EMBOSS: Project Meeting (Mon 13th Jun 11)


EBI: Peter Rice, Jon Ison, Mahmut Uludag,
Apologies: Alan Bleasby, Michael Schuster

1. Minutes of the last meeting

Minutes of the meeting of 6th June 2011 are here.

2. Maintenance etc.

2.1 Applications

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.

2.2 Libraries

Peter fixed a bug in table merging that was detected by the extended testing of the query language.


2.4 SoapLab

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 ChEBI.

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 this week.

New applications for other data types can be added after the release.

3.3 EDAM

Jon is completing the definition of all relations and the cleanup of the EDAM namespaces. A completed version will be ready later this week.


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.

4. Administration

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 a problem.

5. Documentation and Training


6. User queries and answers

All done.

7. AOB

Peter attended a successful testing session for the new EBI e-Learning courses last week. New EMBOSS courses can follow the release.

8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 20th June, relocated to room A2-33.