GAF file 2.0 survey (Retired): Difference between revisions
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However, I will try to get the option added to the curation tool so that i can curate the additional information, even if I can't display it. | However, I will try to get the option added to the curation tool so that i can curate the additional information, even if I can't display it. | ||
Column 16: | Column 16: | ||
Column 17: | Column 17: Fission yeast does not have many alternatively spliced genes although there are a couple of examples of alternative transcripts. These are not currently suitable for GO annotation as all of the experimentation is done on the canonical form. For some examples the alternative transcripts are regulatory, but do not produce a protein coding gene and so have been given a separate identifier as a non-codingRNA (I can think of one example). I don't think i would use this column much for alternative splice forms. If I remember correctly this column will also be used for representing a modified (for example phosphorylated form) of a protein. I can see that potentially I would use the column for this, but at present I do not have identifiers to represent modified/non modified forms, so I wouldn't be sure how to do this and there is not a pressing need for this. | ||
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|RGD | |RGD |
Revision as of 10:07, 2 April 2009
- GAF file header: (please fill in)
- Column 2 should represent the 'canonical gene', and should map to column 1 of the Gene2geneproduct_file
- Column 12 now refers to the information in column 17 (or in Column 2 if Column 17 is empty).
- Column 16: can be left blank
- column 17: should represent the unit annotated (if different from that in column 2)
Can all groups provide the new file? (Yes or No, if not please explain):
Reference Genome Group | Contact Person | Y/N | Reason |
---|---|---|---|
SGD | Stacia Engel | ||
MGI | Li Ni | ||
FlyBase | Susan Tweedie | No | FlyBase does not currently support curation of column 16 or 17 data during GO annotation. Like ZFIN, the required changes to DB, curation interface, data checking/integration tool and web pages are not a high priority but I will continue to push for this. I will also try to generate some example data and will also use this to try to convince the other curators that the extra effort involved in capturing this information is worthwhile (they have expressed concern that it could be very time consuming to find out which isoform has been used in an experiment for col 17). |
dictyBase | Pascale Gaudet | ||
E.coli | Jim Hu | ||
TAIR | Tanya Beradini | ||
WormBase | Kimberly Van Auken | ||
S. pombe | Val Wood | No | GeneDB does not currently support curation of column 16 or 17 data during GO annotation. The required changes to curation interface, database and web pages are not a high priority for GeneDB.
However, I will try to get the option added to the curation tool so that i can curate the additional information, even if I can't display it. Column 16: Column 17: Fission yeast does not have many alternatively spliced genes although there are a couple of examples of alternative transcripts. These are not currently suitable for GO annotation as all of the experimentation is done on the canonical form. For some examples the alternative transcripts are regulatory, but do not produce a protein coding gene and so have been given a separate identifier as a non-codingRNA (I can think of one example). I don't think i would use this column much for alternative splice forms. If I remember correctly this column will also be used for representing a modified (for example phosphorylated form) of a protein. I can see that potentially I would use the column for this, but at present I do not have identifiers to represent modified/non modified forms, so I wouldn't be sure how to do this and there is not a pressing need for this. |
RGD | Victoria Petri | ||
Human | Emily Dimmer | ||
Zebrafish | Doug Howe | No | ZFIN does not currently support curation of column 16 or 17 data during GO annotation. We are not likely to support curation of this type of data into ZFIN any time soon as it will require DB, curation interface, and public display changes that we are not likely to have time to implement any time soon....though I wish we could. I may still try to drum up some example data, but will have to manually manufacture a GAF with col. 16/17 data added on. |
Chicken | Fiona McCarthy |