Wednesday, January 14, 2009

Web Wednesday--NAR's Annual Database Issue

The annual Database Issue from Nucleic Acids Research is now available on-line. Free full text.

RNA biology in general seems to be prominent this year--several tools and databases dedicated to miRNAs, tRNAs and so on.

In terms of things relevant to Drosophila and/or cell-based RNAi screens, a number of things jumped out on an admittedly quick glance:

siRecords, which is cataloging effectiveness of specific siRNAs and displays them with a kind of 'heat bar' slightly reminiscence of Amazon's five-star customer ratings system. Mammalian focus. Example IDs NM_032147, NM_023662, and NM_204702. Read the NAR paper here.

FlyBase, which uses this year's issue to focus on their efforts to improve the quality of GO annotation data. Read the NAR paper here.

PIG, the Pathogen Interaction Gateway, which catalogs interactions between pathogen and host proteins. I expect this information may be useful for follow-up of the several completed, ongoing and planned screens for host-pathogen interactions done at the DRSC. Read the NAR paper here.

Cell Line Data Base or HyperCLDB, which has molecular and other information about human cell lines, and is working to apply a standard nomenclature. May be relevant to mammalian RNAi screens (and has particular relevance to researchers in Europe). Read the NAR paper here.

And as usual there are a fair share of awkward acronyms and crazy names to entertain us. My favorite for the "Yuck!" factor (although of course I recognize the scientific value) is Sys-BodyFluid (NAR paper here). And my pick for "Really?" is SysPIMP (NAR paper here) where "pimp" is for Systematic Platform for Identifying Mutated Proteins.

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