Index of /external2go

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory                             -   
[   ] cog2go                  01-Mar-2007 08:40  8.6K  
[TXT] ec2go                   02-Jul-2009 10:40  287K  
[   ] egad2go                 22-Jun-2009 05:40  4.5K  
[   ] genprotec2go            01-Mar-2007 08:40   28K  
[   ] hamap2go                02-Jul-2009 10:40  209K  
[   ] interpro2go             02-Jul-2009 10:40  2.2M  
[TXT] metacyc2go              20-Jun-2009 08:40  386K  
[TXT] mips2go                 01-Mar-2007 08:40  117K  
[   ] multifun2go             01-Mar-2007 08:40   61K  
[   ] pfam2go                 02-Jul-2009 10:40  672K  
[   ] pirsf2go                02-Jul-2009 10:40  217K  
[   ] prints2go               02-Jul-2009 10:40  310K  
[   ] prodom2go               02-Jul-2009 10:40   61K  
[   ] prosite2go              02-Jul-2009 10:40  265K  
[   ] reactome2go             30-Jun-2009 17:10  747K  
[TXT] resid2go                20-Jun-2009 08:40   41K  
[   ] rfam2go                 19-Oct-2007 03:10   45K  
[   ] smart2go                02-Jul-2009 10:40   61K  
[   ] spkw2go                 02-Jul-2009 10:40   53K  
[   ] spsl2go                 02-Jul-2009 10:40   23K  
[   ] tigr2go                 01-Mar-2007 08:40   27K  
[TXT] tigrfams2go             11-Aug-2008 16:10  568K  
[TXT] um-bbd_enzymeid2go      20-Jun-2009 08:40   61K  
[TXT] um-bbd_pathwayid2go     20-Jun-2009 08:40  9.6K  
[   ] wikipedia2go            20-Jun-2009 08:40   46K  

!version: $Revision: 1.7 $
!date: $Date: 2008/07/11 16:37:34 $
!

Indices of Other Classification Systems to GO

GO is not the only attempt to build structured controlled vocabularies
for genome annotation. Nor is it the only such series of catalogs in
current use. We have, in a series of files in the folder

   /external2go

attempted to make translation tables between these catalogs and GO. We
caution that these mappings are neither complete nor exact; they are
to be used as a guide. One reason for this is absence of definitions
from many of the other catalogs and of a complete set of definitions
in GO itself. The line:

!Uses:

e.g. 
!Uses:http://www.tigr.org/docs/tigr-scripts/egad_scripts/role_reports.spl, 15 aug 2000.

gives the source of the external file. 

The line syntax is: 

database:<identifier> > GO:<term> ; GO:<GO_id>

e.g.: 

TIGR_role:11030 73 Amino acid biosynthesis Glutamate family > GO:glutamine family amino-acid biosynthesis ; GO:0009084

For entries that map to more than one GO term, put each GO term on a separate line, e.g.

InterPro:IPR000011 Ubiquitin-activating enzyme, E1 > GO:protein modification ; GO:0006464
InterPro:IPR000011 Ubiquitin-activating enzyme, E1 > GO:protein modification process ; GO:0006464


Those available so far are: 


cog2go
 - The correspondence between COGs or KOGs (clusters of orthologous
   groups) and GO terms.
 - Constructed by Michael Ashburner and Jane Lomax.

ec2go:
 - The correspondence between EC numbers and GO terms. Parsed from the
   molecular function ontology.
 - Original version parsed by Michael Ashburner. Current file parsed
   from function.ontology Revision 2.537 flat file by Daniel Barrell,
   EBI

egad2go:
 - The correspondence between the TIGR EGAD categories and GO terms.
 - Constructed by Michael Ashburner.

genprotec2go:
 - The correspondence between the GenProtEC functional categories and
   GO terms.
 - Constructed by Heather Butler and Michael Ashburner

hamap2go
 - The correspondence between HAMAP families and GO terms.
 - Constructed byKarine Michoud, SIB, Geneva; maintained by Daniel
   Barrell, EBI

interpro2go:
 - The correspondence between InterPro entries and GO terms.
 - Constructed and maintained by Nicola Mulder and Sandra Orchard.

metacyc2go
 - The correspondence between MetaCyc pathways and GO process terms,
   and between MetaCyc reactions and GO function terms.
 - Constructed by Michael Ashburner, Midori Harris, Suparna Mundodi
   and Amelia Ireland.

mips2go
 - The correspondence between MIPS Funcat categories and GO terms.
 - Constructed by Michael Ashburner and Midori Harris.

multifun2go
 - The correspondence between MultiFun classifications and GO terms.
 - Constructed by Michael Ashburner, Jane Lomax and Margrethe Hauge Serres.

pfam2go
 - The correspondence between Pfam domains and GO terms; a subset of
   interpro2go.
 - Constructed and maintained by Nicola Mulder and Sandra Orchard.

prints2go
 - The correspondence between PRINTS protein fingerprints and GO
   terms; a subset of interpro2go.
 - Constructed and maintained by Nicola Mulder and Sandra Orchard.

prodom2go
 - The correspondence between ProDom domains and GO terms; a subset of
   interpro2go.
 - Constructed and maintained by Nicola Mulder and Sandra Orchard.

prosite2go
 - The correspondence between Prosite domains and GO terms; a subset
   of interpro2go.
 - Constructed and maintained by Nicola Mulder and Sandra Orchard.

reactome2go
 - The correspondence between Reactome events and GO terms.
 - Constructed and maintained by Reactome curators and Amelia Ireland.

rfam2go
 - The correspondence between Rfam families and GO terms.
 - Constructed and maintained by Sam Griffiths-Jones and Jennifer Daub.

smart2go
 - The correspondence between SMART domains and GO terms; a subset of
   interpro2go.
 - Constructed and maintained by Nicola Mulder and Sandra Orchard.

spkw2go: 
 - The correspondence between SWISS_PROT keywords and GO terms.
 - Original mapping constructed by David Hill of MGI. Current version
   constructed and maintained by Evelyn Camon, EBI

tigr2go:
 - The correspondence between the TIGR role categories and GO terms.
 - Constructed by Michael Ashburner.

tigrfams2go
 - The correspondence between TIGRFAMS protein families and GO terms.
 - Constructed by Mihcelle Gwinn and other TIGR staff.

um-bbd_enzymeid2go
 - The correspondence between UM-BBD enzymes and GO terms.
 - Constructed and maintained by Amelia Ireland.

um-bbd_pathwayid2go
 - The correspondence between UM-BBD pathways and GO terms.
 - Constructed and maintained by Amelia Ireland.