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Please download and help test a potential 1.2.1 release candidate that is available at http://bioperl.org/ftp/birney/bioperl-1.2.1-rc2.tar.gz

If all goes well the official bioperl-1.2.1 will be released early next week.

GO::TermFinder will take a list of genes (any name that appears in an annotation file will do, though there are caveats for ambiguous names), an ontology file, and an annotation file, and determine the P_values for the observed frequency of annotation to those genes for each GO node. There are currently some differences between how the P-values are

The full announcement can be read here: http://bio.perl.org/pipermail/bioperl-l/2003-March/011707.html

In the March 2003 issue of Genome Technology, “Opposite Strand” contributor Gerald Barnett’s insightful article on “free choice for open source” is blighted by a gross misattribution. He writes that Open Bioinformatics Foundation has proposed that “all federally funded bioinformatics software should be released as open source.” In fact, the O|B|F has explicitly rejected this extreme and inflexible view, as specified in our January 2002 statement on public funding & open source, which states:

A new mailing list has been created for discussion of software system for genotypes, pedigrees, and linkage data at /mailman/listinfo/bioped-l

This is intended to build off the initial work done in Perl for bioperl-pedigree but is applicable to all who want to contribute to the design or implementation in any language. Database persistence and pedigree rendering are initial areas that will be addressed.

A release candidate for an eventual Bioperl 1.2.1 release is online at: http://bioperl.org/ftp/birney/bioperl-1.2.1-rc1.tar.gz

We need people to install and test this package on as many systems and architectures as possible.

Members of the caCORE team at the NCICB have been discussing if and how best to use LSIDs. Attached is an analysis of the two LSID Resolution proposals. The document also includes brief descriptions of two use cases that seem appropriate to us. We would be very interested in any responses to this analysis.

The document is also available at: ftp://ftp1.nci.nih.gov/pub/cacore/caBIO/lsid/lsid_memo.doc

Joshua Phillips SAIC Advanced Information Technology Center, Annapolis, MD NCI Center for Bioinformatics, Gaithersburg, MD Phone: (301) 402-7087

Andrew Farmer writes:

Here’s the current revision of my writeup on semantic standards; the only major difference between this and the version I sent out earlier is the addition of a section covering DAML-S, the extension of DAML to develop an upper ontology for describing services (complementary to WSDL).

MOBY PROJECT: TECHNICAL REPORT ON SEMANTIC STANDARDS

Date: 3/12/03 Author: Andrew Farmer Version: 1.1

This is intended to give a high-level overview of the work that others are doing in the area of “semantic” representation standards for the web.

MOBY PROJECT: TECHNICAL REPORT ON WEB MESSAGING LAYER

Date: March 9, 2003 Author: Lincoln Stein Version: 1.0

This report concerns the messaging layer of the Moby project, that point at which semantic information is exchanged between the data consumer (the biologist or client process) and the data provider (the model organism system database).

Full report can be read at: http://open-bio.org/pipermail/moby-l/2003-March/000433.html

This is the last call for people to test drive and/or criticize the Bio::Ontology & Bio::OntologyIO re-design and implementation.

The interfaces and modules to look at comprise of Bio::Ontology::OntologyI, Bio::Ontology::TermI, and Bio::OntologyIO. If you care about implementations (as Aaron says most people do rather than bothering with interfaces), check out Bio::Ontology::Ontology, Bio::Ontology::Term, and Bio::OntologyIO.