EVS Weekly Status Report (January 14 – January 18, 2008)
NCI Center for Bioinformatics and Information Technology
Project: EVS API
1. Key Accomplishments
1.1. EVS API
§ [GF#8678] User wishes to search by Synonym.
o The capability for searching synonyms is already available in EVSAPI 4.0. The user can use the searchDescLogicConcepts method to search for concepts that match with a specific property. In NCI Thesaurus, synonyms can also be found in FULL_SYN properties.
o Will extend the capability of the searchDescLogicConcepts method in EVSAPI 4.1 to allow users to search concepts by matching a property type such as PRESENTATION. Both Synonym and FUL_SYN are of this particular property type. Other property types are COMMENT, DEFINITION, INSTRUCTION, and GENERIC.
o Posted a code segment in GForge to illustrate how to use the existing searchDescLogicConcepts method to search for concepts by FULL_SYN or any other property.
o Started to implement a findCodedEntriesWithPropertyTypeMatching method in LexWrapper and make necessary modifications to LexAdapter to support search by property type.
§ [#7857] Grid Enable 3.2 EVS API
o Setting up local environment – Installation of JBOSS, LexBig, SDK and EVS API.
o Installed CaGrid training application
o Currently I’m running the caGrid tutorial for Introduce and trying to understand the product.
1.2. LexBIG API
§ None.
2. Production Support
§ None
3. Meetings
§ 1/15/2007 EVSAPI weekly meeting.
4. Planned Activities:
§ Enhancement of existing EVS tools
§ Execution of EVS/LexBIG task plan.
5. Issues and Recommended Resolutions:
§ None.
Project: Terminology Browser Applications
1. Key Accomplishments
1.1 NCI BioPortal
§ [GF#10877] Advanced Search does not accept multiple word search terms.
· Implemented. Search NCI Thesaurus for "Cellular Stress" using role "Biological_Process_Has_Initiator_Process" now returns:
§ Homeostasis
§ Inflammatory Response
§ Stress Response Signaling
§ [#11143] Major performance degradation over short timeframe
· Tested a new path finding algorithms on DEV. The new algorithm converges much faster than the previous one.
· Continue to explore other available means to improve the performance including root node and coding scheme caching
§ [#11241] List of ontologies should be alphabetized throughout the system.
· Implemented.
§ [#11076] Cannot browse SNOMED ontology.
· Mayo indicated that this issue can be resolved by loading SNOMED using the RRF loader that comes with LexBIG, version 2.2.1 alpha.
· Will reload SNOMED accordingly.
§ [#10996] ] Roles are duplicated in association drop down.
· Modified SearchResultsBean and DataConstants to show roles only for NCI Thesaurus.
§ In responding to caDSR team inquiry (subject: Source Identifiers in lWEXbig), developed a program for retrieving URN, formal name, local name, and version of ontologies from a LexBIG terminology server.
1.1. Terminology Open Portal (TOP)
§ Reviewed design artifacts on the NCBO Gforge Site.
2. Production Support
§ None
3. Meetings
§ 1/15/2008 BioPortal Weekly Meeting.
4. Planned Activities:
§ Continued execution of NCI BioPortal 1.1 task plan.
5. Issues and Recommended Resolutions:
§ None.
Project: Terminology Development Tools
1. Key Accomplishments
§ NCI Protégé GUI/Workflow
§ No status reported
§ NCI Semantic Wiki (BioMedGT Wiki)
o No status reported
§ OWL Classification Services
o No new items
2. Production Support
§ None reported.
3. Meetings
4. Planned Activities:
5. Issues and Recommended Resolutions:
General: Operations
1. Key Accomplishments
§ JP (10947) – Reviewed all external sites for CBIIT references.
§ JP, RW Completed Protégé Server Build in Dev with Rob observing.
§ JP Completed Protégé Server Build in QA environment.
§ JP Released new version of Protégé into Production w/ Gilberto.
§ TS – (10465, 10471)Finished Snomed and Meta load procedures.
§ TS – Finished list of NCI Thesaurus BioPortal QA searches
2. Other Support
§ RW (11031) Load Metathesaurus 2007_09D for Metaphrase Browser
§ RW (11406) NCI Thesaurus 07.12e (DTS)
§ JP (10365) – Latest version of NCI Thesaurus (7.10d) is now up on Bioportal QA site, and is awaiting stage.
§ JP (10788) – December GO load awaiting QA.
§ JP (10149) – MedDRA 10 now up in Bioportal production site.
3. Meetings
§ TS,RW,JP – Mon - EVS Operations
§ RW, JP – Tue - LM staff meeting
§ TS, RW, JP – Wed - Mayo weekly meeting
§ TS, RW, JP – Fri – SMW weekly meeting
§ TS, RW, JP – Fri - Protégé weekly meeting
§ TS – Fri Gilberto meeting about LexBIG QA
4. Issues and Recommended Resolutions:
§ EVS DEV and QA database tiers are under maintenance this weekend to address a bug found with the last Oracle patch, which is affecting our internal database updates.
5. Planned Activities:
§ RW (11759) Compare MGED in LexBIG to DTS
§ RW (11755) Compare GO in LexBIG to DTS
§ RW (11754) Compare representation of NCIt in LexBIG to DTS
§ RW (11797) January GO for DTS
§ TS Continue working with Sima and Konrad to resolve her caCORE 3.2 issue
§ TS (10466) Document loading MGED into LexBIG
§ TS (11758) Compare Snomed in DTS to LexBIG
§ TS (11760) Compare MedDRA in DTS to LexBIG
§ TS (11764) Compare Meta in Metaphrase to LexBIG
§ JP (10471) – Currently reviewing documentation of Metathesaurus load into Lexbig.
§ JP (11839) Perform Snomed Load once the loader machine is available.
§ JP Perform Protégé QA build for 1.2.1 release.
Cross Project Technical Leadership/Management
Staff: C. Griffin, J. Beasley
1. Key Accomplishments
§ Generated Weekly Report
2. Meetings
§ Many AdHoc Meetings
3. Planned Activities:
§ Finalize Communications Plan in support of new EVS Organization, review and distribute
§ Finalize EVS Coding Standards
§ Finalize Standard Task Plan Template
§ Finalize Technical Document Templates
§ Use Case Document
§ Design Document
§ Implementation Specification Document
4. Issues and Recommended Resolutions:
§ None.