Difference between revisions of "Data Resources"

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(Hovergen, hogenom)
(Resources)
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==questions to ask for each resource==
 
==questions to ask for each resource==
  
==Resources==
 
  
===Pandit===
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== Phylogeny Services ==
 +
 
 +
=== Phylogeny.Fr ===
 +
 
 +
http://www.phylogeny.fr
  
[http://www.ebi.ac.uk/goldman-srv/pandit/ Pandit]
+
output formats are Newick, NHX and Phylip, but apparently no means to export alignment and tree together.
  
* [http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=desc format description]
+
==Data Resources==
* citations (from Web of Science):
 
** 7 for 2006 paper
 
** 16 for 2003 paper
 
  
 
===TreeBase===
 
===TreeBase===
  
 
[http://www.phylo.org/sub_sections/databases 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).
 
[http://www.phylo.org/sub_sections/databases 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).
 
===pPOD===
 
[http://phylodata.seas.upenn.edu/cgi-bin/wiki/pmwiki.php pPOD] (not really a data resource, its a db tech project led by computer scientists)
 
  
 
===TreeFam===
 
===TreeFam===
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* hovergen 1994 paper cited '''157''' times
 
* hovergen 1994 paper cited '''157''' times
 +
 +
===Pandit===
 +
 +
[http://www.ebi.ac.uk/goldman-srv/pandit/ Pandit]
 +
 +
* [http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=desc format description]
 +
* citations (from Web of Science):
 +
** 7 for 2006 paper
 +
** 16 for 2003 paper
 +
 +
===pPOD===
 +
[http://phylodata.seas.upenn.edu/cgi-bin/wiki/pmwiki.php pPOD] (not really a data resource, its a db tech project led by computer scientists)
  
 
=== organism-centered===
 
=== organism-centered===
  
 
organism-centered gene-family databases, e.g., for plasmodium
 
organism-centered gene-family databases, e.g., for plasmodium

Revision as of 15:27, 22 May 2008

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

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).

TreeFam

TreeFam

  • citations for 2006 paper: 36

Hovergen, hogenom

Hovergen, hogenom

  • hovergen 1994 paper cited 157 times

Pandit

Pandit

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