Difference between revisions of "Data Resources"

From Evolutionary Informatics Working Group
Jump to: navigation, search
(Data Resources)
(Data Resources)
Line 31: Line 31:
  
 
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):
 
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, can't track citing papers  
+
* Sanderson, et al., 1994 (Am. Jour. Bot.), cited 59 times, can't track citing papers
 
* Sanderson, et al., 1993 (Syst. Biol.) cited 29 times, most citing papers are meta-analyses ! (that's good)
 
* Sanderson, et al., 1993 (Syst. Biol.) cited 29 times, most citing papers are meta-analyses ! (that's good)
 
* Morel, 1996, cited 21 times
 
* Morel, 1996, cited 21 times
Line 47: Line 47:
 
[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)
 
[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===
+
=== Tree o' Life ===
 +
** [http://tolweb.org Tree of Life], note example implementation, e.g. [http://nexml.org/nexml/phylows/tolweb/16299 hominidae subtree (node 16299)]
  
organism-centered gene-family databases, e.g., for plasmodium
+
=== Microbes Online ===
 +
Arkin lab's [http://microbesonline.org MicrobesOnline] server has cool [http://www.microbesonline.org/cgi-bin/treeBrowse.cgi?locus=392933 tree-based view of sequence families]
 +
 
 +
=== PhylomeDB ===
 +
[http://phylomedb.bioinfo.cipf.es/ PhylomeDB]
 +
 
 +
=== PhyLoTA ===
 +
[http://loco.biosci.arizona.edu/pb/ PhyLoTA]
 +
 
 +
=== PhyloFacts ===
 +
[http://phylogenomics.berkeley.edu/phylofacts/ PhyloFacts]
 +
 
 +
=== TimeTree ===
 +
[http://www.timetree.org TimeTree]
 +
 
 +
=== MorphoBank ===
 +
[http://morphobank.geongrid.org/ MorphoBank]
 +
 
 +
=== MorphBank ===
 +
[http://www.morphbank.net/ MorphBank]

Revision as of 14:33, 23 September 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

TreeFam

TreeFam

  • citations for 2006 paper: 36

Hovergen, hogenom

Hovergen, hogenom

  • hovergen 1994 paper cited 157 times

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, can't track citing papers
  • Sanderson, et al., 1993 (Syst. Biol.) cited 29 times, most citing papers are meta-analyses ! (that's good)
  • Morel, 1996, cited 21 times

Pandit

Pandit

pPOD

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

Tree o' Life

Microbes Online

Arkin lab's MicrobesOnline server has cool tree-based view of sequence families

PhylomeDB

PhylomeDB

PhyLoTA

PhyLoTA

PhyloFacts

PhyloFacts

TimeTree

TimeTree

MorphoBank

MorphoBank

MorphBank

MorphBank