EMBOSS: Project Meeting (Mon 11th April 11)


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

1. Minutes of the last meeting

Minutes of the meeting of 4th April 2011 are here.

2. Maintenance etc.

2.1 Applications

Mahmut fixed an issue in dassources and is now searching for DAS servers that provide parent tags for multiple location features.

The application now reads more DAS sources, with a fix to HTTP redirection where the redirect omits the host address.

2.2 Libraries

Peter found and fixed a bug in tables with numeric keys. As the key is always passed by reference, the key must be created each time. The bug only affects the new query language - in the other case where numeric keys are used the key is the address of a page number in a cache in ajindex.c which is a new address for each cached page. The fix is to create Const versions of all the numeric key table constructors (for use by ajindex.c and to ensure keys for non-const tables are allocated each time they are put into the table.

Mahmut has updated the dbfetch access method to look for "Error 12 No entries returned" which is implemented by EBI external services as a 2002 open bioinformatics standard originally proposed by BioPerl.


2.4 Other

Mahmut has checked in changes to SoapLab job records.

3. New developments

3.1 Access methods

3.1.1 BioMart
Alan continues to work on BioMart caches.
3.1.2 Ensembl
Michael continues to work on the updates to support Ensembl release 61. Ensembl 62 is due for release later this month.

Ensembl uses tables with numeric keys, but passes them by value rather than by reference so will continue to use its own key and value functions.

3.2 Query language

Peter has implemented functions to merge two tables using the operators (OR, AND, NOT, EOR) of the new query language. Both tables are resized to the size of the largest table. Keys at the same hash array position are compared, and matches are processed. Any unmatched keys are then processed. Remaining keys in the second table are deleted at the end.

These functions make the implementation of the query language across all access methods very easy, with only a few lines of similar code for each of the 4 possibilities.

3.3 EDAM

Jon has created an identifier branch within EDAM and moved terms from the data branch where they are clearly identifiers.

4. Administration

Peter will submit to BOSC and to the ISMB technology track.

Jon will submit an EDAM presentation to the Bio-Ontologies SIG.

5. Documentation and Training

Peter circulated the response to the first Annual Report on the current grant. Most suggestions to update the website and provide training courses are already in hand, waiting for the books to be published.

6. User queries and answers

All done.

7. AOB


8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 18th April. Peter will be away.

The following two Mondays will be public holidays.