Data Resources

From Evolutionary Informatics Working Group
Revision as of 13:47, 29 May 2008 by Arlin.stoltzfus@nist.gov (talk) (TreeBase)
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Quick analysis of data resources to target for interop hackathon

The idea is that each of these resources has comparative data that we might want to make interoperable.

questions to ask for each resource

Phylogeny Services

Phylogeny.Fr

http://www.phylogeny.fr

output formats are Newick, NHX and Phylip, but apparently no means to export alignment and tree together.

Data Resources

TreeFam

TreeFam

  • citations for 2006 paper: 36

Hovergen, hogenom

Hovergen, hogenom

  • hovergen 1994 paper cited 157 times

Pandit

Pandit

TreeBase

TreeBaseII has the kind of granular schema that would be a good challenge to try to accommodate using cdao. What is missing from cdao (and nexml) is the notion of a "study" with various types of metadata, including publication/reference metadata (which is somewhat dc-like).

Its not clear what reference to site. The TreeBase "Intro" page cites about 7 different references up to 2000, including posters and papers. Some of the papers apparently are scientific studies and not implementation papers. Some of the most likely candidates for a TreeBase citation are as follows (perhaps we should include all of these):

  • Sanderson, et al., 1994 (Am. Jour. Bot.), cited 59 times
  • Sanderson, et al., 1993 (Syst. Biol.) cited 29 times
  • Morel, 1996, cited 21 times

pPOD

pPOD (not really a data resource, its a db tech project led by computer scientists)

organism-centered

organism-centered gene-family databases, e.g., for plasmodium