EMBOSS: Project Meeting (Mon 25th January 10)
Alan reported that a new JASPAR database release is available, with a new directory and FTP structure. The developers have been asked to provide advance warning of such changes in future. Alan rewrote jaspextract and jaspscan. The transcription factor binding site matrices now have version numbers as a '.1' suffix. There are many more files in the directory. jaspextract has to use the suffixes to find the file types and create JASP subdirectories. Peter will update the QA tests.
Jon has renamed data structures specific to applications to remove any 'Aj' or 'Emb' prefix.
Alan has updated edamclean to meet the coding standards.
Alan suggested replacing system calls, for example to run "mkdir", with code that can be supported on Windows. Peter offered to work through the system calls replacing them with new functions.
Peter has modified ajFileoutNameDirS to always add a file extension.
Peter has fixed a bug in reading refseqp format protein data.
Peter is testing eclipse as a development workbench. The spell checker has been used to update documentation in the source code. There is a very useful function index. To make the views of source files easier, .cvsignore files have been defined.
Peter would like to add new data formats, including completing work on SAM and BAM sequence and alignment data. Further work is needed to provide coverage for non-sequence data resources.
Jon raised issues of maintenance for the database registry. We need to agree a maintenance format, possibly in addition to a distribution format.
Jon noted that OBO recommends "intersection_of" as a way to combine two terms.
The ONDEX group at Rothamsted are considering using EDAM internally within ONDEX, but they will need a model of relationships between entities (e.g. 'gene encodes protein').
Jon reported on the Amsterdam workshop on EDAM and BioXSD. A WSDL syntax was agreed and the format for a purl.org reference. We need the registry to define the syntax of the page to which a persistent URL will resolve. As an initial proposal, we could use the OBO format of the term definition.
The coverage of EDAM is good, with very few extra terms needed. Some additions are needed to support BiOXSD annotations.
Heinz Stockinger (SIB) has asked colleagues to review the content of EDAM. SIB will use EDAM to support their website tools.
A beta release of EDAM will be needed soon to provide a stable starting point for users. At this point term identifiers will have to be fixed and terms can no loner be removed. Changes will have to be through obsolete terms and definitions of synonyms.
DTU will organize a workshop on annotation. There will be a follow-up third EDAM meeting in Amsterdam.
EBI has started a series of internal meetings for those interested in ontologies.
Alan will try building on Tom's old mini Mac.
Peter has tested the new Thunderbird 3.0 which seems to be working well now.
The XML documents reflect the new package structure. Personal email addresses have been removed from the application documentation, replacing them with the emboss-bug address.
EBI training and outreach are interested in trying the book text as online training courses.
The EMBOSS web site will need a new home page and new structure using the book text and Wiki contents.