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 4.6 (May 8, 2014) ==
+
'''<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Please note: this page is deprecated and no longer updated.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>'''
  
−
* Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.
+
BioPortal REST API release notes: https://github.com/ncbo/ontologies_api/releases<br>
−
* Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.
+
BioPortal web application release notes: https://github.com/ncbo/bioportal_web_ui/releases
−
* Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)
 
−
* Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)
 
−
* Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything.
 
−
* Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.
 
−
* Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.
 
−
* Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.
 
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* Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.
 
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* Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.
 
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* Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.
 
−
* Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.
 
−
 
−
 
−
We have today shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We have provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at:
 
−
http://data.bioontology.org/documentation
 
  
−
== BioPortal Release 4.0 ==
 
  
−
The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.
+
''This page contains software release notes for the 5.x series of [http://bioportal.bioontology.org/ BioPortal].'' 
  
−
The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today).  We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive.  Draft documentation for the new API is available at
+
Use the following links to access release notes for the BioPortal Virtual Appliance, and older versions of BioPortal:
−
http://data.bioontology.org/documentation
 
  
−
BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.
+
* [[BioPortal_Virtual_Appliance_Release_Notes|BioPortal Virtual Appliance release notes]]
 +
* [[BioPortal_4_Release_Notes|BioPortal 4.x release notes]]
 +
* [[BioPortal_Release_3_Release_Notes|BioPortal 3.x release notes]]
 +
* [[BioPortal_Release_2_Release_Notes|BioPortal 2.x release notes]]
  
−
With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.
 
  
−
Temporary Changes
+
__TOC__
−
* All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.
 
−
* “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet
 
−
* The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type.
 
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* We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.
 
−
* Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.
 
  
−
Permanent Additions
 
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* New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.
 
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* We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.
 
  
−
Permanent Subtractions
+
== BioPortal 5.22.1 (2021-July-08, 2021-August-10) ==
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* Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.
 
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* We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.
 
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* We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.
 
  
−
== BioPortal Release 3.12 ==
+
'''Bug Fixes'''
−
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.
 
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* Improved some default layouts in the visualization system.
 
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* Updated automated mappings for all ontologies.
 
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* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.
 
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* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].
 
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* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.
 
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* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.
 
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** NIF PubMed Health: Tests
 
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** NIF Drug Related Gene Database
 
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** NIF Gemma
 
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** NIF Integrated Disease View
 
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* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.
 
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* Fixed web service failure when attempting to retrieve all concepts from several ontologies.
 
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* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.
 
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* Fixed Search to work correctly in MeSH.
 
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* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses
 
  
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(Release February 2013)
+
* 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])
 +
* Fixed a bug that prevented UMLS ontologies from being processed in AllegroGraph ([https://github.com/ncbo/bioportal-project/issues/215 ncbo/bioportal-project#215])
 +
* Fixed a security vulnerability
  
−
== BioPortal Release 3.10 ==
 
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* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.
 
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* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.
 
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* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.
 
−
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.
 
  
−
(Release July 2012)
+
== BioPortal 5.21.0 (2021-May-18) ==
  
−
== BioPortal Release 3.9 ==
+
'''New Features'''
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* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better”  ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org.  *
 
−
 
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* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *
 
−
 
−
* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).
 
−
 
−
<nowiki>*</nowiki>  This item was requested via the User Support mailing list. Thank you for your comments and suggestions!
 
  
−
(Release June 2012)
+
* 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])
  
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== BioPortal Release 3.8 ==
+
'''Bug Fixes'''
−
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other.  The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*
 
−
 
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* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies.  A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*
 
−
 
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* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs).  A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*
 
−
 
−
We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.
 
  
−
<nowiki>*</nowiki>This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!
+
* Fixed the 4store health status check API ([https://github.com/ncbo/goo/issues/112 ncbo/goo#112])
  
−
(Release May 2012)
 
  
−
== BioPortal Release 3.7 ==
+
== BioPortal 5.20.0 (2021-April-02) ==
−
* Updated term mappings generated by LOOM
 
−
* Added boolean functionality to Search Web service and UI
 
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* Updated ontology content for the Resource Index
 
−
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org
 
−
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*
 
−
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*
 
  
−
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!
+
'''New Features'''
  
−
(Release April 2012)
+
* 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])
  
−
== BioPortal Release 3.6 ==
+
'''Bug Fixes'''
−
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:
 
−
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org
 
−
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org
 
−
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org
 
−
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org
 
−
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org
 
−
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org
 
−
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org
 
−
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org
 
−
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.
 
−
* Major Updates and Fixes
 
−
** Updated the ontologies used by the Annotator Web Services*
 
−
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*
 
  
−
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!
+
* 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])
  
−
(Release January 2012)
 
  
−
== BioPortal Release 3.5 ==
+
== BioPortal 5.19.0 (2020-September-04) ==
−
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display
 
−
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation
 
−
* Improved Annotator Web service response performance by 5-10x*
 
−
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)*
 
−
* Updated Ontology Recommender algorithm to provide better recommendations*
 
−
* Added display of matched terms for Ontology Recommender*
 
−
* Added Web service to get all namespaces for an ontology*
 
−
* Bug Fixes
 
−
** Display user-friendly names for RxNorm ontology properties
 
  
−
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!
+
'''New Features'''
  
−
(Release December 2011)
+
* 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
  
−
== BioPortal Release 3.4 ==
+
'''Bug Fixes'''
−
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*
 
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* Limited access to “Private” ontologies via the Browse and Search pages
 
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* Added backend support to allow multiple administrators for a single ontology*
 
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* Added ability to copy to the clipboard a permanent link to any BioPortal term* 
 
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* Bug Fixes  
 
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** Resolved issue causing search to not display all matching terms*
 
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** Fixed Term Mappings tab display for IE 7 & 8*
 
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** Fixed RDF Ontology Download Web service
 
−
** Fixed link to the list of resources included in the Resource Index*
 
  
−
<nowiki>*</nowiki> This item was requested via the User Support mailing list and the NCBO User Group. Thank you for your comments and suggestions!
+
* 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])
  
−
(Release October 2011)
 
  
−
== BioPortal Release 3.3 ==  
+
== BioPortal 5.18.0 (2020-July-14) ==
−
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
 
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* Updated Search page to remove Flash
 
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* 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
 
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* 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.
 
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* Bug Fix
 
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** Fixed the Filter by Account on the Mappings tab
 
  
−
(Release date September 2011)
+
'''New Features'''
  
−
== BioPortal Release 3.2 ==
+
* 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])
−
New features include updates to the Web interface and Web services:
+
* 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])
−
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender 
+
* 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])
−
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service
+
* 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])
−
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples
+
* 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])
−
* Added support for access control for viewing ontologies
 
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* Added link to subscribe to BioPortal Notes emails 
 
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* Synchronized “Jump To” feature with ontology parsing and display
 
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* Added documentation on Ontology Groups
 
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* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter
 
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* Removed the metric "Number of classes without an author"
 
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* 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
 
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** 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
 
  
 +
'''Bug Fixes'''
  
−
'''''Firefox Extension for NCBO API Key''''':
+
* 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])
−
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''''':
 
−
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 5.17.0 (2020-June-22) ==
−
New features include updates to the Web interface and Web services:
 
−
* Support for loading OWL 2 ontologies
 
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* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key.
 
−
* Browsing of ontologies that contain large numbers of sibling terms
 
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* Icons for is_a and part_of  are displayed for OBO format ontologies
 
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* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology
 
−
Bug Fix
 
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* 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)
+
'''New Features'''
  
−
== BioPortal Release 3.0 ==
+
* 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
−
New features include updates to the Web interface and Web services:
+
* 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
−
* Web interface updates
+
* 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])
−
* 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
+
<pre>
−
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology
+
Usage: bundle exec ruby run_tests.rb [options]
−
* 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
 
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** Data indexed with new ontologies from BioPortal
 
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** PubMed data now available for abstracts published in 2010
 
  
−
(Release date May 19, 2011)
+
    -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>
  
−
== BioPortal Release 2.6.4 ==
+
'''Bug Fixes'''
−
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)
+
* 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 Release 2.5 ==
 
−
New features in this release include the following:
 
−
* 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.
 
  
−
* 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.)
+
== BioPortal 5.16.0 (2020-April-16) ==
  
−
* Prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).
+
'''New Features'''
  
−
* Prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org
+
* 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])
  
−
* Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for  viewing instances shortly.
+
'''Bug Fixes'''
  
−
* 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.
+
* 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])
  
−
* Preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings
 
  
−
[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services
+
== BioPortal 5.14.0 (2019-December-09) ==
  
−
(Release date June 9, 2010)
+
* 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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