Remaining annotation to move out of the contig files

[kimrutherford]

Here are the counts of the /controlled_curation annotation still in the contig files.

@ValWood Are any of these a priority for moving to their own files in SVN?

     26 catalytic activity
      6 complementation
     22 experimental tools
      6 external_link
   1935 gene expression
    159 genome organization
   1484 misc
     76 misc functional group
   1011 name description
     23 pathway
  25147 species distribution
    196 subunit composition
   1692 warning

[ValWood]

6 external_link should move to externam link (either general, or publication associated)

23 pathway we will review and remove as they should be in captured by GO-CAMs

6 complementation we will remanp.

I would say 1
935 gene expression
could be in the flat files (we have the format, and I thought they already were in the flat files?)
But no hurry.

1011 name description could also be moved into a flat file

We can discuss the others tomorrow.

[kimrutherford]

I thought they already were in the flat files?

I can't find a GitHub issue about that. All the gene expression data I can see SVN is in: pombe-embl/external_data/qualitative_gene_expression_data/ and in pombe-embl/external_data/Quantitative_gene_expression_data/. I don't think any of it came from the contig files.

[ValWood]

1. Move legacy gene expression file into PHAF
2. Move name description
3. @PCarme will do legacy external links
4. Remember the "misc" contains a lot of "external links" for single mutant expression data (old microarray datasets) - we refactor these when we have all the remining data in an export file
5. move everything else to a TSV file

[kimrutherford]

Documentation for adding links on the reference page:
https://github.com/pombase/website/wiki/Config-file#reference_page_extra_links

[PCarme]

3. @PCarme will do legacy external links

That's done.