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HUPO-PSI / psi-mi-CV

Molecular Interactions Controll Vocabulary
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feature clarification: cross-linker/cross-linked residue #420

Open lukasz99 opened 4 years ago

lukasz99 commented 4 years ago

There is a cross-linker (MI:0911) but no cross-linked residue. It is not clear how to use it. is it supposed to refer to cross-linked residue or actual cross-linker ? if latter (although I cannot come up with a use case) than a new term is needed in order to annotate cross-linking sites. Otherwise definition of the term got to be modified...

pporrasebi commented 4 years ago

Cross linker refers to the cross-likning agent used, as I infer from the definition and also the children terms indicate. Do you need a 'cross-linked residure' feature in the CV? There can be use cases for it, but it is not currently IMEx practice to capture cross-linked residues.

lukasz99 commented 4 years ago

On 10/31/19 7:31 AM, Pablo Porras wrote:

Corss linker refers to the cross-likning agent used, as I infer from the definition and also the children terms indicate. Do you need a 'cross-linked residure' feature in the CV? There can be use cases for it, but it is not currently IMEx practice to capture cross-linked residues.

my guess it's not captured b/c at the time the decision was made the infrmation was not there (apart from special cases it is hard to identify x-linked sites other then disulfides; this got changed with MS development/accessibility). getting 'crosslinked residue/crosslink site' term makes it possible to annotate these at all (at the moment it is not possible). the curation policy seems to be a separate issue that can be discussed at the next imex meeting.

personally I think location of x-links is at least as valuable as binding region info and, as there's not too many experiment to curate, I don't have a problem curating these without formal imex requirement.

lukasz

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Lukasz Salwinski PHONE: 310-825-1402 UCLA-DOE Institute FAX: 310-206-3914 UCLA, Los Angeles EMAIL: lukasz@mbi.ucla.edu

pporrasebi commented 4 years ago

Sure, I agree with your argument. I am just asking if you need the term for curation outside IMEx boundaries. I just do not want to create the term if there is not actual use case for it. If your answer is a definitive 'yes', I'll create the term.