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PomBase website v2
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Displaying modified residues, part 1 (active form, column17) #1623

Closed ValWood closed 4 years ago

ValWood commented 4 years ago

Currently we display a label from PRO, or the PRO id (It's different in different contexts).

The PRO display label looks like this:

binding section https://www.pombase.org/gene/SPAPB1A10.09 active form anaphase spindle elongation protein 1 unmodified form

https://www.pombase.org/gene/SPAC1782.09c active form tyrosine-protein phosphatase Clp1 phosphorylated 1

https://www.pombase.org/gene/SPAC1782.09c mediator of replication checkpoint protein 1 phosphorylated 2

These are sub-optimal in a number of ways 1) won't really mean very much to our users 2) use the UniProt description as a base, which is always different to our description, and sometimes incorrect or out of date- also it's a long label the gene name would be much more succinct (taking up less space in individual annotations) and less prone to changes over time 3) Exclude the critical information for our users, the actual residue(s)

So we will need to have a system in place where we create a more meaningful label from the PRO entry.

Ideally we would display active form anaphase spindle elongation protein 1 unmodified form A -> Ase1-unmodified

active form tyrosine-protein phosphatase Clp1 phosphorylated 1 ->Clp1-P-S396,408,467,468,493,513

mediator of replication checkpoint protein 1 phosphorylated 2 -> -> Mrc1-P-S604

This information is available in one of the synonym forms: https://github.com/PROconsortium/PRoteinOntology/issues/197

Darren said: "You're in luck, because the synonym with the information you need is always labeled "PRO-proteoform-std" and, as the name of the synonym type indicates, it is a standardized representation of modifications. Some updates are in the works--mostly to handle glycans--but the basic description is given in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210558/ (figure 1)."

ValWood commented 4 years ago

from

https://github.com/pombase/website/issues/67 Darren Natale has created some SPARQL queries https://sourceforge.net/p/pro-obo/term-requests/115/ which should be able to get the required info? We can discuss after pombe 2017...

ValWood commented 4 years ago
Screenshot 2020-10-14 at 22 15 15

non-binding example:

would become:

histone methyltransferase activity (H3-K9 specific)

  | has substrate hht1-Ub-K14, hht2-Ub-K14, hht3-Ub-K14   | involved in pericentric heterochromatin assembly occurs in regional_centromere_outer_repeat_region   | involved in silent mating-type cassette heterochromatin assembly occurs in mating-type region heterochromatin   | occurs in regional_centromere_inner_repeat_region

(note we will need to deal with the Methionine removal, but this is really maturation, not modification. I'm hoping we can get PRO to handle this)

ValWood commented 4 years ago

Cut12

modelling modifications

Would become:

GO:0035591 signaling adaptor activity
cut12-unP has input dis2 part of G2/M transition of mitotic cell cycle in mitotic spindle pole body  during mitotic G2 phase IPI with dis2 Grallert A et al. (2013)
cut12-P-T75,78 has input plo1 part of G2/M transition of mitotic cell cycle  in mitotic spindle pole body  during mitotic G2 phase IPI with plo1 Grallert A et al. (2013)

Essentially the modified entity would be displayed as the annotated entity, rather than as an extension.

ValWood commented 4 years ago

open a new ticket for the configuration