PAINT-GONUTS integration

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For at least some test cases, GONUTS will be used to display PAINT-based annotations so MODs can do quality control.

Importing the PAINT GAF into GONUTS

known issues

  1. The underlying code for GONUTS relies heavily on mappings to UniProt. Using the gp2protein files it is possible to translate the UniProt Identifiers/Accessions to MOD ids to make pages in GONUTS; it is almost impossible to map NCBI identifiers automatically. i.e. They get made by hand and sometimes get skipped completely.
    --DanielRenfro 15:16, 10 September 2009 (UTC)

Display in GONUTS

GONUTS GOsummary extension pulls all gene associations for a gene into the summary table and graph, not just those added from the PAINT GAF.

  • Currently IEA is excluded from the summary table and graph. Should other evidence codes be excluded [Mary comment: the refG graphs display only experimental evidence code annotations (EXP, IDA, IPI,IMP, IGI, IEP); IC; and the ISS codes (ISS, ISO, ISA, ISM), which are only displayed (and labeled as "ISS_only") if there is no experimental annotation to the term.]
  • ISS to an ancestor node is now displayed as ISS-An in the table
  • How should qualifiers be handled. From the electronic jamborees, it was important to display NOT in the table. What about other qualifiers?


Examples

  • To show only the graph, enter this line on a category page.
<GOsummary>notable</GOsummary>
  • Alternatively, you can show only the table with:
<GOsummary>nograph</GOsummary>