SPKW mapping transport/electron transport

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In Uniprot, some gene products like

cytochrome b5 O94391 have the keywords transport AND electron transport

Can the keyword 'transport' be removed from these entries?

In GO, electron transport (Midori, did we once discuss making the primary name 'electron transfer' to remove confusion?)

anyway, the point here is that 'electron transfer/transport' is not 'transport' as defined in GO.

So if these keywords cannot be removed, then 'transport' cannot map to 'transport' which is a bit drastic as it will loose lots of mappings

Reported by: ValWood

Original Ticket: "geneontology/annotation-issues/339":https://sourceforge.net/p/geneontology/annotation-issues/339

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> did we once discuss making the primary name 'electron transfer'?

'Electron transport' has 'electron transfer' as an exact synonym. I can't find anything to suggest that we were going to swap the name and synonym.

m

Original comment by: mah11

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• milestone: --> GOA
• assigned_to: nobody --> ecamon

Original comment by: mah11

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I thought it was discussed at a consortium meeting, but could be my imagination, and if it was it was ages ago.

Would it make sense though, as it isn't a direct child of transport? I think it could be helpful for curators.....

Original comment by: ValWood

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OK, I still get back transport mappings pulled in from this, so can it be assigned to Ev?

eg Uniprot entires include O94523 P00046

Original comment by: ValWood

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Hi Ev,

Is this still on your radar?

This could be another one to deal with via some logic,

i.e only map to GO 'transport' if has keyword 'transport' BUT NOT keyword 'electron transport'.

Val

Original comment by: ValWood

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• assigned_to: ecamon --> edimmer

Original comment by: mah11

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Can this be looked into, its still generating lots of problem mappings.

e.g. P87111

Its affecting some of my analysis, so I think I may have to remove all of my SPKW mapping to transport to work round it but its also affecting lots of protein in other organisms.

Cheers

Val

Original comment by: ValWood

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Sorry again for not closing this item...

Right..

GO Electron transport def is: The transport of electrons from an electron donor to an electron acceptor. with synonym electron transfer

SPKW definition is: ID Electron transport. AC KW-0249 DE Protein involved in the transport of electrons, a process by which electrons are transported through a series of reactions from the reductant, or electron donor, to the oxidant, or electron acceptor, with concomitant energy conversion. Necessary for both photosynthesis and aerobic respiration. GO GO:0006118; electron transport HI Biological process: Transport; Electron transport. CA Biological process.

sorry i think the mapping might be correct from the defs...however maybe the kw hiearchy to general 'transport' term is causing a problem.

Is Jen re-doing transport part of GO anything new I should know..

SPKW def for 'transport ; is ID Transport. AC KW-0813 DE Protein involved in the transport of a molecule (metabolite, protein, etc), a ion or an electron across cell membranes, inside the cell or in a tissue fluid. (mapped to 29801 Swiss-Prot entries)

GO transport def: The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

now a mapping from GO transport to KW transport still looks ok to me...

again do you think its the hierarchy of kws...i'm stumped on this one...help?

Evelyn

evelyn

Original comment by: camon

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The keyword hierarchy is the problem; the direct GO mappings look fine, nay obvious. After much discussion, GO has moved 'electron transport' so that it's not under 'transport', and it would make sense for the keywords to mirror that arrangement.

There's no major work going on on transport at the moment, although the transport interest group plans to work on processes at some point.

m

Original comment by: mah11

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Hi Ev,

I think the problem is that

GO transport def: The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells.

does not cover electron transport (you will see that

electron transport The transport of electrons from an electron donor to an electron acceptor.

is not a child of transport.

This is because it does not fit the transport def:

Midori, perhps we could add a comment to 'transport' that it exludes 'electron transport'?

The only way to fix this is

i) to remove 'transport' kw from all entries where the 'transport' refers to 'electron transport'

ii) lose the Go mapping to transport, which would be a bit drastic.

iii) do some fancy logic post processing of Unirpot entries i.e only map to GO 'transport' if has keyword 'transport' BUT NOT keyword 'electron transport'.

(we haven't adressed the transport part of the process ontology, but there are no plans to change this part of the heirarchy)

Original comment by: ValWood

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Ah I see, midori already responded. I think we have said the same thing. val

Original comment by: ValWood

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yep, it's actually fairly simple after all: uniprot just has to change this bit of the electron transport kw:

HI Biological process: Transport; Electron transport.

the rest should follow on from that fix, if I understand rightly

comment added to transport; can't hurt.

m

Original comment by: mah11

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Passing this one to Emily as mapping is ok, needs to be discussed with Claire and perhaps also serenella to change kw hierarchy

Evelyn

CHANGE TO PENDING EMILY

Original comment by: camon

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• status: open --> pending

Original comment by: edimmer

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This Tracker item was closed automatically by the system. It was previously set to a Pending status, and the original submitter did not respond within 90 days (the time period specified by the administrator of this Tracker).

Original comment by: sf-robot

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• status: pending --> closed

Original comment by: sf-robot

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• status: closed --> pending

Original comment by: mah11

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This Tracker item was closed automatically by the system. It was previously set to a Pending status, and the original submitter did not respond within 90 days (the time period specified by the administrator of this Tracker).

Original comment by: sf-robot

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• status: pending --> closed

Original comment by: sf-robot