A List Of Test Systems to Compare with Descriptron:

Mapping services

AliasServer
http://cbi.labri.fr/outils/alias/
Tool for identifier translation using CRC64 hash of the protein sequence
as a primary key. Provides unification, linkout and translation services
for a handful (~35) species for proteins only.  Supports use cases 2, 3.

Freely available for download. Regularly updated.

MD Anderson GeneLink
http://bioinformatics.mdanderson.org/GeneLink.html
ID translation and search service for human IDs (10 ID types).  Supports
use case 2, 3.

EnsMart
http://www.ensembl.org/Multi/martview
ID translation services for Ensembl genomes. Supports use case 2.

MatchMiner
http://discover.nci.nih.gov/matchminer/html/index.jsp
ID translation service for mouse and human. Supports use cases 2, 3.

Ariadne Genomics ID Mapping Service
http://www.ariadnegenomics.com/services/idmap.html
Tool for identifier translation. Supports 7 species and maps between 12
different ID types mainly for proteins and genes.
Commercial service, not available for download
Supports use case 3

GeneLynx
http://www.genelynx.org/
Provides linkout services for human, mouse and rat.  Supports use case 2.

NetAffx
http://www.affymetrix.com/products/software/specific/netaffx.affx
Provides ID translation services for Affy probe set IDs.  Supports use
case 3.

http://openbns.sourceforge.net/ - Supports use cases 2,3

Databases

International Protein Index
http://www.ebi.ac.uk/IPI/IPIhelp.html
A cross reference database for proteins in higher eukaryotic organisms
(5 species). Provides protein and gene cross references. Supports use
case 1.

Entrez Gene
Provides detailed information on genes from multiple organisms including
gene aliases and links to NCBI related resources. Supports use case 4
(and 2 to some degree).

UniProt (SwissProt, PIR, TrEMBL) provides some information on links to
related resources and protein names.




> In the ISMB Semantic web for Life Science BOF,
> an issue was raised about the ambiguity of how people
> refer to a protein in the literature.
>
> For example, let's say, you find a description such as
> "JNK activates JUN" but acctually this "JNK" stands for
> a bunch of proteins ("concrete entities") and JUN
> also stands for a set of proteins.
>
> This isssue is known as the "generic entitity" problem.
> If you read the literature, you typically encounter these
> "generic protein" names.
> And there should be a mechanism that tells you how many
> proteins you have for each generic name.
>
> An ontology for generic/concrete protein names, called
> "MoleculeRole Ontology" is available from
> http://www.inoh.org/ontology-viewer/.
> Actually, it is a DAG structured controled vocabulary (CV).
> The current version covers about 4400 Uniprot IDs which means
> that the CV defines generic/concrete protein relations for
> more than 4400 concrete proteins.
>
> The CV is available in OBO format (Gene Ontology native format).
> http://www.inoh.org/download.html
>
> PS.
> There are some OBO->OWL converters, but some argued they didn't
> fit their needs. It would be nice to know how people like to
> convert an OBO ontology into an OWL file.