bug #562: When downloading mapping the user list is not up to date

Bug #515: After registration failure, can still edit metadata -- But no edits saved

Bug #644: Problem with Root to concept when on a top level node

Bug #490: Get a mapping icon next to a class that has no mappings

Bug #651: Cell Cycle Ontology - Incorrect Relationship and Ontology Navigation

Bug #496: Marginal note icon appears when there are no marginal notes

Bug #656: The "download" link for remote ontologies points to a wrong URL

Bug #493: Commas in the wrong place for properties with multiple values

Bug #560: The term "Element" in the resource tab must be replaced by "Annotations"

Bug #677: Flex visualization problem with deep paths

Bug #662: Cell Cycle Ontology Search and User problems

Bug #679: BioPortal hangs when clicking on some "Latest marginal notes"

Bug #593: Many ontology (ex Cell Type) have Explore links that are broken

Bug #482: Search Results - Concept does not load for NCI Thesaurus:Aspirin_Clopidogrel-Bisulfate

Bug #652: Exploring big ontologies in the Tree has very large lag time

Bug #550: Simply closing an ontology browsing tab can sometime take hours

Bug #521: Strip out language prefix (e.g. "~#en") from Owl rdfs:comment fields in the REST XML

Support #691: URL Links to an existing TAO concepts is not working

Support #699: Proxy Error - Human Disease Ontolgoy - Prostate Cancer

New features

1. Protégé knowledge base caching enhancements

2. Protégé Lucene implementation (OWL and PROTÉGÉ ontologies now use Lucene index instead of a direct database search)

3. Protégé based search results are now correctly ordered by ranking

4. Latest Marginal Notes and Latest Mappings sidebars added to the “Browse Ontologies” page

New REST Service Base URL

Note that we have updated the URL to rest services to a more permanent and intuitive version: http://rest.bioontology.org/bioportal and the port has changed from 8080 to the standard, 80. The old REST service links will still work, but going forward, we should distribute the above base URL for all our RESTful services.