EMBOSS: Project Meeting (Mon 22nd November 10)
Minutes of the meeting of 8th November 2010 are here.
Peter has updated list and select types in ACD to support the use of '*' for all values. This is useful for several applications as a default or a user-supplied value.
Peter has added applications to index EDAM, OBO files and DRCAT.
Mahmut is working on a vectorstrip issue.
Valgrind also reports an error from get_addrinfo which should be added to the suppression list.
Peter has modified the ajindex code to automatically convert keys to lower case and to replace spaces with underscores. A new function ajStrFmtQuery does the transformations.
Peter has extended the possible inputs for lists and selects in ACD to support the use of '*' for "all options". This is only allowed where the maximum number of values matches the number of possible values.
Michael has some configure changes to support the Intel icc compiler.
Ensembl now has a version 60 which will need migration.
Generating a cachefile will need access to DB definition internals. This may be a common issue with BioMart access, and possibly also DAS.
One approach is an application to connect once to a server and dump a list of databases which can become a public list with a link in the emboss.standard configuration file.
For Ensembl, it would be helpful to have a list of database aliases to avoid duplicating DB definitions for all possible names. This may also apply to BioMart and DAS.
The topic name space has been simplified into fields of study for use by BioCatalogue.
Peter will add new applications that use the EDAM relationships for searches. Each relationship is specific to certain name spaces or branches.
Jon has removed the inverse relationships as these can be automatically generated or inferred by reasoners. For example, is_format_of is retained, but has_format has been removed. If users need them, we can regenerate them for any release.
EDAM term names are being standardized with the consistent use of prediction, detection, etc.
Matus is updating EDAM format terms using new terms found in DRCAT.
Matus will continue to work on EDAM. A paper is in preparation. Matus will visit next week, then go to the Berlin semantic web conference with Jon.
Two other ontology projects at EBI are interested in OWL representations of OBO data.
Jon has checked with EBI's ontology lookup service (OLS) who have access to a developer machine to avoid the need to use anonymous CVS on Open Bio.
The EMBOSS distributed with fedora 14 failed to run any application. There is a problem with the va_list architecture when AMD64 is defined. There is also an issue with using an external plplot, but it is now using the EMBOSS_supplied version.
After the recent air conditioning failure in the EBI machine room, the EMBOSS server rebooted successfully.
The indexes will be sent today.