modification up/down +Torin1

[mah11]

Follow-up from helpdesk (ticket 9292) for modifications that increase or decrease upon adding Torin1 ...

Canto and the website already allow increased during and decreased during extensions of modification annotations, so one job for me is to update the upload format documentation. (I'll be lazy and not make a separate website ticket for it, tho.)

@ValWood So, given that Torin1 inhibits both TORs, do you think it would be OK to use increased or decreased during GO:0032007 negative regulation of TOR signaling? That option wouldn't be available in Canto, because we've restricted that to phases and response-to processes, but we can put any BP ID in a a bulk load file.

If that won't do, I'll add configurations for yada_in_presence_of(CHEBI:nnn) extensions.

[mah11]

Come to think of it, is it worth adding the presence_of(CHEBI) extension option anyway, on spec?

[ValWood]

Come to think of it, is it worth adding the presence_of(CHEBI) extension option anyway, on spec?

It could be useful. Should I add both the TOR signalling and the presence_of in that case?

[mah11]

Up to you what to do for this set of annotations ... I suppose both are true; the chemical is the tool used to get at the "real" process that affects the modifications.

I also remembered where else to add the new stuff: the mini-ontology in svn (pombe-embl/mini-ontologies/PSI-MOD_extension_relations.obo). That and the config edits are done.

[ValWood]

sanity check increased_in_presence_of(CHEBI:84327),increased_during(GO:0032007) decreased_in_presence_of(CHEBI:84327),decreased_during(GO:0032007)

look OK?

[mah11]

yup!