Help:Annotation Pipeline: Difference between revisions

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==Overview==
Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts.
==Detailed Description==
{{NeedsEditing}}
{{NeedsEditing}}


==Overview==
A standardized method of loading annotations into [[EcoliWiki]] is in the works:
Each quarter [[EcoliWiki]] incorporates the ''E. coli'' annotations from [[EcoCyc]] into our website. Upon each [[EcoCyc]] release the annotations are parsed and loaded into the wiki using automated scripts.
# remove (to a file) the ecocyc.removed annotations
# remove (to a file) the IEAs that are older than 1 year
# validate the EcoCyc GAF
#* send the output and reasoning for the changes back to [[EcoCyc]] (Markus)
# sort the file on the appropriate columns
# convert to [[IFALT]]
# collapse the IEAs
# add metadata and load into [[EcoliWiki]]
 
 


==Known Issues==
==Known Issues==
* Currently [[EcoliWiki]] has not been removing annotations that were removed from [[EcoCyc]].  
* Currently [[EcoliWiki]] has not been removing annotations that were removed from [[EcoCyc]].  
: (<small>A fix is in the works. --[[User:DanielRenfro|Daniel]] 16:34, 9 March 2010 (UTC)</small>)
: (<small>A fix is in the works. --[[User:DanielRenfro|Daniel]] 16:34, 9 March 2010 (UTC)</small>)
==Detailed Description==


===IEA Collapsing===
===IEA Collapsing===
* In order to keep the number of computational annotations rows down to a manageable level (and so they don't overwhelm the tables) EcoliWiki "collapses" these rows. This means ''computational'' annotations for any particular product that are assigned to the same GO term will be collapsed into one row.  
In order to keep the number of computational annotations rows down to a manageable level (and so they don't overwhelm the tables) EcoliWiki "collapses" these rows. This means ''computational'' annotations for any particular product that are assigned to the same GO term will be collapsed into one row.  


An example, these rows are from a gene_associations.ecocyc file that was imported:
An example, these rows are from a gene_associations.ecocyc file that was imported:
Line 31: Line 41:
                                         GO_REF:0000020                                          HAMAP:MF_01152
                                         GO_REF:0000020                                          HAMAP:MF_01152
                                         GO_REF:0000002                                          InterPro:IPR001305
                                         GO_REF:0000002                                          InterPro:IPR001305


==See Also==
==See Also==
* [[Help:Gene Association File]]
* [[Help:Gene Association File]]

Revision as of 22:26, 4 May 2010

Overview

Each quarter EcoliWiki incorporates the E. coli annotations from EcoCyc into our website. Upon each EcoCyc release the annotations are parsed and loaded into the wiki using automated scripts.

Detailed Description

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

A standardized method of loading annotations into EcoliWiki is in the works:

  1. remove (to a file) the ecocyc.removed annotations
  2. remove (to a file) the IEAs that are older than 1 year
  3. validate the EcoCyc GAF
    • send the output and reasoning for the changes back to EcoCyc (Markus)
  4. sort the file on the appropriate columns
  5. convert to IFALT
  6. collapse the IEAs
  7. add metadata and load into EcoliWiki


Known Issues

  • Currently EcoliWiki has not been removing annotations that were removed from EcoCyc.
(A fix is in the works. --Daniel 16:34, 9 March 2010 (UTC))

IEA Collapsing

In order to keep the number of computational annotations rows down to a manageable level (and so they don't overwhelm the tables) EcoliWiki "collapses" these rows. This means computational annotations for any particular product that are assigned to the same GO term will be collapsed into one row.

An example, these rows are from a gene_associations.ecocyc file that was imported: 

EcoCyc  EG10240-MONOMER DnaJ            GO:0051082      GOA:hamap|GO_REF:0000020        IEA     HAMAP:MF_01152  F       chaperone with DnaK; heat shock protein dnaJ|groP|grpC|b0015|ECK0015    protein taxon:511145    20091214        UniProtKB
EcoCyc  EG10240-MONOMER DnaJ            GO:0051082      GOA:interpro|GO_REF:0000002     IEA     InterPro:IPR012724      F       chaperone with DnaK; heat shock protein dnaJ|groP|grpC|b0015|ECK0015    protein taxon:511145    20091214        UniProtKB
EcoCyc  EG10240-MONOMER DnaJ            GO:0051082      GOA:interpro|GO_REF:0000002     IEA     InterPro:IPR008971      F       chaperone with DnaK; heat shock protein dnaJ|groP|grpC|b0015|ECK0015    protein taxon:511145    20091214        UniProtKB
EcoCyc  EG10240-MONOMER DnaJ            GO:0051082      GOA:interpro|GO_REF:0000002     IEA     InterPro:IPR003095      F       chaperone with DnaK; heat shock protein dnaJ|groP|grpC|b0015|ECK0015    protein taxon:511145    20091214        UniProtKB
EcoCyc  EG10240-MONOMER DnaJ            GO:0051082      GOA:interpro|GO_REF:0000002     IEA     InterPro:IPR002939      F       chaperone with DnaK; heat shock protein dnaJ|groP|grpC|b0015|ECK0015    protein taxon:511145    20091214        UniProtKB
EcoCyc  EG10240-MONOMER DnaJ            GO:0051082      GOA:interpro|GO_REF:0000002     IEA     InterPro:IPR001305      F       chaperone with DnaK; heat shock protein dnaJ|groP|grpC|b0015|ECK0015    protein taxon:511145    20091214        UniProtKB


Notice that these 5 annotations are assigned to only 2 GO terms. After processing (and formatting for EcoliWiki), they look like this: 

GO:0051082     unfolded protein binding GO_REF:0000002  IEA: Inferred from Electronic Annotation InterPro:IPR001305   F   Seeded from EcoCyc 12.5    complete 
                                        GO_REF:0000002                                           InterPro:IPR002939
                                        GO_REF:0000002                                           InterPro:IPR003095
                                        GO_REF:0000002                                           InterPro:IPR008971
                                        GO_REF:0000002                                           InterPro:IPR012724
                                        GO_REF:0000020                                           HAMAP:MF_01152
                                        GO_REF:0000002                                           InterPro:IPR001305

See Also

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