Difference between revisions of "BioPortal Release Notes"

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(Noted that this page is no longer used, in favor of GitHub releases. Added links to release notes pages for API and UI.)
 
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== BioPortal Release 3.3 ==
+
'''<span style="color:red;">Please note: this page is deprecated and no longer updated. To view current release notes for BioPortal, please refer to one of the following pages:</span>'''
−
New features include updates to the Web interface and Web services:
 
−
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services
 
−
* Updated Search page to remove Flash
 
−
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies.
 
−
* Added Help documentation
 
−
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.
 
−
* Bug Fix
 
−
** Fixed the Filter by Account on the Mappings tab
 
  
−
== BioPortal Release 3.2 ==
+
BioPortal REST API release notes: https://github.com/ncbo/ontologies_api/releases<br>
−
New features include updates to the Web interface and Web services:
+
BioPortal web application release notes: https://github.com/ncbo/bioportal_web_ui/releases
−
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender 
 
−
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service
 
−
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples
 
−
* Added support for access control for viewing ontologies
 
−
* Added link to subscribe to BioPortal Notes emails 
 
−
* Synchronized “Jump To” feature with ontology parsing and display
 
−
* Added documentation on Ontology Groups
 
−
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter
 
−
* Removed the metric "Number of classes without an author"
 
−
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release. 
 
−
* Bug Fix
 
−
** Fixed calculation of “Classes with no definition” metric
 
−
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results
 
  
  
−
'''''Firefox Extension for NCBO API Key''''':
+
''This page contains software release notes for the 5.x series of [http://bioportal.bioontology.org/ BioPortal].'' 
−
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org.  
 
  
−
'''''Upcoming software license change''''':
+
Use the following links to access release notes for the BioPortal Virtual Appliance, and older versions of BioPortal:
−
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.
 
  
−
== BioPortal Release 3.1 ==
+
* [[BioPortal_Virtual_Appliance_Release_Notes|BioPortal Virtual Appliance release notes]]
−
New features include updates to the Web interface and Web services:
+
* [[BioPortal_4_Release_Notes|BioPortal 4.x release notes]]
−
* Support for loading OWL 2 ontologies
+
* [[BioPortal_Release_3_Release_Notes|BioPortal 3.x release notes]]
−
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key.  
+
* [[BioPortal_Release_2_Release_Notes|BioPortal 2.x release notes]]
−
* Browsing of ontologies that contain large numbers of sibling terms
 
−
* Icons for is_a and part_of  are displayed for OBO format ontologies
 
−
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology
 
−
Bug Fix
 
−
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response
 
  
−
(Release date July 8, 2011)
 
  
−
== BioPortal Release 3.0 ==
+
__TOC__
−
New features include updates to the Web interface and Web services:
 
−
* Web interface updates
 
−
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology
 
−
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology
 
−
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.
 
−
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms
 
−
* Form auto-complete Widget - Option to include term definition in display
 
−
* Resource Index
 
−
** Data indexed with new ontologies from BioPortal
 
−
** PubMed data now available for abstracts published in 2010
 
  
−
(Release date May 19, 2011)
 
  
−
== BioPortal Release 2.6.4 ==
+
== BioPortal 5.22.1 (2021-July-08, 2021-August-10) ==
−
New features include additional Web services and Web interface enhancements:
 
−
* Mapping Web services - Access to ontology term mappings, including UMLS, OBO DbXref, and LOOM mappings ( http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service ) ''Please note, the prototype Mapping Web service will be removed March 23''
 
−
* RDF Download Web service - Access any BioPortal ontology in RDF ( http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service and http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service )
 
−
* Notes - Ability to archive Notes, e.g. accepted term proposals, and filter from display
 
−
* Annotator
 
−
** Updated ontology content
 
−
** Offsets corrected for non-ASCII characters
 
−
** Link to Annotator Web interface using parameters
 
−
** Web interface enhancements
 
−
* Display of ontology development status
 
−
* Hyperlinks on term details page
 
−
* Ability to add comments on Mappings
 
  
−
(Release date February 2011)
+
'''Bug Fixes'''
  
−
== BioPortal Release 2.5 ==
+
* Fixed a bug that caused Mapping Submission IDs query to fail in AllegroGraph ([https://github.com/ncbo/ontologies_linked_data/issues/120 ncbo/ontologies_linked_data#120])
−
New features in this release include the following:
+
* Fixed a bug that prevented UMLS ontologies from being processed in AllegroGraph ([https://github.com/ncbo/bioportal-project/issues/215 ncbo/bioportal-project#215])
−
* Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms or update other ontology content. BioPortal provides a structured template for making such requests,  allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.
+
* Fixed a security vulnerability
  
−
* Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If  you would like to subscribe to notifications about a particular ontology, please send email to support at bioontology.org.  We will have an interactive form to sign-up for notifications shortly.)
 
  
−
* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).
+
== BioPortal 5.21.0 (2021-May-18) ==
  
−
* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org
+
'''New Features'''
  
−
* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for  viewing instances shortly.
+
* Further optimize the mapping counts generation job, including periodic 4store health checks ([https://github.com/ncbo/ncbo_cron/issues/40 ncbo/ncbo_cron#40])
 +
* Added incremental progress logging to the Annotator dictionary generation job ([https://github.com/ncbo/ncbo_annotator/issues/16 ncbo/ncbo_annotator#16])
  
−
* New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.
+
'''Bug Fixes'''
  
−
* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings
+
* Fixed the 4store health status check API ([https://github.com/ncbo/goo/issues/112 ncbo/goo#112])
  
−
[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services
 
  
−
(Release date June 9, 2010)
+
== BioPortal 5.20.0 (2021-April-02) ==
 +
 
 +
'''New Features'''
 +
 
 +
* A new CRON job that allows regenerating total mapping count and mapping count pairs on demand ([https://github.com/ncbo/ncbo_cron/issues/37 ncbo/ncbo_cron#37])
 +
* An enhancement to the ontology pull process to allow clearing caches after the full run ([https://github.com/ncbo/ncbo_cron/issues/38 ncbo/ncbo_cron#38])
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* The mapping counts generation script failed to properly count mappings between ontoloigies ([https://github.com/ncbo/ontologies_linked_data/issues/88 ncbo/ontologies_linked_data#88])
 +
* Reported mapping counts between ontologies are always higher than the actual counts ([https://github.com/ncbo/ontologies_linked_data/issues/115 ncbo/ontologies_linked_data#115])
 +
* Incorrect mapping count statistics generated for some ontologies ([https://github.com/ncbo/ontologies_linked_data/issues/94 ncbo/ontologies_linked_data#94])
 +
* Empty pages in paged result sets ([https://github.com/ncbo/ontologies_linked_data/issues/66 ncbo/ontologies_linked_data#66])
 +
 
 +
 
 +
== BioPortal 5.19.0 (2020-September-04) ==
 +
 
 +
'''New Features'''
 +
 
 +
* A new CRON job that synchronizes the search index with the master data stored in the triple store ([https://github.com/ncbo/ncbo_cron/issues/34 ncbo/ncbo_cron#34])
 +
* An enhancement to the test runner script that uses a Dockerized instance of Redis for the tests run against
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* A fix to the test runner script that detects when a test fails instead of always reporting SUCCESS ([https://github.com/ncbo/ontologies_linked_data/issues/111 ncbo/ontologies_linked_data#111])
 +
* Fixed a bug that prevented the ontologies report refresh from completing successfully ([https://github.com/ncbo/ncbo_cron/issues/35 ncbo/ncbo_cron#35])
 +
 
 +
 
 +
== BioPortal 5.18.0 (2020-July-14) ==
 +
 
 +
'''New Features'''
 +
 
 +
* Upgraded OWL API to version 4.5.17; updated the OWL API Wrapper to reflect this upgrade ([https://github.com/ncbo/owlapi_wrapper/releases/tag/v1.3.6 owlapi_wrapper/releases/tag/v1.3.6])
 +
* In OWL API Wrapper, expanded the list of allowed suffixes for ontology files to include .n3, .nt, .nq, .skos, .rdf, and .rdfs ([https://github.com/ncbo/owlapi_wrapper/releases/tag/v1.3.6 owlapi_wrapper/releases/tag/v1.3.6])
 +
* Implemented a script to allow an on-demand regenerating of the ontology admin report ([https://github.com/ncbo/ncbo_cron/issues/32 ncbo/ncbo_cron#32])
 +
* Implemented a script to allow an on-demand regenerating of the ontology analytics data ([https://github.com/ncbo/ncbo_cron/issues/19 ncbo/ncbo_cron#19])
 +
* Implemented a script to allow an on-demand regenerating of the ontology rank data ([https://github.com/ncbo/ncbo_cron/issues/31 ncbo/ncbo_cron#31])
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* Fixed a deprecation warning `Redis#exists(key)` will return an Integer in redis-rb 4.3 ([https://github.com/ncbo/sparql-client/issues/3 ncbo/sparql-client#3], [https://github.com/ncbo/ncbo_annotator/issues/12 ncbo/ncbo_annotator#12])
 +
 
 +
 
 +
== BioPortal 5.17.0 (2020-June-22) ==
 +
 
 +
'''New Features'''
 +
 
 +
* Implemented the ability to retrieve sorted ontology classes via the search endpoint ([https://github.com/ncbo/bioportal_project/issues/165 ncbo/bioportal_project#165]). The API signature is as follows:<br/>http://data.bioontology.org/search?ontologies=NCIT&sort=prefLabel
 +
* Implemented the ability to retrieve sorted descendant classes via the subtree search endpoint ([https://github.com/ncbo/bioportal_project/issues/165 ncbo/bioportal_project#165]). The API signature is as follows:<br/>http://localhost:9393/search?subtree_ontology=NCIT&subtree_root_id=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16275&sort=prefLabel
 +
* Implemented a test runner script that uses Dockerized versions of 4store and AllegroGraph to run the test suite. The triple store backends and their versions can now be switched seamlessly when running unit tests ([https://github.com/ncbo/ontologies_linked_data/issues/105 ncbo/ontologies_linked_data#105])
 +
<pre>
 +
Usage: bundle exec ruby run_tests.rb [options]
 +
 
 +
    -b, --backend [4store|ag]        An optional backend name. Default: 4store
 +
    -v, --version VERSION            An optional version of the server to test against. Default: 'latest'
 +
    Must be a valid image tag published on repositories:
 +
https://hub.docker.com/r/bde2020/4store/tags for 4store
 +
https://hub.docker.com/r/franzinc/agraph/tags for ag
 +
    -p, --port PORT                  An optional port number of the server to test against. Default: 9000 for 4store, 10035 for ag
 +
    Must be a valid integer value
 +
    -f, --file TEST_FILE_PATH        An optional path to a test file to be run. Default: all test files
 +
    -t, --test TEST_NAME            An optional name of the test to be run. Default: all tests
 +
    -h, --help                      Display this screen
 +
</pre>
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* Fixed an issue running against AllegroGraph v7+ that prevented paged calls from completing properly ([https://github.com/ncbo/goo/issues/106 ncbo/goo#106])
 +
* Fixed an issue running against AllegroGraph v7+, where a test for ontology properties failed ([https://github.com/ncbo/ontologies_linked_data/issues/106 ncbo/ontologies_linked_data#106])
 +
* Fixed an issue that caused Zlib::GzipWriter runtime errors during ontology processing ([https://github.com/ncbo/ontologies_linked_data/issues/107 ncbo/ontologies_linked_data#107])
 +
* Removed a workaround that was implemented to address a bug in AllegroGraph v6+, which caused certain SPARQL queries to fail. AllegroGraph v7.0.1 release has addressed the issue ([https://github.com/ncbo/goo/issues/104 ncbo/goo#104])
 +
* Fixed an issue that caused runtime errors when running the code against Ruby 2.7.0 and Ruby 2.7.1 ([https://github.com/ncbo/ontologies_api/issues/69 ncbo/ontologies_api#69])
 +
* Fixed an issue, where a search on term id with exact match returns irrelevant results ([https://github.com/ncbo/ontologies_api/issues/57 ncbo/ontologies_api#57])
 +
* Fixed an issue, where a call to the class descendants endpoint fails if properties are included ([https://github.com/ncbo/ontologies_api/issues/54 ncbo/ontologies_api#54])
 +
 
 +
 
 +
== BioPortal 5.16.0 (2020-April-16) ==
 +
 
 +
'''New Features'''
 +
 
 +
* Full integration with the AllegroGraph Semantic Graph Database; 4store backwards compatibility assured ([https://github.com/ncbo/bioportal_project/issues/122 ncbo/bioportal_project#122], [https://github.com/ncbo/goo/issues/100 ncbo/goo#100])
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* Fixed an issue with AllegroGraph request chain breaking with existing Goo code ([https://github.com/ncbo/goo/issues/101 ncbo/goo#101])
 +
* Fixed an issue, where no parsed ontology records appeared in AllegroGraph after ontology has been parsed ([https://github.com/ncbo/goo/issues/102 ncbo/goo#102])
 +
* Fixed an issue with the paging calls returning wrong results in AllegroGraph ([https://github.com/ncbo/goo/issues/103 ncbo/goo#103])
 +
 
 +
 
 +
== BioPortal 5.14.0 (2019-December-09) ==
 +
 
 +
* Implemented a number of enhancements that drastically improved performance of the class descendants call ([https://github.com/metadatacenter/cedar-project/issues/980 metadatacenter/cedar-project/issues/#980])
 +
* Introduced a new version of owlapi-wrapper (OWL API v4.5.13)
 +
* Updated Solr to version 8.2.0; introduced changes to the config files to conform to the latest version of Solr
 +
* Updated code to use secure protocol for password reset URLs ([https://github.com/ncbo/ontologies_linked_data/issues/98 ncbo/ontologies_linked_data#98])
 +
 
 +
 
 +
== BioPortal 5.11.0 (2019-February-13) ==
 +
 
 +
* Implemented the ability to index and efficiently search ontology branches ([https://github.com/ncbo/ontologies_linked_data/issues/90 ncbo/ontologies_linked_data#90])
 +
* Added path_to_root functionality to provisional classes
 +
* Migrated code to Google Analytics API v0.10; updated the library and the method calls to the new signatures
 +
* Added the ability to query properties on class descendants endpoint
 +
 
 +
 
 +
== BioPortal 5.8.0 (2018-April-26) ==
 +
 
 +
* Implemented a configurable number of retries for 4store failures ([https://github.com/ncbo/ontologies_linked_data/issues/84 ncbo/ontologies_linked_data#84])
 +
* Added a script for running SPAM deletion form the command line, added provisional classes to SPAM deletion artifacts ([https://github.com/ncbo/ncbo_cron/issues/13 ncbo/ncbo_cron#13])
 +
* Bug Fix: Recommender fails when input includes the word "concept" ([https://github.com/ncbo/ncbo_ontology_recommender/issues/7 ncbo/ncbo_ontology_recommender#7])
 +
* Fixed the pull process to ignore submission candidates that do not pass the OWLAPI parser ([https://github.com/ncbo/ncbo_cron/issues/10 ncbo/ncbo_cron#10])
 +
 
 +
 
 +
== BioPortal 5.6.0 (2017-December-19) ==
 +
 
 +
* Added ontologyId field to the schema in preparation for Solr upgrade
 +
* Implemented the ability to browse flat ontologies in tree view ([https://github.com/metadatacenter/cedar-project/issues/407 metadatacenter/cedar-project/issues/#407])
 +
* Developed an endpoint to retrieve all ontologies with extended metadata ([https://github.com/metadatacenter/cedar-project/issues/660 metadatacenter/cedar-project/issues/#660])
 +
* Added the ability to sort terms in "/roots" and "/tree" endpoints ([https://github.com/metadatacenter/cedar-project/issues/409 metadatacenter/cedar-project/issues/#409])
 +
 
 +
 
 +
== BioPortal 5.3.1 (2017-May-22) ==
 +
 
 +
* Fixed an issue that prevented the [http://bioportal.bioontology.org/ontologies/HIV HIV ontology] from parsing.
 +
* Fixed an issue that caused a 404 error in the BioPortal user interface when attempting to view the class tree of the HIV ontology.
 +
* Fixed an issue that prevented proper calculation of the set of root classes for the [http://bioportal.bioontology.org/ontologies/HP HP ontology].
 +
 
 +
 
 +
== BioPortal 5.3.0 (2017-May-02) ==
 +
 
 +
This API-only release adds a suite of REST endpoints for retrieving ontology properties. It also addresses limitations with our auto-generated API documentation.
 +
 
 +
'''New Features'''
 +
 
 +
* Implemented an endpoint for retrieving property trees ([https://github.com/ncbo/ontologies_api/issues/27 ontologies_api/issues/27]). [http://data.bioontology.org/documentation#ObjectProperty Documentation]. [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002210/tree Example link].
 +
* Implemented an endpoint for retrieving property roots ([https://github.com/ncbo/ontologies_api/issues/28 ontologies_api/issues/28]). [http://data.bioontology.org/ontologies/UBERON/properties/roots Example link].
 +
* Implemented an endpoint for retrieving property parents ([https://github.com/ncbo/ontologies_api/issues/29 ontologies_api/issues/29]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002210/parents Example link].
 +
* Implemented an endpoint for retrieving property children ([https://github.com/ncbo/ontologies_api/issues/30 ontologies_api/issues/30]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002203/children Example link].
 +
* Implemented an endpoint for retrieving property ancestors ([https://github.com/ncbo/ontologies_api/issues/31 ontologies_api/issues/31]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002210/ancestors Example link].
 +
* Implemented an endpoint for retrieving property descendants ([https://github.com/ncbo/ontologies_api/issues/32 ontologies_api/issues/32]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002286/descendants Example link].
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* Fixed a bug that prevented the API documentation from being auto-generated for ontology properties endpoints ([https://github.com/ncbo/ontologies_api/issues/33 ontologies_api/issues/33]).
 +
 
 +
 
 +
== BioPortal 5.1.0 (2017-Apr-05) ==
 +
 
 +
This is an API release, which adds two new REST endpoints as well as a number of fixes and enhancements, designed to improve the asynchronous processing of ontology data.
 +
 
 +
'''New Features'''
 +
 
 +
* Implemented an endpoint for searching ontology properties ([https://github.com/ncbo/ontologies_api/issues/21 ontologies_api/issues/21]). [http://data.bioontology.org/documentation#nav_prop_search Documentation]. [http://data.bioontology.org/property_search?q=pref+label Example link].
 +
* Implemented an endpoint for retrieving a specific ontology property by its ID ([https://github.com/ncbo/ontologies_api/issues/22 ontologies_api/issues/22]). [http://data.bioontology.org/ontologies/BIBFRAME/properties/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FvoiceType Example link].
 +
 
 +
'''Enhancements'''
 +
 
 +
* Improved logging of the CRON job processing
 +
* A more robust error handling of the CRON batch operations
 +
* A new CRON task that allows indexing ontology properties
 +
* An enhanced ontology processing script that now accepts a list of tasks to be performed
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* Fixed a bug that prevented mappings from being saved in a file correctly during processing ([https://github.com/ncbo/ontologies_linked_data/issues/70 ontologies_linked_data/issues/70]).
 +
 
 +
 
 +
== BioPortal 5.0.0 (2017-Feb-06) ==
 +
 
 +
This release represents an overhaul of our user interface, using bootstrap as the front-end framework to enable immediate and longer-term improvements. (Since the October 2016 release, we have also made a number of minor changes, mostly under the hood, and recently added a few significant features to the Recommender; Release Notes will be added shortly for those changes.)
 +
 
 +
Please Note: Although we are aware of some bugs that have surfaced since the transition, so far they have been relatively minor and most can be worked around by re-sizing the page or changing tabs. We will be working to squash those bugs in the next few days, so please bear with us for this brief period.
 +
 
 +
'''Enhancements'''
 +
 
 +
* Released new BioPortal user interface, including the features described below.
 +
* Implemented new UI framework based on boostrap, enabling cleaner management of all UI elements.
 +
* Redesigned the front page to provide cleaner and more informative look and feel, and put key features front and center.
 +
* Added graph to show top ontology access counts, replacing table with similar information.
 +
* Redesigned header to move most links to the menu bar, simplifying header and unifying it across all pages.
 +
* Redesigned footer to include appropriate and cleanly presented content, including social links, unified across all pages.
 +
 
 +
'''Bug Fixes'''
 +
 
 +
* Fixed an issue with the prompt for the ontology search on the front page, which would not produce desired results.
 +
* Fixed layout issues in front page header.

Latest revision as of 12:56, 4 February 2022

Please note: this page is deprecated and no longer updated. To view current release notes for BioPortal, please refer to one of the following pages:

BioPortal REST API release notes: https://github.com/ncbo/ontologies_api/releases
BioPortal web application release notes: https://github.com/ncbo/bioportal_web_ui/releases


This page contains software release notes for the 5.x series of BioPortal.

Use the following links to access release notes for the BioPortal Virtual Appliance, and older versions of BioPortal:



BioPortal 5.22.1 (2021-July-08, 2021-August-10)

Bug Fixes


BioPortal 5.21.0 (2021-May-18)

New Features

  • Further optimize the mapping counts generation job, including periodic 4store health checks (ncbo/ncbo_cron#40)
  • Added incremental progress logging to the Annotator dictionary generation job (ncbo/ncbo_annotator#16)

Bug Fixes


BioPortal 5.20.0 (2021-April-02)

New Features

  • A new CRON job that allows regenerating total mapping count and mapping count pairs on demand (ncbo/ncbo_cron#37)
  • An enhancement to the ontology pull process to allow clearing caches after the full run (ncbo/ncbo_cron#38)

Bug Fixes


BioPortal 5.19.0 (2020-September-04)

New Features

  • A new CRON job that synchronizes the search index with the master data stored in the triple store (ncbo/ncbo_cron#34)
  • An enhancement to the test runner script that uses a Dockerized instance of Redis for the tests run against

Bug Fixes


BioPortal 5.18.0 (2020-July-14)

New Features

  • Upgraded OWL API to version 4.5.17; updated the OWL API Wrapper to reflect this upgrade (owlapi_wrapper/releases/tag/v1.3.6)
  • In OWL API Wrapper, expanded the list of allowed suffixes for ontology files to include .n3, .nt, .nq, .skos, .rdf, and .rdfs (owlapi_wrapper/releases/tag/v1.3.6)
  • Implemented a script to allow an on-demand regenerating of the ontology admin report (ncbo/ncbo_cron#32)
  • Implemented a script to allow an on-demand regenerating of the ontology analytics data (ncbo/ncbo_cron#19)
  • Implemented a script to allow an on-demand regenerating of the ontology rank data (ncbo/ncbo_cron#31)

Bug Fixes


BioPortal 5.17.0 (2020-June-22)

New Features 

Usage: bundle exec ruby run_tests.rb [options]

    -b, --backend [4store|ag]        An optional backend name. Default: 4store
    -v, --version VERSION            An optional version of the server to test against. Default: 'latest'
				     Must be a valid image tag published on repositories:
					https://hub.docker.com/r/bde2020/4store/tags for 4store
					https://hub.docker.com/r/franzinc/agraph/tags for ag
    -p, --port PORT                  An optional port number of the server to test against. Default: 9000 for 4store, 10035 for ag
				     Must be a valid integer value
    -f, --file TEST_FILE_PATH        An optional path to a test file to be run. Default: all test files
    -t, --test TEST_NAME             An optional name of the test to be run. Default: all tests
    -h, --help                       Display this screen

Bug Fixes

  • Fixed an issue running against AllegroGraph v7+ that prevented paged calls from completing properly (ncbo/goo#106)
  • Fixed an issue running against AllegroGraph v7+, where a test for ontology properties failed (ncbo/ontologies_linked_data#106)
  • Fixed an issue that caused Zlib::GzipWriter runtime errors during ontology processing (ncbo/ontologies_linked_data#107)
  • Removed a workaround that was implemented to address a bug in AllegroGraph v6+, which caused certain SPARQL queries to fail. AllegroGraph v7.0.1 release has addressed the issue (ncbo/goo#104)
  • Fixed an issue that caused runtime errors when running the code against Ruby 2.7.0 and Ruby 2.7.1 (ncbo/ontologies_api#69)
  • Fixed an issue, where a search on term id with exact match returns irrelevant results (ncbo/ontologies_api#57)
  • Fixed an issue, where a call to the class descendants endpoint fails if properties are included (ncbo/ontologies_api#54)


BioPortal 5.16.0 (2020-April-16)

New Features

Bug Fixes

  • Fixed an issue with AllegroGraph request chain breaking with existing Goo code (ncbo/goo#101)
  • Fixed an issue, where no parsed ontology records appeared in AllegroGraph after ontology has been parsed (ncbo/goo#102)
  • Fixed an issue with the paging calls returning wrong results in AllegroGraph (ncbo/goo#103)


BioPortal 5.14.0 (2019-December-09)

  • Implemented a number of enhancements that drastically improved performance of the class descendants call (metadatacenter/cedar-project/issues/#980)
  • Introduced a new version of owlapi-wrapper (OWL API v4.5.13)
  • Updated Solr to version 8.2.0; introduced changes to the config files to conform to the latest version of Solr
  • Updated code to use secure protocol for password reset URLs (ncbo/ontologies_linked_data#98)


BioPortal 5.11.0 (2019-February-13)

  • Implemented the ability to index and efficiently search ontology branches (ncbo/ontologies_linked_data#90)
  • Added path_to_root functionality to provisional classes
  • Migrated code to Google Analytics API v0.10; updated the library and the method calls to the new signatures
  • Added the ability to query properties on class descendants endpoint


BioPortal 5.8.0 (2018-April-26)


BioPortal 5.6.0 (2017-December-19)


BioPortal 5.3.1 (2017-May-22)

  • Fixed an issue that prevented the HIV ontology from parsing.
  • Fixed an issue that caused a 404 error in the BioPortal user interface when attempting to view the class tree of the HIV ontology.
  • Fixed an issue that prevented proper calculation of the set of root classes for the HP ontology.


BioPortal 5.3.0 (2017-May-02)

This API-only release adds a suite of REST endpoints for retrieving ontology properties. It also addresses limitations with our auto-generated API documentation.

New Features

Bug Fixes

  • Fixed a bug that prevented the API documentation from being auto-generated for ontology properties endpoints (ontologies_api/issues/33).


BioPortal 5.1.0 (2017-Apr-05)

This is an API release, which adds two new REST endpoints as well as a number of fixes and enhancements, designed to improve the asynchronous processing of ontology data.

New Features

Enhancements

  • Improved logging of the CRON job processing
  • A more robust error handling of the CRON batch operations
  • A new CRON task that allows indexing ontology properties
  • An enhanced ontology processing script that now accepts a list of tasks to be performed

Bug Fixes


BioPortal 5.0.0 (2017-Feb-06)

This release represents an overhaul of our user interface, using bootstrap as the front-end framework to enable immediate and longer-term improvements. (Since the October 2016 release, we have also made a number of minor changes, mostly under the hood, and recently added a few significant features to the Recommender; Release Notes will be added shortly for those changes.)

Please Note: Although we are aware of some bugs that have surfaced since the transition, so far they have been relatively minor and most can be worked around by re-sizing the page or changing tabs. We will be working to squash those bugs in the next few days, so please bear with us for this brief period.

Enhancements

  • Released new BioPortal user interface, including the features described below.
  • Implemented new UI framework based on boostrap, enabling cleaner management of all UI elements.
  • Redesigned the front page to provide cleaner and more informative look and feel, and put key features front and center.
  • Added graph to show top ontology access counts, replacing table with similar information.
  • Redesigned header to move most links to the menu bar, simplifying header and unifying it across all pages.
  • Redesigned footer to include appropriate and cleanly presented content, including social links, unified across all pages.

Bug Fixes

  • Fixed an issue with the prompt for the ontology search on the front page, which would not produce desired results.
  • Fixed layout issues in front page header.
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