See also:  http://baderlab.org/IdentifierMapping and:  http://hum-molgen.org/NewsGen/08-2009/000020.html

Identifier Systems

MIRIAM resources

•  http://www.ebi.ac.uk/miriam/
• Laibe et al, BMC Syst Bio '07  pubmed
• MIRIAM resources provides a curated ontology of data sources.
• relation to BridgeDb?: Most identifiers in BridgeDb? can be converted to a valid MIRIAM URI using the Xref.getURI() method.

LSID

• Unfortunately most of the data sources that are interesting to us do not support the LSID identifier resolution system. For this reason we do not provide support for LSID identifiers.

Mapping Services

AliasServer

• Iragne et al, Bioinformatics04  pubmed
•  http://cbi.labri.fr/outils/alias/
• Web service: yes, SOAP. See  http://cbi.labri.fr/outils/alias/API_SOAP.html
• Relation to BridgeDb: SOAP webservice could be implemented as IDMapper implementation. Planned for the future: #33. Please contact our mailinglist if you want to help us out.

Babelomics ID-Converter (Rosetta)

•  http://babelomics.bioinfo.cipf.es/
• Al-Shahrour, F., et al. NAR 2006  pubmed
• Al-Shahrour, F., et al. NAR 2005  pubmed
• Web application: yes
• Web service: no, as far as I can tell.
• Relation to BridgeDb: as there is no official webservice, integration with BridgeDb? may be hard.

BioDbNet? db2db

•  http://biodbnet.abcc.ncifcrf.gov/db/db2db.php

caBIG geneConnect

•  https://cabig.nci.nih.gov/tools/GeneConnect
• No journal publication
• Web application: yes
• Web service: yes, XML-RPC
• Relation to BridgeDb: XML-RPC webservice could be integrated. Planned for the future: #34. Please contact our mailinglist if you want to help us out.

CRONOS

• Waegele et al, Binf08  pubmed
•  http://mips.gsf.de/genre/proj/cronos/index.html
• mapping based on symbolic name matches, mix of uniprot, refseq and ensembl.
• last updated summer 2009 (last checked Nov. 2009)
• Supports 6 species: human, mouse, rat, cow, dog, fly
• Web application: yes
• Web service: WSDL. See  http://mips.helmholtz-muenchen.de/genre/export/sites/default/cronos/WSREADME.txt
• Relation to BridgeDb: IDMapperCronos has been implemented. Identifier mapping through CRONOS is supported.

CTS, Chemical Translation Service

•  http://uranus.fiehnlab.ucdavis.edu:8080/cts/homePage
• Both website and WSDL webservice
• based on data extracted from HMDB
• As far as I know, the only webservice for translating chemicals

DAVID gene ID Conversion tool (DICT)

• Huang et al, Bioinformation 2008  pubmed
•  http://david.abcc.ncifcrf.gov/conversion.jsp
• Web application: yes
• Web service: no
• Backend database is available for download, which makes it potentially possible to create an IDMapper for DAVID. Please contact our mailinglist if you want to help us out.

Ensembl BioMart (formerly known as EnsMart)

• Smedley et al, BMC Genomics 2009  pubmed
• Kasprzyk et al, Geneome res 04  pubmed
•  http://www.ensembl.org/Multi/martview
• Web application: yes
• Web service: yes
• Relation to BridgeDb: an IDMapper for BioMart has been implemented. Identifier mapping through EnsMart is fully supported by BridgeDb?

GeneCruiser

• Liefeld, bioinformatics05  pubmed
•  http://genecruiser.broadinstitute.org/
• Web application: yes. requires user registration to use
• Web service: unknown

GeneMerge

• Castillo-Davis, Binf03  pubmed
•  http://genemerge.bioteam.net/
• Site seems down (Nov 5 2009)

g:Convert / g:Profiler Gene ID Converter

• J. Reimand, M. Kull, H. Peterson, J. Hansen, J. Vilo: g:Profiler -- a web-based toolset for functional profiling of gene lists from large-scale experiments (2007) NAR 35 W193-W200
•  http://biit.cs.ut.ee/gprofiler/gconvert.cgi
• Web application: yes

HMS/IDCS

• Imanishi, NAR09  pubmed
•  http://biodb.jp/#ids
• Web application: yes
• Webservice: yes, REST-based. See  http://biodb.jp/help/ws_en.html
• Relation to BridgeDb: Integration planned for the future: #35. Please contact our mailinglist if you wish to help us out.

HMDB

•  http://www.hmdb.ca
• HMDB is primarily a metabolite database, but it also provides metabolite identifier mapping information and a webservice.
• Relation to BridgeDb: Integration planned for the future, please contact our mailinglist if you wish to help us out.

IDConnect / IDClight

• Alibes et al, BMCBinf07
•  http://idconverter.bioinfo.cnio.es/
• Web site: yes

MatchMiner

• Bussey et al, GenBio03
•  http://discover.nci.nih.gov/matchminer/index.jsp
• Web site: yes
• Web service: no, as far as I can tell.

MiMI

• Jayapandian, NAR07
•  http://mimi.ncibi.org/MimiWeb/main-page.jsp

MyGene?

•  http://mygene.info/doc
• web service: yes (REST)

Onto-translate

• Khatri et al, NAR06  pubmed; Draghici et al, Bioinformatics06  pubmed
•  http://vortex.cs.wayne.edu/ontotoolshelp/ontoconvert.htm
• Web site: requires user registration

PICR

• Cote et al, BMCBinf07  pubmed
•  http://www.ebi.ac.uk/Tools/picr/
• PICR can perform identifier translation as well as sequence lookup, with a focus on protein identifiers. It has support for over 70 different data sources. Gene identifiers such as ENSG... or ENST... can't be looked up.
• Web application: yes:  http://www.ebi.ac.uk/Tools/picr/
• Web service: yes, both REST and SOAP
• Relation to BridgeDb: an IDMapper for PICR has been implemented. Identifier mapping through PICR is fully supported by BridgeDb

PIR ID Mapping

• Huang et al
•  http://pir.georgetown.edu/pirwww/search/idmapping.shtml
• Web application: yes

Progmap

•  http://nar.oxfordjournals.org/cgi/content/short/gkp462v1
• website:  http://progmap.bioinformatics.nl/
• Webservice available upon request

RESOURCERER

• Tsai et al, 2001  pubmed
• (Moved to  http://compbio.dfci.harvard.edu/tgi/)
• No web service as far as I can tell
• Last release Dec 2006 (Last checked Nov 2009)

SOURCE

• Diehn et al, NAR03  pubmed
• Web application:  http://source.stanford.edu/
• No web service as far as I can tell

Synergizer

•  pubmed
• Relation to BridgeDb: an IDMapper for Synergizer has been implemented. Identifier mapping through Synergizer is fully supported by BridgeDb?
• Data comes directly from two "authorities" ncbi and ensembl.

Uniprot

•  http://uniprot.org/mapping

Other

Alitora

•  http://wiki.alitora.com/publicWiki/index.php/Main_Page
• 2 years old; actively maintained
• Open access content; closed source code
•  API javadocs
• Data from literature processing and primary data sources
• Unique qualities:
  • data is stored as a hypergraph, not as tables. This could support interesting filters and analysis built-in to queries.
  • database is writable. Users could add their own mappings based on network analysis.
• Relation to BridgeDb: an IDMapper for Alitora would be implemented as part of the SBIR aims, pending approval...

Template

• web link
• paper link and citation
• Institute
• Age and mainenance? First release, last release? Release schedule?
• Open access / open source license?
• Web site?
• Programatically accessible Web service?
• Command line tool?
• Limits to batch operation?
• Supported species?
• Supported types (genes, metabolites, proteins, reporters, etc.)?
• Supported data sources (Ensembl, Entrez, etc).
• Basis for identifier mapping (alignment, other)?
• Comments