This script will print the erroneous lines with short descriptions of the problem. Some of these errors will be easy to fix and will not have any biological significance. A common error is misspellings or disallowed entries in the ''Assigned_by'' column (column 15.) Other errors are non-trivial and should be kept track of for further curation.
This script will print the erroneous lines with short descriptions of the problem. Some of these errors will be easy to fix and will not have any biological significance. A common error is misspellings or disallowed entries in the ''Assigned_by'' column (column 15.) Other errors are non-trivial and should be kept track of for further curation.
{{Info|I need to make sure this information gets back to EcoCyc. <br />--[[User:DanielRenfro|Daniel]] 22:43, 8 March 2010 (UTC)}}
{{Info|I need to make sure this information gets back to EcoCyc. <br />--[[User:DanielRenfro|Daniel]] 22:43, 8 March 2010 (UTC)}}
* Get the ''good'' lines from the EcoCyc release, for later inclusion into the GAF.
* Just like with the EcoCyc annotations, we must validate the annotations. The lack of restrictions in the annotation table makes for some interesting errors, most of which can be fixed by hand. These errors need to be fixed in the wiki as well, or they will show up again next month.
* Using a text editor, the errors are fixed. Some sample errors are:
a.) unprintable character found on this line, may not be this column
b.) Line identical to previous line
c.) Qualifier column=4 allowed type not present, found "Deprecated"
d.) DB:Reference column=6 format of reference not DB:REFID
Some characters, such as 'β', cannot be included as there is no standard encoding for the GAF and they can become garbled. Also, EcoliWiki does not enforce strict reference notation, so some lines may need a PubMed number.
* After the file has been fixed to an acceptable degree, the good lines are obtained for inclusion into the GAF.
The two sites' annotations are prepared by the EcoliWiki team (mostly [[User:DanielRenfro|Daniel,) and submitted via CVS to the GO Consortium. The figure at right shows the four basic steps to this process:
Obtain annotations from EcoCyc (quarterly)
Obtain annotations from EcoliWiki (monthly)
Merge them and resolve name-conflicts
Submit to the GO
Detailed Description
There are actually two files that get submitted each month. The gene association file and the gp2protein file. A detailed description of each can be found in the GO Consortium's documentation.
header information
Occasionally the header information in the gene_association file needs to be updated. This information can be found in the gene_assocation.ecocyc.conf file in the go/gene-associations/submission/ directory of the GO CVS.
To change this information, just edit the file from the CVS checkout and resubmit it. It will get prepended to the gene_assocation file automatically.
gene_association.ecocyc
The following is the process by which the annotation file is prepared, broken into managable steps.
Step 0.5 - Setup the environment
The process requires some files and scripts from the GO Consortium. Instead of do this by hand each month, Daniel wrote a script to handle this part of the process. To use this bash script, copy this code into a file and make it executable. On our servers it is named gaf_setup.sh.
The first step is to run this script. Alternatively, you can follow the directions below to do this by hand.
EcoCyc's quarterly releases contain their annotations in the gene_association file format. The file is typically named gene_associations.ecocyc.... (Notice the plural on associations). In order to prepare their annotations, we must first parse the annotations for validity.
This script will print the erroneous lines with short descriptions of the problem. Some of these errors will be easy to fix and will not have any biological significance. A common error is misspellings or disallowed entries in the Assigned_by column (column 15.) Other errors are non-trivial and should be kept track of for further curation.
I need to make sure this information gets back to EcoCyc. --Daniel 22:43, 8 March 2010 (UTC)
Get the good lines from the EcoCyc release, for later inclusion into the GAF.
Just like with the EcoCyc annotations, we must validate the annotations. The lack of restrictions in the annotation table makes for some interesting errors, most of which can be fixed by hand. These errors need to be fixed in the wiki as well, or they will show up again next month.
Using a text editor, the errors are fixed. Some sample errors are:
a.) unprintable character found on this line, may not be this column
b.) Line identical to previous line
c.) Qualifier column=4 allowed type not present, found "Deprecated"
d.) DB:Reference column=6 format of reference not DB:REFID
Some characters, such as 'β', cannot be included as there is no standard encoding for the GAF and they can become garbled. Also, EcoliWiki does not enforce strict reference notation, so some lines may need a PubMed number.
After the file has been fixed to an acceptable degree, the good lines are obtained for inclusion into the GAF.
