Help:Annotation Pipeline

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

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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

Quarterly EcoliWiki incorporates the recent changes in annotations from EcoCyc. These changes are reflected in the monthly submission to the Gene Ontology.

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

• Help:Gene Association File