Help:Annotation Pipeline: Difference between revisions

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==Overview==
==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.  
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. This is reflected in the montly annotation file submitted to the [[Help:Gene_ontology|Gene Ontology]] each month.  


==Detailed Description==
==Detailed Description==
{{NeedsEditing}}
; Obtain the latest [[EcoCyc]] release
: Quarterly annotations are fetched from [[EcoCyc]] and parsed for validity.


A standardized method of loading annotations into [[EcoliWiki]] is in the works:
; Calculate the changes
# remove (to a file) the ecocyc.removed annotations
: The most recent release is compared to the previous release and two files are generated:
# remove (to a file) the IEAs that are older than 1 year
:# <tt>differences.lost.gaf</tt>
# validate the EcoCyc GAF
:# <tt>differences.gained.gaf</tt>
#* send the output and reasoning for the changes back to [[EcoCyc]] (Markus)
: These two files contain the annotatations (in [http://www.geneontology.org/GO.format.gaf-1_0.shtml GAF 1.0] format) that have been lost or gained since the last release, respectively.
# sort the file on the appropriate columns
# convert to [[IFALT]]
# collapse the IEAs
# 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]].
; Use a script to add/remove annotations from [[EcoliWiki]]
: A [[wikipedia:PHP|PHP]] script adds and removes the annotations from the wiki based on the file.
: Specifically, does the following things:
:# looks in the <tt>differences.lost.gaf</tt> file
:# determines which gene products need annotations removed
:# visits those pages in the wiki
:# finds the annotation to remove from the [[Help:Gene_ontology|Gene Ontology]] table
:# saves the page to commit the edit
:# does the same steps for adding annotations


==Known Issues==
==Known Issues==
* Currently [[EcoliWiki]] has not been removing annotations that were removed from [[EcoCyc]].
* A number of ''old'' annotations are still in [[EcoliWiki]]. These were added early in the life of [[EcoliWiki]], and were not tagged with the appropriate metadata that allows us to add/delete annotations. These are spurious and do not contribute to the total set of annotations, as these annotations could be out of date or incorrect.  
: (<small>A fix is in the works. --[[User:DanielRenfro|Daniel]] 16:34, 9 March 2010 (UTC)</small>)
 
===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


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


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==
[[Category:Help]]
* [[Help:Gene Association File]]

Latest revision as of 20:01, 15 June 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. This is reflected in the montly annotation file submitted to the Gene Ontology each month.

Detailed Description

Obtain the latest EcoCyc release
Quarterly annotations are fetched from EcoCyc and parsed for validity.
Calculate the changes
The most recent release is compared to the previous release and two files are generated:
  1. differences.lost.gaf
  2. differences.gained.gaf
These two files contain the annotatations (in GAF 1.0 format) that have been lost or gained since the last release, respectively.
Use a script to add/remove annotations from EcoliWiki
A PHP script adds and removes the annotations from the wiki based on the file.
Specifically, does the following things:
  1. looks in the differences.lost.gaf file
  2. determines which gene products need annotations removed
  3. visits those pages in the wiki
  4. finds the annotation to remove from the Gene Ontology table
  5. saves the page to commit the edit
  6. does the same steps for adding annotations

Known Issues

  • A number of old annotations are still in EcoliWiki. These were added early in the life of EcoliWiki, and were not tagged with the appropriate metadata that allows us to add/delete annotations. These are spurious and do not contribute to the total set of annotations, as these annotations could be out of date or incorrect.

See Also

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