Difference between revisions of "Data Resources"

From Evolutionary Informatics Working Group
Jump to: navigation, search
m
m (Resource Matrix)
Line 74: Line 74:
 
| Evolutionary systematists' descriptive taxonomy CMS
 
| Evolutionary systematists' descriptive taxonomy CMS
 
| [[mx|Info]]
 
| [[mx|Info]]
| [[User:Myoder|Matt Yoder]]  
+
| [[User:Myoder|Matt Yoder]]
 
|-
 
|-
! [http://paleodb.org/ PaleoDB]]
+
! [http://paleodb.org/ PaleoDB]
 
| Fossil taxonomy and distribution
 
| Fossil taxonomy and distribution
 
| [[PaleoDB|Info]]
 
| [[PaleoDB|Info]]

Revision as of 20:22, 27 February 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


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

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

TreeFam

TreeFam

  • citations for 2006 paper: 36

Pandit

Pandit

Tree of Life

Microbes Online

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

PhylomeDB

PhylomeDB

MorphBank

MorphBank

PhyLoTA

PhyLoTA

PhyloFacts

PhyloFacts

TimeTree

TimeTree

MorphoBank

MorphoBank

pPOD

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