2010Jan07

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Welcome to the newest member of our group, Chinua, who is a computer science graduate student at UMass.

Reports:

Maureen, David, and Zhimin have been working on the FP Eclipse project environment.

Zhimin made a mock-up implementation of the hadoop service. This will be very helpful for testing. He is refactoring some of the FP code. There will be multiple phases of query processing, including stages for creating the query from the incoming xml, transforming to target query format, query execution, and post-processing. Post-processing can involve "filters" for applying fuzzy-matching or security policies, for example.

Zhimin is also looking as JSF as an implementation for GUI work that perhaps will be taken over by Chinua.


Bob reports on the PubMed Central dtd. PubMed is an indexing and abstract service by the National Library of Medicine. PubMed Central is an archiving service for open published documents. They archive immutable documents marked up to an xml dtd, the PMC dtd. Bob has been involved in a project to extend the PMC dtd to include taxonomic literature. The new dtd is likely to change. There are applications for Flora of N. America, and serveral issues raised concerning the nature of annotations that we should consider for FP.

Bob has been working on making Golden Gate into an FP client. He has an Eclipse project with both the GG and FP jars working in it. GG has an interface that supports annotations to internal documents. It maps a segment of a document to a user-defined text annotation. The goal is to have the annotations delivered to the FP network.

Two questions arise: what should an annotation be? do we have enough on the FP end to support this?

umbfp has been down but new parts are on the way.

James reports he's been in contact with a phd student who has been working on FNA and how different treatments can be compared to eachother. The biodiversity informatics group is supporting a proposal by Webb & Mathews which addresses the biogeography of Indonesia. Bob, James, and possibly Paul may be invited to a workshop in Missouri at which FP/networking will be a major topic.


For discussion: annotating published literature.

Administration: meeting agenda format

Next meeting: 2010Jan14 morning.