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GenMAPP Collaborators
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Several groups have contributed to GenMAPP by creating
custom databases or submitting pathway MAPPs. Here are
some examples of these collaborations.
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Escherichia coli
K12 Gene Database
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Dr. Kam Dahlquist, Dr. John David N. Dionisio, and the
Bioinformatics group at Loyola Marymount University
(http://myweb.lmu.edu/kdahlqui/Contact.htm) have created
a gene database for
Escherichia coli K12. The database was created
programmatically using XMLPipeDB
based on the UniProt complete proteome
set and
GOA gene associations to Gene Ontology. The database contains several gene
ID systems,
including UniProt, Blattner, EchoBASE and EcoGene. It
also contains annotation information from EMBL,
Gene
Ontology,
InterPro, PDB and Pfam. The database is available for
download through the Downloader tool in GenMAPP, as well
as at
http://www.cs.lmu.edu/~xmlpipedb/download.shtml.
A detailed ReadMe document describing the database
schema is packaged with the database.
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Schizosaccharomyces pombe
Gene Database and pathway MAPPs
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Through a
collaboration with NIPER (National Institute of
Pharmaceutical Education and Research) in Punjab,
India, GenMAPP has been implemented for fission
yeast, Schizosaccharomyces pombe.
The database and MAPP archive are available at
http://www.databases.niper.ac.in/Pombe/
The database is based on Sanger GeneDB IDs, and also
contains UniProt IDs and Pfam, InterProt and EC
number annotation.
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NetPath pathway MAPPs
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A set of 10 cancer and 10
immune signaling pathways have been added to the GenMAPP
Contributed MAPP archive, as part of an ongoing
collaboration with NetPath. NetPath (http://www.netpath.org/)
is a human pathway annotation project, initiated by the PandeyLab at Johns Hopkins University (http://pandeylab.igm.jhmi.edu)
and the Institute of Bioinformatics (http://www.ibioinformatics.org).
The 10 cancer signaling pathways were developed in
collaboration with the Computational Biology Center at
Memorial Sloan-Kettering Cancer Center (http://cbio.mskcc.org)
and with Gary Bader's lab at the University of Toronto (http://baderlab.org)
for the Cancer Cell Map (http://cancer.cellmap.org).
All 20 pathways are freely available in GenMAPP, PSI-MI
and BioPAX formats at
http://www.netpath.org.
The 10 cancer signaling pathways are also available for
download and browsing from
http://cancer.cellmap.org. All 20 pathways have been
inferred from human to all other GenMAPP supported
species.
These pathways are unpublished at this time; please cite
these websites until the pathways are described in a
publication. Feedback about the NetPath site and its
contents can be sent to:
info@netpath.org
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SGD metabolic pathway MAPPs
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Students at Vassar College
worked with Dr. Kam Dahlquist to adapt a set of pathway
MAPPs for S.cerevisiae
based on the metabolic pathways at SGD,
http://pathway.yeastgenome.org/biocyc/. The 120
pathways are packaged as a MAPP archive, available for
download through the Downloader feature in GenMAPP.
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Rat pathway MAPPs |
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A set of
pathway MAPPs representing processes relevant to
toxicology have been submitted by Dr. Sebastien
Burel at
Neurocrine Biosciences Inc. A total of 8 MAPPs
were submitted for rat, and they have also been
inferred to all other supported species.
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