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[bioontology-support] new BioPortal release, and introduction

John Graybeal jbgmeta1 at stanford.edu
Wed Nov 11 19:28:39 PST 2015


Hello everyone,

We're pleased to announce a new release of BioPortal (version 4.22)! Highlights of this release are included below, and in the release notes [1].

Also, I'd like to introduce myself. I'm John Graybeal, the new lead for BioPortal, replacing Ray Fergerson. I'm filling tall shoes, but Ray did a great handoff and the BioPortal support team is great, so I'm looking forward to providing continued high value with the BioPortal services.

If you have concerns, we encourage you as always to make requests via the support at bioontology.org<mailto:support at bioontology.org> email. And if you have something that isn't appropriate for the list, you can email me directly. (If it looks like a routine request, I'll forward it to the list, so please indicate if you don't want that.)

Thanks for using BioPortal and letting us know your thoughts. And now, back to our list of improvements.

Enhancements

* New functionality at the REST API level in support of our collaboration with the CEDAR [2] project:
   * Added the ability to search for, and retrieve all value sets. (A value set is an unstructured collection of terms.)
   * Implemented search for value set items [3].
   * Implemented search for ontology classes and value set items [4].
   * Added the ability to exclude value set collections from search [5].
   * Added the ability to search for value set values across all value sets in an ontology.
* Clicking the Add Comment and/or Add Proposal buttons in the Notes sections for ontologies will navigate unauthenticated users to the login page.
* Ontologies are now sortable by creation date on the Admin page.

Bug Fixes

* Fixed an issue that caused Projects page load times in excess of 3 minutes.
* Fixed an issue that caused the UI to go blank after selecting the root node of the CCO ontology.
* Admin page: the ontologies table now refreshes after deleting an ontology.
* Fixed an issue that caused a 404 error when trying to view the DINTO ontology.
* Fixed an inconsistency in the metadata for the CHMO ontology that caused the parsing process to fail.

[1] http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes
[2] http://www.metadatacenter.org/
[3] http://data.bioontology.org/search?q=melanoma&also_search_provisional=true&valueset_exclude_roots=true&ontology_types=VALUE_SET_COLLECTION
[4] http://data.bioontology.org/search?q=melanoma&also_search_provisional=true&valueset_exclude_roots=true
[5] http://data.bioontology.org/search?q=melanoma&ontology_types=ONTOLOGY&also_search_provisional=true
========================

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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