Version 39 (modified by antonialock, 10 years ago) (diff)


1-2 December, 2011

NOT annotations
again....ok to put just 'NOT' in col 16? And then tack on any other extension as they apply?

Ste11 paper
PMID: 10867006. Only annotated "HMG box domain binding" - possible to capture more information? E.g C-term binds outside of the consensus sequence, loop 1/2 binds consensus.

Protein IDs
PR:xxx and PRO:xxx when to use what ID
Also, certain gene products, either repeats that are cleaved into multiple proteins after transcr/transl (P-factor), or where there are multiple genes for the same product (M-factor) or if you want to refer to a family of proteins (histones). What is best to use? GeneID? (multiple annotations). Protein ID?

Get artemis running
I'm still mac inept!

Protein sequence features
another example in PMID 21118960 of promoter mutagenesis

cnx1Protein cleavage site (protein feature, SO:0100011)within aa residue 438-455

This is a bit like the NLS situation i described earlier.

Midori has supplied Kim with a mapping with the use of these exisiting protein feature terms to SO terms

So I added this in artemis as:

/controlled_curation="term=protein sequence feature, cleavage site; M438-K455|region; db_xref=PMID:19606215; date=20111027"

(is this what you meant, the cleavage site is somewhere in the region of 438-455)

so this one will go through to PomBase. We will do protein sequence features like this for a while as it will be some time before these can be done fully in the curation tool, and there aren't too many of them.

Note that if we use any SO terms which aren't in the list we will need to supply a mapping to Kim to make it appear in Pombase.

14-15 November, 2011 (3-4 November, 2011)

done - Retreat
Stuff to talk about and discuss at the retreat [BR]]

done - has_substrate
use systematic ID for now. Is inferred from context. Can add .1 for transcripts (mRNA substrates).
At the moment I annotate the has_substrate relationship on the underlying assumption that the user should be able to infer whether the substrate is a protein product or RNA (for instance kinase X has the substrate GeneDBSpombe Y). I suspect that this might be quite an inaccurate way of doing it and might come back and haunt us in the future (especially if we want to build automated pathway overviews etc). Should I actually be crossreferencing PRO ID's (and what about mRNA?).

done - TermGenie
How do I know what things to run through TermGenie? Just things like "regulation" etc relating to existing terms?

done - helpdesk
Will go through this next time.
a tour

done - Relations
Keep this as it is for MF. Requires regulation by for process control.
make list of ontologies used for relations and examples
the 'requires_regulator' term is very specific (the annotated gene product is a catalytic subunit of a complex, and requires a regulatory subunit for activity). Should it only be applicable to complexes e.g if it is shown that a MF doesn't occur if another gene is not present (which might be upstream....) then this should not be used (and only annotate to the other gene product as being involved in the process...)?

17-18 October, 2011

Capturing diploid phenotypes
There is a CL term for diploid (CL:0000415 - A cell whose nucleus has two haploid genomes)
This does not distinguish between homozygous or heterozygous. I did ask for a term but not sure they will make one. If not --> allele=heterozygous/homozygous?

eg PMID 12557273 
pik3 deletion --> sterile
pik3 deletion in diploid --> inviable spores produced
pik3 heterozygote --> all spores viable (even pik3 deletion)
therefore - pik3 is required for the formation of spore but not germination

What is the standard
Perhaps more of a philosophical question, but what are the standard conditions? e.g MM or YE, exponential growth, stationary? etc.
I think it would be nice to have the standard conditions defined, especially for phenotype annotations. Of course not to the fine experimental set-up details, but capturing general deviations from the standard would, in my opinion, be more rigorous.

Cell morphology
It would be useful to get some (image) examples of shapes. {{{E.g what is snowman? And what morphology do these cells have in D? (8380233)

  • Make a wiki page linking to different examples. Name examples FYPO[term]_img. Record reference.

Phenotype terms
To discuss: DNA binding terms and enzymatic activity.

||sxa2||Normal carboxypeptidase activity||K309A||
This mutant cannot process P-factor. It was an in vitro assay as opposed to monitoring the pheromone response

Phenotype 2
For the term "abolished protein modifications", how do you specify which protein mod is abolished if there are multiple annotated. For the time being I have just used qualifier=MOD...

  • add child terms

What are appropriate annotations to "regulation" terms?
I.e. Do you have to have some level of the response initially, the level which is further upregulated by a gene product.
or if the loss of a gene cause the absence of a response is it then +vly regulating? I'm guessing not - it is just essential for the pathway?

Modifying frames