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HUPO-PSI / psi-mod-CV

Reactivated PSI-MOD ontology for molecular mass modifications
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Adding terms to psi-mod-CV to link modifications with amino acids #11

Open pmt706 opened 4 years ago

pmt706 commented 4 years ago

Would everyone be ok if I were to run through the psi-mod CV and put in appropriate links to the amino acids modified? For instance, right now, MOD:01356 is_a MOD:00916 (modified serine), when I would categorize it instead as MOD:01356 is_a MOD:00002 (O-glycosyl serine, which itself is_a MOD:00916). There are many such circumstances in the MOD:01157 (protein modification characterized by amino acid modified) side of the CV that need addressing.

pabinz commented 4 years ago

In that respect, if we want to reorganise the strict relationships of terms, which makes perfect sense, yes, there are many instances. MOD:01356 would have is_a MOD:00002 ! O-glycosyl-L-serine (instead of MOD:00916) is_a MOD:00517 ! Hex1HexNAc1NeuAc1 glycosylated residue

And I would keep the order of the is_a by starting with the proximal childhood of MOD:01157 followed by the proximal childhood of MOD:01156 (although this priorization has no impact on the relationship itself. Only a human reading convenience)

Cheers

De : pmt706 notifications@github.com Envoyé : lundi 10 février 2020 20:43 À : HUPO-PSI/psi-mod-CV psi-mod-CV@noreply.github.com Cc : Subscribed subscribed@noreply.github.com Objet : [HUPO-PSI/psi-mod-CV] Adding terms to psi-mod-CV to link modifications with amino acids (#11)

Would everyone be ok if I were to run through the psi-mod CV and put in appropriate links to the amino acids modified? For instance, right now, MOD:01356 is_a MOD:00916 (modified serine), when I would categorize it instead as MOD:01356 is_a MOD:00002 (O-glycosyl serine, which itself is_a MOD:00916). There are many such circumstances in the MOD:01157 (protein modification characterized by amino acid modified) side of the CV that need addressing.

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pmt706 commented 4 years ago

Agreed! My goal is to connect these leaf nodes to as few parents as possible and to root them ultimately to MOD:01157 and MOD:01156 (and to MOD:00538 where necessary)... also to pick up any missing links to UniMod/RESID if they exist.

edeutsch commented 4 years ago

Although I didn't realize we had this problem, in that I thought it was already very nicely hierarchical, if you see ways to make the parent-child relationships better, I am all for it! Agreed!