EMBOSS: Project Meeting (Mon 29th March 10)
Peter has updated the handling of missing values in ACD. Past releases used '.' as a general missing value, but this is inappropriate for directories. The missing value is now an empty string, specified as '' for a parameter. A bug in processing -qualifier='' has been fixed to correctly return an empty string.
Alan has timeouts and SIGALRM working under Windows. The function name is the same but the underlying method is different.
Alan added some casts to the new ajsys.c code for compilation on Microsoft compilers and modified the use of open and read to use Microsoft preferred variants on Windows systems.
Alan reported that the sequence type can be inferred from the name of an attribute for current marts. We can make a list of known sequence attribute names to generate a sequence type of 'nucleotide' or 'protein'.
The EDAM tool function and datatype branches could be simplified for use by BioXSD and by the reviewers at the Swiss Institute of Bioinformatics.
The datatypes branch should be specifically for semantic descriptions of datatypes. Terms that relate to syntax should be moved to a separate "formats" branch with relations between the formats and datatypes.
Jon mentioned possibilities for maintaining the list of databases in other formats. NO final decision was reached.
Jon has been evaluating ontology editors, especially for managing OWL definitions. One possibility is TopBraid which costs $500. Jon will check what other OBO Foundry ontologies use where they provide (or maintain) an OWL version.
Jon described the Sequence Ontology teams new browser which gives a useful graphical view of ontology terms and structure.
Alan described the mount point for the internal web server. Files moved to /shared/www/html will appear in the internal web server. So far we are only using the Wiki.
A future meeting should consider requirements for the next release.
Peter will write a script to check all URLs in the book source files.
Alan updated the Developer's Manual to cover the setting of compiler warnings and configuring SQL access through MySQL or PostGres.
Jon welcomes suggestions for the front covers. We may need to let the publishers choose something appropriate.