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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.

Nat Goodman gave a talk on his impressions with BioPerl at a recent OReilly Bioinformatics Technology Conference.

The powerpoint slides can be downloaded here: http://conferences.oreillynet.com/presentations/bio2003/goodman_nat.ppt

All of the conference talks can be downloaded here (worth checking out): http://conferences.oreillynet.com/pub/w/21/presentations.html

From the session info:

Goodman

Hilmar writes:

Here’s the background.

The current code in the bioperl-db adaptors to biosql run the connection with AutoCommit off, which means the client determines the transaction. Load_seqdatabase.pl (the main script for loading databases into biosql) treats one sequence entry as one transaction. If any sql statement required for loading the sequence fails unexpectedly, the whole transaction is rolled back, otherwise it is committed once the entry and all its annotation went in successfully. The emphasis rests on ‘unexpectedly’: INSERTs may fail due to unique key violations, which is caught and triggers a look-up of the affected entry by unique key. E.g. a dbxref may already exist; if so, it needs to be looked up in order to establish the association with the bioentry.

Hilmar writes:

Triggered by what happened during the hackathon in Singapore, the Bioperl Ontology object model needs to undergo a number of changes that I’m going to describe below, along with a proposal how to resolve the issues. I have largely implemented the proposal and barring major objections I’m ready to commit tonight or tomorrow morning. Even though some of these things significantly change the API, we (I, backed by the core people) propose to migrate these changes over to the ‘stable’ 1.2 branch, to be able to release bioperl-db (bridges to the biosql schema) in dependency on a stable bioperl branch.