Difference between revisions of "Taxon-GO Implementation April 2009 onwards"

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Set up WinXP laptop to run the perl scripts to generate the tab delimited file that the users need to act on these links.
 
Set up WinXP laptop to run the perl scripts to generate the tab delimited file that the users need to act on these links.
  
'''TODO''': There are a bunch of terms that currently have two only_in_taxon links and they mess up the converstion to tab-delimited. Need to resolve these relationships. Have deleted them from the file for now.
+
'''TODO''': There are a bunch of terms that currently have two only_in_taxon links and they mess up the converstion to tab-delimited. Need to resolve these relationships. Have deleted them from the file for now. This is the list:
 +
 
 +
GO:0048494 chromatophore ribulose bisphosphate carboxylase complex
 +
GO:0030075 plasma membrane-derived thylakoid
 +
GO:0030094 plasma membrane-derived photosystem I
 +
GO:0030096 plasma membrane-derived thylakoid photosystem II
 +
GO:0031676 plasma membrane-derived thylakoid membrane
 +
GO:0031979 plasma membrane-derived thylakoid lumen
 +
GO:0048493 plasma membrane-derived thylakoid ribulose bisphosphate carboxylase complex
 +
GO:0009521 photosystem
 +
GO:0030077 plasma membrane light-harvesting complex
 +
GO:0042716 chromatophore
 +
GO:0009760 C4 photosynthesis
 +
GO:0009761 CAM photosynthesis
 +
GO:0016168 chlorophyll binding
 +
GO:0030093 chloroplast photosystem I
 +
GO:0030095 chloroplast photosystem II
 +
GO:0030089 phycobilisome

Revision as of 06:54, 1 April 2009

1st April 2009

This work has been on hold for a while as we were waiting for more sophisticated filtering in OBO-Edit to let all editor edit the file while doing normal live file editing. However Chris has asked that we push on without the filtering for a while.

Today:

Loaded the files in OE2 and found some file problems. The UnionTerm stanzas were a bit messed up, but were fixed by adding a Typedef for the the union_of relationship, and removing the top term.

Other file errors found and fixed:

Two entire taxa had gone missing from the taxon slim, and we had also lost a union_of term from the UnionTerms file. I do not know how that happened but I have replaced them.

Midori had added a new only_in_taxon link to a union_of term that did not exist. I have made the union_of stanza and added it to the file. I should talk with Midori about how to edit these files. I did not know she had started.

I have recommitted the edited source files and also saved out and recommitted the all_files_mid_edit.obo file. I did not make any edits so the perl scripts do not need to be run.

Fixed this misformed tag 'name: synonym: "synonym: "synonym: "'in both edit file and source.

Set up WinXP laptop to run the perl scripts to generate the tab delimited file that the users need to act on these links.

TODO: There are a bunch of terms that currently have two only_in_taxon links and they mess up the converstion to tab-delimited. Need to resolve these relationships. Have deleted them from the file for now. This is the list:

GO:0048494	chromatophore ribulose bisphosphate carboxylase complex
GO:0030075	plasma membrane-derived thylakoid
GO:0030094	plasma membrane-derived photosystem I
GO:0030096	plasma membrane-derived thylakoid photosystem II
GO:0031676	plasma membrane-derived thylakoid membrane
GO:0031979	plasma membrane-derived thylakoid lumen
GO:0048493	plasma membrane-derived thylakoid ribulose bisphosphate carboxylase complex
GO:0009521	photosystem
GO:0030077	plasma membrane light-harvesting complex
GO:0042716	chromatophore
GO:0009760	C4 photosynthesis
GO:0009761	CAM photosynthesis
GO:0016168	chlorophyll binding
GO:0030093	chloroplast photosystem I
GO:0030095	chloroplast photosystem II
GO:0030089	phycobilisome