EMBOSS: Project Meeting (Mon 29th June 09)
Peter Rice (at BOSC/ISMB/ECCB 2009 conference)
1. Minutes of the last meeting
Minutes of the meeting of 22nd June 2009 are
2. Maintenance etc.
Mahmut reported logging problems and issues of multiple
deployment in the same tomcat when using METRO. The issues were
resolved by returning to JAXWS 2.1.7.
The new SoapLab2 release on Friday looks healthy. Two rarely used
methods are missing from the API. Mahmut will restore them.
Mahmut will check the documents directory for the 'i' box in Jemboss.
3. New developments
Alan continues to work on the Ensembl API. He has a test
program that successfully downloads information from the main server at
Jon is working on the public data resources cross-reeferenced
by SwissProt and EMBL. He has updated "dbxref.dat" which is derived
from SwissProt's "dbxref.txt" file. The new file has additional known
data resources from the recently published ELIXIR database survey by
Chris Southan, giving a total of 600 databases, of which 150 are
cross-referenced by the current main databases.
The fields in the file are:
- ID - unique name, using the DR ine code or acronym if available
- DESC - a short text usually taked from dbxref.txt
- SERVER - The URL of the main database server
- DB_CATEGORY - defined in dbxref.txt
- EDAM_TYPE - parent node from EDAM if listed
- SWISSPROT_LINK - type of link (explicit, implicit, noen) from SwissProt
- QUERY_TERMS - Accession, ec_number etc with associated URL
- LITERATURE_REF - PubMed or DOI reference (difficult to maintain,
dropped from the file)
- CONTACT_INFO - removed from the public copy
- STATUS - supported by EMBOSS, referenced from sequence databases,
Jon has also been working on library code to use the dbxref.dat
5. Documentation and Training
Jon sent sample documents to the publishers in Word 2003
Peter is away, but will work on the book texts between now and
6. User queries and answers
All done this week.
8. Date Of Next Meeting
The next meeting will be on Monday 6th July.