EMBOSS: Project Meeting (Mon 27th Jun 11)
1. Minutes of the last meeting
Minutes of the meeting of 20th June 2011 are
2. Maintenance etc.
Peter has redefined application groups for all EMBOSS and
EMBASSY applications. Each group has a defined EDAM term which should
be in the ancestry path for at least one topic relation in an ACD file
that includes the group. New groups were added for data retrieval, and
missing groups added to the hierarchy. A new
application ontogetcommon> to return the common ancestor of a
list of terms was written specifically to test group definitions.
Peter looked into a report from a user at EBI that
concatenated PDB files failed. As this is not valid PDB format it can
be treated as a feature, not a bug.
Mahmut fixed a problem caused by primer3_core compiled under
the wrong operating system for LSF.
Peter reported QA tests and valgrind tests were all working on
Peter has scripts to update the html and text documentation
Makefiles, preserving the current records where no split is needed..
Mahmut is testing Jemboss interfaces and adding a Nimbus look
and feel option selectable under "preferences".
3. New developments
3.1 Access methods
Peter has added several OBO ontologies to the release,
including the Gene Ontology and Sequence Ontology. They are defined as
GO, SO, etc. and have dbxobo index files.
Mahmut has updated CHADO access.
Mahmut can use the dbfetch access method to find
cross-reference information. It is possible to retrieve and parse the
full entry, or to retrieve reference information.
Michael is preparing cache files for Ensembl data sources.
3.2 New applications
Peter is adding applications to fetch URLs from DRCAT entries
where no EMBOSS-parsable format is available. The applications will
use definitions from EMBL and SwissProt cross-references to guess at
the identifier, or an explicit user definition, where there are
several queries to choose from.
Peter has added new applications godef and goname
to search the gene ontology in the same way as the equivalent EDAM
New applications could be added to use GO cross-references.
Application edamid is not useful. Retrieval from EDAM by
identifier is trivial with ontoget. The edamid
application has been deleted.
Peter is adding ACD datatypes for assembly and variation though
these will not be used until after the release.
Peter has added conditional tests to the emboss.default and
emboss.standard file parsers. This allows servers dependent on AXIS2C
or on SQL to be included only when they were part of the build.
5. Documentation and Training
The Open Bio cvs view is not working. Anonymous CVS is also occasionally failing.
Peter proposed considering github in future for shared
Jon will set up a new website on emboss.open-bio.org for testing.
Peter will copy application documentation to the Wiki.
Copies of the CUP books have arrived and look good.
Peter will take sample copies to ISMB and BOSC.
6. User queries and answers
Michael suggested following discussions on BioStar and
SeqAnswers to catch EMBOSS_related issues.
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 4th July.