|
From: <ja...@op...> - 2001-03-09 04:18:23
|
Hey All, This is the report from the OMG meeting that just happen in Irvine CA. It was a surprisingly productive meeting. I still feel that the OpenSource process: release early, release often is a better approach than the OMG process. But since many corporate players feel very uncomfortable with that approach, I guess the OMG process is as good as you get. Executive Summary ================= * we were extremely productive, and were able to agree on big pieces of the data format. These pieces had to do with sample tracking, and higher level annotations. * we spent most of the first 1/3 of the time discussing the glossary and agreeing on nomenclature. This was a GoodThing (TM). We now have a fairly broad group of academics (MGED) and three major corporate players (Rosetta, NetGenix, and Agilent) agreeing on terminology. It is my assigned duty to write up a new glossary, and when I do I will distribute it to this list. * The big discussion came to the actual data encoding for the spot values. The two major options were Rosetta's very verbose but explicit row-by-row XML encoding (much like GeneXML) or MAML's very loose, flexible and un-tested matrix approach. Paul and I agreed to implement some examples of the matrix approach before we would decide anything, but it seemed likely that support for the row-based approach would be manditory, and the matrix approach optional. * We decided that a description of spots on an ArrayLayout (which we agreed to call an ArrayPattern) needed to include at least three levels: 1) the SequenceFeature -- the nucleic acid (or other stuff) bound to the array; 2) the Reporter the higher level entity that SF was to represent (we used to call this the *canonical* sequence feature; 3) the BiosequenceCluster -- for example a UniGene set. * We uncovered that Rosetta's and NetGenix submission's had missed the concept of between array comparisons (i.e. ratio's of two different time points). Michael Miller was going to address this. * Rosetta had an elegant way to encode spot position which did not require massive numbers of attributes * There was an enormous amount of technical discussion about what would be the *normative* output of this groups effort, i.e. what is the actual document that will hold the specification. Should it be UML, a CORBA IDL, or XML? We decided to absolutely produce UML, and that the UML can be used to produce an IDL and an XML specification, but that we are likely to produce both the IDL and XML specification as well. So, all in all, we learned a lot, and it was worth the trip. jas. |