EMBOSS: Project Meeting (Mon 13th Jun 11)
1. Minutes of the last meeting
Minutes of the meeting of 6th June 2011 are
2. Maintenance etc.
Peter has a test script to compare ACD groups with the
hierarchy of EDAM topics. The aim is to check that applications are in
the correct groups according to their annotation. Some new groups may
be needed. Some applications clearly should move, for example the
"Editing" group which includes seqret.
Peter has added a new application ontogetcommon to find
the closest common ancestor for a set of EDAM terms. This is used by
the validation script to check that there is a common ancestor below
the top level 'topic'.
Peter has updated the documentation of input and output
formats to cover all ACD datatypes, and replaced some incorrect
references in the application documentation. The updated paged need
checking before uploading to the Wiki.
Peter fixed a bug in table merging that was detected by the
extended testing of the query language.
Mahmut reported on discussions about SoapLab release dates. The
EMBOSS release will come first, with SoapLab testing once we have
frozen the 6.4.0 code.
3. New developments
3.1 Access methods
Mahmut is implementing additional dbfetch formats so that
users can choose the data format more freely. Formats will be
included in the server cache file if they are supported.
Peter suggested adding more ontologies to the standard
distributed set, especially GO and SO. Jon also suggested
Peter proposed naming all server cache generation applications
with the prefix 'cache' and the name of the access method or resource.
3.2 New applications
Jon suggested some new applications to navigate ontology
hierarchies, and to report on the relations between terms.
All OBO relations are transitive, inherited by all terms below.
Peter believes that the current applications do honour this
inheritance, but will check before the release.
Peter is aiming to implement "URL" data retrieval from DRCAT
New applications for other data types can be added after the release.
Jon is completing the definition of all relations and the
cleanup of the EDAM namespaces. A completed version will be ready later
Peter will run the validation script on DRCAT to update any
changes to EDAM terms references.
Jon would like to create web pages for DRCAT
entries. Peter suggested making this a new output format
for drget to generate the pages automatically.
Mahmut reported that Alan has added a test to the
configure script to warn users of the need to run rsync to download
the taxonomy data and the index files.
has updated Jemboss install for one user who reported
5. Documentation and Training
6. User queries and answers
Peter attended a successful testing session for the new EBI
e-Learning courses last week. New EMBOSS courses can follow the
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 20th June, relocated to room