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HUPO-PSI / psi-mi-CV

Molecular Interactions Controll Vocabulary
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New terms: phosphotransfer/phosphotransfer assay #120

Closed noedelta closed 8 years ago

noedelta commented 17 years ago

Relevant PMID: 16712436

In this particular case the phosphate is transferred between two proteins of a phosphorelay system. Phosphorylation/dephosphorylation terms cannot be used as both should be applied whereas interaction cannot be annotated with more than one interaction type term.

'phosphotransfer assay' can be, in principle, bypassed by using, depending on circumstances, kinase/phosphatase terms but having an assay term mirroring the enzymatic reaction type seems reasonable...

in addition, 'phosphate donor' and 'phosphate acceptor' as biological roles seem to be appropriate...

lukasz

Reported by: lukasz99

noedelta commented 17 years ago

Logged In: YES user_id=545117 Originator: NO

A point for consideration however - if we are now going to be able to do a mapping to a wider range of external CVs and eventually intend to replace the PTMs with PSI-MOD should we also map the "enzymatic study" terms to GO and leave them to further develop these, as we are redundant to their efforts. They already have a full description of 2-component signal transduction btw.

Sandra

Original comment by: orchard

noedelta commented 17 years ago

Logged In: YES user_id=653048 Originator: NO

Ok for the biological roles, I am not clear wheather you want the assay or the interaction type or both.

Original comment by: luisa_montecchi

noedelta commented 17 years ago

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>Ok for the biological roles, I am not clear wheather you want the assay or >the interaction type or both.

to clarify, the optimal (at least from my point of view :o) would be: enzymatic reaction: phosphotransfer enzymatic reaction assay: phosphotransfer assay biological role: phosphate acceptor, phosphate donor

Sandra, can you point me to the place with the relevant PSI-MOD info ? I've tried OLS but found nothing about reactions under PSI-MOD branch :o(

lukasz

Original comment by: lukasz99

noedelta commented 17 years ago

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added see from MI:0841 to MI:0844

Original comment by: luisa_montecchi

noedelta commented 17 years ago

Original comment by: luisa_montecchi