BioPortal Release Notes

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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:


Contents


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

  • A fix to the test runner script that detects when a test fails instead of always reporting SUCCESS (ncbo/ontologies_linked_data#111)
  • Fixed a bug that prevented the ontologies report refresh from completing successfully (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 (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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