BioPortal Release Notes

Please note: this page is deprecated and no longer updated.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 Virtual Appliance release notes
• BioPortal 4.x release notes
• BioPortal 3.x release notes
• BioPortal 2.x release notes

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

Bug Fixes

• Fixed a bug that caused Mapping Submission IDs query to fail in AllegroGraph (ncbo/ontologies_linked_data#120)
• Fixed a bug that prevented UMLS ontologies from being processed in AllegroGraph (ncbo/bioportal-project#215)
• Fixed a security vulnerability

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

• Fixed the 4store health status check API (ncbo/goo#112)

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

• The mapping counts generation script failed to properly count mappings between ontoloigies (ncbo/ontologies_linked_data#88)
• Reported mapping counts between ontologies are always higher than the actual counts (ncbo/ontologies_linked_data#115)
• Incorrect mapping count statistics generated for some ontologies (ncbo/ontologies_linked_data#94)
• Empty pages in paged result sets (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 (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

• Fixed a deprecation warning `Redis#exists(key)` will return an Integer in redis-rb 4.3 (ncbo/sparql-client#3, 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 (ncbo/bioportal_project#165). The API signature is as follows:
  http://data.bioontology.org/search?ontologies=NCIT&sort=prefLabel
• Implemented the ability to retrieve sorted descendant classes via the subtree search endpoint (ncbo/bioportal_project#165). The API signature is as follows:
  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 (ncbo/ontologies_linked_data#105)

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

• Full integration with the AllegroGraph Semantic Graph Database; 4store backwards compatibility assured (ncbo/bioportal_project#122, ncbo/goo#100)

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)

• Implemented a configurable number of retries for 4store failures (ncbo/ontologies_linked_data#84)
• Added a script for running SPAM deletion form the command line, added provisional classes to SPAM deletion artifacts (ncbo/ncbo_cron#13)
• Bug Fix: Recommender fails when input includes the word "concept" (ncbo/ncbo_ontology_recommender#7)
• Fixed the pull process to ignore submission candidates that do not pass the OWLAPI parser (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 (metadatacenter/cedar-project/issues/#407)
• Developed an endpoint to retrieve all ontologies with extended metadata (metadatacenter/cedar-project/issues/#660)
• Added the ability to sort terms in "/roots" and "/tree" endpoints (metadatacenter/cedar-project/issues/#409)

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

• Implemented an endpoint for retrieving property trees (ontologies_api/issues/27). Documentation. Example link.
• Implemented an endpoint for retrieving property roots (ontologies_api/issues/28). Example link.
• Implemented an endpoint for retrieving property parents (ontologies_api/issues/29). Example link.
• Implemented an endpoint for retrieving property children (ontologies_api/issues/30). Example link.
• Implemented an endpoint for retrieving property ancestors (ontologies_api/issues/31). Example link.
• Implemented an endpoint for retrieving property descendants (ontologies_api/issues/32). Example link.

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

• Implemented an endpoint for searching ontology properties (ontologies_api/issues/21). Documentation. Example link.
• Implemented an endpoint for retrieving a specific ontology property by its ID (ontologies_api/issues/22). 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 (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.