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Category:RefGenome Electronic Jamboree 2009-07 ETFDH
See the talk page for discussion. See also Help:Annotation Jamborees
Contents
Orthoset
Participants
| Name | Group | Organism(s)/Genome(s) | Notes |
|---|---|---|---|
|
Kimberly Van Auken |
WormBase |
C. elegans |
worm ortholog: WBGene00002855 = let-721 |
|
Stan Laulederkind |
RGD |
Rat |
|
|
Debby Siegele |
ecoliwiki |
E. coli |
|
|
Li NI |
MGI |
Mouse |
MGI:106100 |
|
Jodi Hirschman |
SGD |
S. cerevisiae |
CIR2 |
|
Susan Tweedie |
flyBase |
D. melanogaster |
|
|
Tanya Berardini |
TAIR |
A. thaliana |
|
|
Ruth Lovering |
BHF-UCL |
Human |
|
| edit table |
GENE
no genes found in this category
Minutes
Attendees: Rob, Jodi, Suzi, Jim, Debby, Brenley, Yasmin, Mike, Kimberly, Emily, Rachael, Susan, Ruth, Varsha, Kara, Stan, Li, Pascale, Petra (who else?)
- Term definition question for human annotation: Because this is a dehydrogenase it would be appropriate to annotate to the process 'GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase', however, it was felt the definition is too narrow.
Def: A fatty acid beta-oxidation pathway in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product.
Objection to the wording "the initial step", makes it more sound like a 'one enzyme function term'. The Dehydrogenase has several steps to it, definition should be broader. Everyone agreed.
Ruth: create SF item about narrowing the def for GO:0033539.
- In general, there's a lack of annotations for ETFDH. Most common annotation is component mitochondrion that can be moved across.
Discussion about annotating experiments from other organisms. Experiments for pig were annotated. There are also annotations from Hamster. These annotations could be propagated at least to all mammals.
Pig annotations were added to GONUTS table. Hamster annotations will also be added to GONUTS. Agreement that experiments from other organisms should be annotated when annotations in the 12 ref genome organisms are scarce.
Annotations can be propagated fom GONUTS to GOA to AmiGO release. Other organisms can also be used in PAINT tool.
Question about which reference to use, not clear in documentation. For pig annotations PPOD reference has been used. If there is no other paper, create/use your own reference.
Action Item: Improve ISS evidence code documentation.
References
See Help:References for how to manage references in GONUTS.
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