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.
- 1 Resource Matrix
- 2 questions to ask for each resource
- 3 Phylogeny Services
- 4 Data Resources
|Resource||6 words or less||Info||Participants|
|Phylogeny.Fr||Robust Phylogenetic Analysis For The Non-Specialist||Info|
|PANTHER||Protein ANalysis THrough Evolutionary Relationships||Info|
|HOVERGEN||Homologous Vertebrate Genes Database||Info|
|HOGENOM||Complete Genome Homologous Genes Families||Info|
|TreeBASE II||Database of Phylogenetic Knowledge||Info|
|TreeFam||Tree Families Database||Info|
|PANDIT||Protein & Nucleotide Domains with Inferred Trees||Info|
|Tree of Life||Everything!||Info|
|MicrobesOnline||Multispecies comparison among prokaryotes.||Info|
|PhylomeDB||A database for phylomes||Info|
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)?
output formats are Newick, NHX and Phylip, but apparently no means to export alignment and tree together.
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.
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 , "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 1994 paper cited 157 times
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
- citations for 2006 paper: 36
- format description
- citations (from Web of Science):
- 7 for 2006 paper
- 16 for 2003 paper
Tree of Life
pPOD (not really a data resource, its a db tech project led by computer scientists)