Initial Meeting- Aug 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.

- one way to reduce the data size: look only at gene models that are not expressed in all tissues – this will reduce by some 50% but it is still a big dataset.

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?

Issues and concerns

• From the POC conference call 8-2-11:

-use of column 16 to designate the different stage descriptions in different sources

• Documentation of the statistical analysis and cut-off used for the microarray data- is this published yet?

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). ''MS sent us the mappings as a spreadsheet and we discussed it on the POC conference call 8-2-11.

• Do we need to add or modify any existing PO terms? Are we going to proceed with getting rid of the Zea "sensu" terms?

• Mary will upload a small file first, (perhaps the annotations to the structure terms first?) and then upload the larger file.