Difference between revisions of "Initial Meeting- Aug 2011"
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from MS by email: | from MS by email: | ||
* In a few cases, there is a classical gene name for the gene model. I assume these could be supplied as synonyms? Or, would you prefer they be supplied as a separate row? | * In a few cases, there is a classical gene name for the gene model. I assume these could be supplied as synonyms? Or, would you prefer they be supplied as a separate row? | ||
| + | ''Need to look at this, and ask PJ'' | ||
*Do you still wish to have separate files for anatomy and growth terms? | *Do you still wish to have separate files for anatomy and growth terms? | ||
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*Note, the instructions on the wiki for field 13. TAXON deal with Field 12 and should be altered. | *Note, the instructions on the wiki for field 13. TAXON deal with Field 12 and should be altered. | ||
''I am not sure I understand to which page you are referring. The info shown here: http://wiki.plantontology.org:8080/index.php/Annotation_File_Format looks like it matches the GO page (http://www.geneontology.org/GO.format.gaf-2_0.shtml), as it should. Could you please send the link?'' | ''I am not sure I understand to which page you are referring. The info shown here: http://wiki.plantontology.org:8080/index.php/Annotation_File_Format looks like it matches the GO page (http://www.geneontology.org/GO.format.gaf-2_0.shtml), as it should. Could you please send the link?'' | ||
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| + | =Plan of action:= | ||
| + | * Mary will work with JE to get SVN access set up, ''done'' | ||
| + | |||
| + | *PO will review the mappings between the maize samples (60) and the PO terms (~52). | ||
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| + | I am thinking about sending a small file first, to make sure all is fine and dandy, and then upload the larger file. Would that work for you? Or do you want to look at the beast in its full glory? | ||
Revision as of 18:28, 3 August 2011
Notes about the dataset:
From email: Mary Schaeffer: These are all new annotations – and there are a lot, as each gene-model has some expression. I am lumping the putative splice variants to one model.
For our 60 tissues for this set, the number of PO terms is some 52 distinct ones.
Questions
from MS by email:
- In a few cases, there is a classical gene name for the gene model. I assume these could be supplied as synonyms? Or, would you prefer they be supplied as a separate row?
Need to look at this, and ask PJ
- Do you still wish to have separate files for anatomy and growth terms?
I think that might be a good idea as well to make the huge file easier to deal with.
- Note, the instructions on the wiki for field 13. TAXON deal with Field 12 and should be altered.
I am not sure I understand to which page you are referring. The info shown here: http://wiki.plantontology.org:8080/index.php/Annotation_File_Format looks like it matches the GO page (http://www.geneontology.org/GO.format.gaf-2_0.shtml), as it should. Could you please send the link?
Plan of action:
- Mary will work with JE to get SVN access set up, done
- PO will review the mappings between the maize samples (60) and the PO terms (~52).
I am thinking about sending a small file first, to make sure all is fine and dandy, and then upload the larger file. Would that work for you? Or do you want to look at the beast in its full glory?
