BioPortal Release Notes

BioPortal Release 4.25 (March 2016)

In this release we fixed problems that were causing regular outages of the Recommender, and sometimes affecting the main BioPortal system. Our troubleshooting documentation has been updated based on our experience.

Other minor changes included fixing issues with acquiring DRON and NCIT ontologies (NCBO-1651, NCBO-1655), and fixing the metrics endpoint (NCBO-1660),

BioPortal Release 4.24 (February 2016)

Enhancements

• Implemented an ability to create and manage provisional relations on a provisional class (NCBO-1614)
• Implemented an ability to search for all subclasses of a class, including provisional classes (NCBO-1624)

Bug Fixes

• Fixed a subtree root search to properly include provisional classes when an appropriate parameter is passed to the endpoint
• Fixed an issue with CHEBI ontology not being pulled from its download location (NCBO-1639)
• Fixed a display issue where BioPortal displayed a nested 404 page when an error occured rendering the class tree (NCBO-1623)
• Fixed a bug in NCBO Tree widget that ommitted a "+" sign for classes that have children (NCBO-1574)
• Fixed an issue with search not returning entries for some existing classes of NCBI Taxonomy (NCBITAXON) (NCBO-1591)
• Added sample link to this section of the API documentation (NCBO-1612)
• Updated the Resource Index UI to default to hierarchical classes (classes and descendants) (NCBO-1622)
• Fixed a broken pull location for ONLIRA ontology (NCBO-1627)

BioPortal Release 4.23 (January 2016)

• Added an additional server to the group that serves the BioPortal UI for improved performance.
• Fixed an issue with the ontology analytics REST endpoint returning an empty set.
• Fixed an issue that caused a breakage of the ontology submissions REST endpoint (NCBO-1590).
• Fixed an issue that prevented search from returning some terms in the DOID and NCBITAXON ontologies (NCBO-1578, NCBO-1588).
• Fixed an issue that caused some of the mapping display dialogs to freeze (NCBO-1562).
• Fixed an issue where using the "Jump To:" search box on the ontology classes page caused the UI to hang (NCBO-1506).
• Fixed an issue that prevented the DDO ontology from parsing (NCBO-1603).
• Fixed an issue that caused an error in the virtual appliance if ontology analytics data is empty. Thanks to Vincent Emonet for the contribution.
• Fixed an issue on the Annotator page with an incorrect parameter in the REST API link to retrieve results formatted as JSON. Thanks (again!) Vincent Emonet for the contribution.

BioPortal Release 4.22.1 (December 2015)

This is a minor release that addresses an issue of system instability caused by a bug in our HTTP caching layer that resulted in a significant load on our backend services.

Enhancements

• Added configuration parameters at the UI layer that allow for a greater control over debugging issues with HTTP caching.

Bug Fixes

• Fixed a bug in the HTTP caching code that caused multiple identical requests to bypass the cache and trigger extraneous requests to the REST API. The bug fix resulted in a significant performance boost to both the front- and back-end services.

BioPortal Release 4.22 (November 2015)

Enhancements

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

Bug Fixes

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

BioPortal Release 4.21 (October 2015)

Bug Fixes

• Fixed an issue that caused class trees to reload every time a class was selected.
• Fixed an issue with BioPortal's term selection widget that caused raw HTML to be displayed in search results.
• Fixed a problem in the REST API that caused an internal server error when accessing nonexistent users. The API now correctly displays a 404 not found message.
• Fixed a bug that prevented flat tree ontologies from displaying in BioPortal.
• Fixed an issue that prevented the latest versions of the Gazetteer and Chemical Entities of Biological Interest ontologies from parsing.
• Fixed a problem that prevented visualization from working with private ontologies (thanks go to Eric Verbeek for this).

BioPortal Release 4.20 (August 2015)

This release includes minor fixes from several previous releases.

• Released a new version of the Ontology Recommender. This version is more flexible than the previous version and allows users to assign weights to the scores for various factors that influence the recommendation. In addition, some edge cases in the old system that resulted in bad recommendations have been addressed. This new recommendation system was developed independently by Marcos Martinez and then incorporated into our base code.
• Instances (individuals) in an ontology can now be accessed through the API. Documentation for this is available at: http://data.bioontology.org/documentation#Instance.
• Components have been added to the Annotator UI to allow users to exercise additional options available through the API.
• Icons now indicate non-subclass relationships in OBO ontologies. Previously it was not possible to distinguish visually OBO subclass from other OBO relations displayed in the tree (such as OBO part-of).
• The UMLS MeSH vocabulary is now displayed hierarchically. Previously it was displayed as a flat list of terms because of some problems with the hierarchical relation in the source that we were using.
• The Search API now allows search-by-name of provisional classes assigned to an ontology.
• The UMLS ontologies have all been updated to the latest 2015AA release.
• A new version of BioMixer with a simpler user interface has been incorporated into the system. This work was done by our collaborators at the University of Victoria.
• Created both a REST service and a UI for BioPortal application administration. This interface is automatically visible to VM administrators.
• Updated the framework of our system from RAILS version 2 to version 4.
• Fixed many bugs, especially those causing failures when parsing an ontology.

BioPortal Release 4.14 (February 2015)

This release includes minor fixes from several previous releases.

• The ontology summary page for each ontology now has a graph of recent history of the level of user-interface (UI) web traffic (number of page views) for that ontology. This graph is available under the “Metrics” box. See, for example, http://bioportal.bioontology.org/ontologies/SNOMEDCT . The raw data is also available for download in CSV format from the same location.
• The BioPortal home page now has a link that displays all ontologies in the system and the number of UI views for each ontology. Previously usage of only the top 5 ontologies were available.
• Users of our virtual machine now have the ability to plug in alternate concept recognizers for use by the annotator. To support these custom annotators, arbitrary parameters can be passed via the rest interface to the underlying concept recognizer. Documentation for how to make use of this feature is available on GitHub. Previously the “mgrep” concept recognizer was hardwired into the system and code modifications were required to employ another recognizer.
• Ontologies views can now be used for annotation. Previously only top level ontologies were available for use by the annotation system.
• All of PubMed has been indexed for use by the Resource Index for all terms in all ontologies in BioPortal. Previously only 18 months of PubMed data was indexed.
• We now provide for download, for all resources in BioPortal, files containing counts for term occurrence and co-occurrence (occurrence of pairs of terms in a document). These files can be used for research in enrichment analysis. Documentation of the files and how they might be used is available on GitHub.
• The ontology browse page now has a faceted interface that allows the list of displayed ontologies to be narrowed as desired. Previously all ontologies appeared in an alphabetical list but this became unwieldy with the 400+ ontologies that we now have.
• There is now a user-interface for displaying all of the properties in an ontology. If the properties were created in a hierarchy then this hierarchy is displayed. Previously only the class hierarchy was displayed. Properties were available programmatically though the REST interface but this information was not surfaced in the UI.
• Ontologies defined using SKOS are now supported. For these ontologies, the hierarchy is determined by the SKOS “broader” and “narrower” properties.
• We now allow download of all publically available ontologies in RDF. UMLS ontologies with restrictive licenses are excluded.
• We fixed a number of non-parsing ontologies and removed a bunch of low-content (“test”) ontologies.
• The system now contains the latest versions (2014AB) of all UMLS ontologies.
• We now treat all OBO synonym types as a BioPortal synonyms. Previously only the OBO “exact” synonym type was treated as a BioPortal synonym.
• We now notify by email the ontology authors if the nightly pull of their ontology fails.

BioPortal Release 4.10 (September 2014)

This release includes minor fixes from several previous releases.

• Reengineered the entire Resource Index to achieve better and more consistent performance and to align the Resource Index with the new BioPortal backend (released last year). In addition to allowing us to support additional resources, this revision removes a number of inconsistencies that resulted from the Resource Index using the old BioPortal backend.
• Upgraded the OWL and OBO parser to the latest version and reparsed all OBO and OWL ontologies. This reprocessing fixed a large number of problems with ontologies that either did not parse or that failed search indexing or metrics calculations.
• We now create and make available for download a comma-separated value (CSV) file for most ontologies. These files have one row/class and a standard set of properties in the columns. We cannot make these files available for ontologies if the license for the ontology does not permit it (e.g. SNOMED-CT and MedDRA).
• Fixed PURLS for all ontologies. There were a large number of ontologies for which the PURLs we created, in the old system or the new one, no longer worked correctly.
• Reworked the entire mappings system so that mappings will be always up-to-date with the latest version of the ontologies.
• Created a web page (http://bioportal.bioontology.org/validate_ontology_file) so that users can validate that their ontologies parse correctly with the latest version of the OWL/OBO parser.
• Removed a number of bogus ontologies and spam notes.
• Fixed implementation of “longest only” parameter in Annotator.
• We now reparse and reindex an ontology if the administrator of the ontology changes the metadata for the ontology. The reparse is necessary because the metadata contains information, such as the properties that contain synonyms or definitions, that influence the parsing and indexing.
• Recalculated metrics for all ontologies. This process filled in metrics for many ontologies that lacked them, and corrected the calculations of some metrics in other ontologies.
• We now allow the download of RDF (Turtle) files for UMLS ontologies whose license allows users to download them.
• Reindexing ontologies for search no longer interferes with the use of search on those ontologies. Previously search for an ontology was either broken or incomplete for an ontology that was being indexed.
• Added an ontology properties endpoint to the REST API. This endpoint allows a user to query for the properties used by an ontology.

As previously noted, we have permanently retired the old NCBO BioPortal API. New API documentation is available at http://data.bioontology.org/documentation.

BioPortal Release 4.6 (May 2014)

• 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.
• 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.
• 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.
• 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.
• 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.
• 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've shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We've 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 (September 2013)

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.

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 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.

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

• 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.
• 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

• 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.
• 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

• 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.
• We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.
• 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.

Previous BioPortal Releases

For release notes for earlier releases, see

BioPortal Release 3 Release Notes

and

BioPortal Release 2 Release Notes