Difference between revisions of "Data Resources"

From Evolutionary Informatics Working Group
Jump to: navigation, search
m (Resource Matrix)
m
Line 147: Line 147:
 
|}
 
|}
  
 +
Many resources have their own page (linked to from the "Info" links above).  Resources that don't have their own page may be described below.
  
 
__TOC__
 
__TOC__
Line 187: Line 188:
 
===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).
+
See [[TreeBASE]].
 
 
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
 
  
 
===TreeFam===
 
===TreeFam===
Line 201: Line 197:
 
===Pandit===
 
===Pandit===
  
[http://www.ebi.ac.uk/goldman-srv/pandit/ Pandit]
+
See [[PANDIT]]
  
* [http://www.ebi.ac.uk/goldman-srv/pandit/pandit.cgi?action=desc format description]
+
=== Tree of Life ===
* citations (from Web of Science):
 
** 7 for 2006 paper
 
** 16 for 2003 paper
 
  
=== Tree of Life ===
+
See [[Tree of Life]].
** [http://tolweb.org Tree of Life], note example implementation, e.g. [http://nexml.org/nexml/phylows/tolweb/16299 hominidae subtree (node 16299)]
 
  
 
=== Microbes Online ===
 
=== 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]
 
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 ===
 
=== PhylomeDB ===
 +
 
[http://phylomedb.bioinfo.cipf.es/ PhylomeDB]
 
[http://phylomedb.bioinfo.cipf.es/ PhylomeDB]
  
 
=== MorphBank ===
 
=== MorphBank ===
[http://www.morphbank.net/ MorphBank]
+
 
 +
See [[MorphBank]].
  
 
=== PhyLoTA ===
 
=== PhyLoTA ===
 +
 
[http://loco.biosci.arizona.edu/pb/ PhyLoTA]
 
[http://loco.biosci.arizona.edu/pb/ PhyLoTA]
  
 
=== PhyloFacts ===
 
=== PhyloFacts ===
 +
 
[http://phylogenomics.berkeley.edu/phylofacts/ PhyloFacts]
 
[http://phylogenomics.berkeley.edu/phylofacts/ PhyloFacts]
  
 
=== TimeTree ===
 
=== TimeTree ===
[http://www.timetree.org TimeTree]
+
 
 +
See [[TiimeTree]].
  
 
=== MorphoBank ===
 
=== MorphoBank ===
[http://morphobank.geongrid.org/ MorphoBank]
+
 
 +
See [[MorphoBank]].
  
 
===pPOD===
 
===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)
+
 
 +
See [[pPOD]].
  
 
[[Category:DB Interop Hackathon]]
 
[[Category:DB Interop Hackathon]]
 +
[[Category:Data Resources]]

Revision as of 20:12, 2 March 2009

This page started as a quick analysis of data resources to target for the Database Interop Hackathon. It has become a hub for information about possible and participating data providers.

Each of these resources may have comparative data that we might want to make interoperable.

Resource Matrix

Resource 6 words or less Info Participants
Dryad Evolutionary publication backing data repository Info Ryan Scherle
Encyclopedia of Life Page for each species on Earth. Info Karen Cranston
GMOD Organism database toolkit, sequence emphasis. info Dave Clements
HOGENOM Complete Genome Homologous Genes Families Info
HOVERGEN Homologous Vertebrate Genes Database Info
iPlant Collaborative Uncover plants' higher order principles Info Karla Gendler, Sheldon McKay
Kepler an open-source scientific workflow system Info Ilkay Altintas
Mesquite Phylogenetic and population genetics analysis software. Info Peter Midford
MicrobesOnline Multispecies comparison among prokaryotes. Info
modENCODE model organism ENCyclopedia Of DNA Elements Info Sheldon McKay
MorphBank Specimen images and annotation Info Katja Seltmann
MorphoBank Homology of phenotypes over the web Info Lucie Chan
mx Evolutionary systematists' descriptive taxonomy CMS Info Matt Yoder
PaleoDB Fossil taxonomy and distribution Info Matt Kosnik
PANDIT Protein & Nucleotide Domains with Inferred Trees Info Greg Jordan
PANTHER Protein ANalysis THrough Evolutionary Relationships Info
Phenoscape Evolutionarily variable morphological characters database Info Jim Balhoff, Hilmar Lapp, Todd Vision
PhyloFacts Universal Proteome Explorer Info
Phylogeny.Fr Robust Phylogenetic Analysis For The Non-Specialist Info
PhylomeDB A database for phylomes Info
PhyLoTA Genbank nucleotide sequence taxonomic distribution Info
PhyloWidget Viewing, editing, publishing phylogenetic trees online. Info Greg Jordan
pPOD Database technologies for integrating AToL information Info Sam Donnelly
TimeTree Species divergence times Info
TreeBASE Database of Phylogenetic Knowledge Info Bill Piel
TreeFam Tree Families Database Info
Tree of Life Everything! Info Katja Schulz

Many resources have their own page (linked to from the "Info" links above). Resources that don't have their own page may be described below.

questions to ask for each resource

  • What is the scope of the resource?
  • Who controls it?
  • How can users access data?
  • How are data organized? Is there an explicit data model, schema, or format description?
  • Is there evidence that this is an important resources (registered users; citations)?

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

The resources below provide comparative data and are listed in order of apparent level of re-use, using literature citations as the measure of apparent data re-use. This is a crude way of prioritizing targets because i) literature citations sometimes do not indicate data re-use; and ii) past re-use is not as important as the potential for future re-use of a resource when semantic tools are used to increase its value.

Panther

The Panther system project is an online data resource for protein families with trees, HMMs, metabolic pathways, and other "functional" information. According to the latest publication [1], "PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles."

  • 279 citations for 2003, 2005 and 2007 papers, but its not clear how data re-use is based on the comparative aspect of this resource, as opposed to using this resource to mine relations between individual proteins and metabolic pathway annotations.

Hovergen

Hovergen,

  • hovergen 1994 paper cited 157 times

Hogenom

hogenom

TreeBase

See TreeBASE.

TreeFam

TreeFam

  • citations for 2006 paper: 36

Pandit

See PANDIT

Tree of Life

See Tree of Life.

Microbes Online

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

PhylomeDB

PhylomeDB

MorphBank

See MorphBank.

PhyLoTA

PhyLoTA

PhyloFacts

PhyloFacts

TimeTree

See TiimeTree.

MorphoBank

See MorphoBank.

pPOD

See pPOD.