BioPortal 1.3 Release Notes
10 February 2009
Introduction
EVS adopted a version of the open source BioPortal as the NCI EVS terminology browser for use with caCORE EVS 4.x. BioPortal was developed by the National Center for Biomedical Ontology (NCBO). NCI modified the BioPortal code to support searching of Metathesaurus data and searching of terminologies by role, property and association name and filler value.
The NCI BioPortal was always intended to be an interim browser solution to support viewing of the NCI-hosted terminologies served through the LexBIG Terminology Server (first available with the EVS 4.0 release). The baseline design was intended to provide a common view to all terminologies and that has proven to be a significant limitation for users of the NCI Thesaurus and the NCI Metathesaurus. As such, the EVS team intends to build browsers that will be specifically architected and designed to address the concerns of our NCI Thesuraus and Metathesaurus users in the 2009 time frame. The details are still being discussed however, please feel free to submit your feedback to the BioPortal Feature Requests (http://gforge.nci.nih.gov/tracker/?atid=2087&group_id=90&func=browse) so that they will be taken into account.
For more information about the NCI BioPortal go to: http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/vocabulary/BioPortal_facts
Release History
Release / DateNCI BioPortal v 1.0 initial release / 07 November 2007
NCI BioPortal v 1.01 Bug Fix Release
/ 25 February 2008
NCI BioPortal v 1.1 Bug Fix Release / 27 June 2008
NCI BioPortal v 1.2 Release / 17 December 2008
NCI BioPortal v 1.3 Release / 10 February 2009
New Features and Updates
18932 - Implement Sort Function in BioPortal - We’ve implemented a more sophisticated method of sorting search results. More meaningful results will be displayed first.
18933 - Change Suggest New Term link to point to Metaphrase – The “Suggest New Term” link will now point to an existing mechanism for requesting new terms.
18934 - Section 508 compliance : text alternatives – This item furthered our efforts to be 508 compliant (accommodations in the application for people with disabilities).
18935 - Section 508: Add link to download PDF reader – This item furthered our efforts to be 508 compliant (accommodations in the application for people with disabilities).
Bugs Fixed Since Last Release
No bug fixes for this release.
Known Issues
For a list of known issues, in BioPortal refer to the GForge Bug Tracker site:
https://gforge.nci.nih.gov/tracker/?atid=1459&group_id=90&func=browse
*======*
* DATA RELATED ISSUES*
*======*
[GF #11256|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=11256&group_id=90&atid=1459] Search Results for MGED and GO ontologies returning unexpected results
--- Description:
Searches against MGED are not displaying expected results.
--- Resolution:
MGED is a data issue. The publishers of MGED put all the information that should
go into properties into comments. This saves them the trouble of actually declaring
and controlling their property types, but it makes it impossible for LexBIG to interpret
the data. This issue is currently being addressed.
NOTE: The Gene Ontology (GO) issues have been resolved.
[GF #14140|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=14140&group_id=90&atid=1459] Advanced Search occasionally returns different results than the Term Browser
--- Description:
Results returned from LexBIG doesn’t always match results returns from DTS.
--- Resolution:
This should be expected behavior. The underlying search algorithms in DTS and LexBIG
differ and that can impact the data results. In most cases you’ll get more data returned
from LexBIG than you do from DTS.
*======*
* FUNCTIONALITY ISSUES*
*======*
Below we make note of issues that we've seen but, may or may not be consistently occurring. If you
encounter any of these problems, please post your experience the EVS Users list
(http://list.nih.gov/archives/ncievs-l.html). We apologize in advance for any inconvenience these
issues may cause and we are working to address them as quickly as possible.
[GF #17335|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17335&group_id=90&atid=1458] Tree view not working
--- Description:
The tree display for source terminologies in Metathesausus is not working. It times out with a communications failure error message.
[GF #17337|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17337&group_id=90&atid=1458] Metathesaurus slow on PROD
--- Description:
Several aspects of performance on PROD are unacceptably slow when dealing with Metathesaurus
data. Concept details are displayed slowly as is the local neighborhood graph. License
acknowledgment click thru is also slow some of the time. The delay between requesting details
and seeing them is often so long that the request seems to have failed or else that there are
no details to display.
[GF #17541|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17541&group_id=90&atid=1458] Problem searching on CTCAE subsets
--- Description:
All results are not being returned for certain "deep" searches.
[GF #17723|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17723&group_id=90&atid=1458] HL7 always searches on attribute
--- Description:
HL7 search returns values that do not have a textualPresentation value containing "agent".
Instead, it is returning values that have ANY property containing the word "agent".
[GF #17731|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17731&group_id=90&atid=1458] Switches to advanced search after multi-terminology second search
--- Description:
Search criteria has switched to advanced search and the value displayed for the number of
results returned is zero even though the correct results were actually returned.
*======*
* FUNCTIONALITY NOTES*
*======*
These are functional items that are not issues or problems but, do need explanation.
[GF #17140|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=14140&group_id=90&atid=2088] Advanced Search occasionally returns different results than the Term Browser
--- Description:
Apelon uses a very straightforward substring matching; while LexBIG applies string
tokenize before comparing each token with the user specified search criteria, or words.
The match is performed according to stemming rules, not simple substring. The result is
that there *should* be a difference expected between results returned from the DTS backed
browsers and BioPortal (depending on the query).
[GF #17687|http://gforge.nci.nih.gov/tracker/index.php?func=detail&aid=17687&group_id=90&atid=2088] Period is treated as a space
--- Description:
The period '.' is used as a space character. For example, the following searches produce the EXACT same results:
Conceptual.Entity
Conceptual Entity
This becomes a problem when trying to do a "contains" search for concepts like: 2.16.840.1.113883.5.132