gocentral
commented
21 years ago Logged In: YES user_id=451873
For the 'part of cell connected by pumps' - do you have a name that you would use to describe this location?
It's difficult to make this a GO term because it's a location that's dependent on a process (i.e. active transport across a membrane).
Original comment by: jl242
Hi,
In the course of working with the GKB group some issues have come up for cellular component. In particular for solutes.
Lincoln Stein wrote:
> > Hi All, > > Enclosed are my edits on > > Homo_sapiens_2,4-Dichlorobenzoate_degradation > Homo_sapiens_3-Chloroacrylic_acid_degradation > Homo_sapiens_Alanine_and_aspartate_metabolism > > I am uncertain about a number of things. First of all, there are a lot of > soluble small molecules, such as H+, which show up everywhere. First I > annotated them as cytosol, but then when I realized that they are also > present in mitochondrion and peroxisome, I moved them to cytoplasm. However, > I'm concerned that they will show up in extracellular matrix and nucleus > next. What should I do?
We need a location which covers everything except mitochondrial matrix, extracellular and some cytoplasmic vesicles, i.e. places which are connected to "the rest of the cell" by pumps.
> Second, none of the enzymes that I examined seem to be complexes, but several > are homotetramers and homodimers. How do I indicate this fact?
Complex:name of the complex hasComponent:monomer hasComponent:monomer hasComponent:monomer hasComponent:monomer
> Third, how do I tell when an enzyme is modified in the reaction? For example, > there's a cytochrome P450 involved in the first pathway, and it is (I think) > transiently oxidized during the reaction. Do I worry about the oxidized > intermediate? If I should, and I didn't happen to know, how could I tell?
3 Possibilities: 1) If it is some sort of prosthetic group which gets modified them you can consider functional P450 as a complex containing an AccessionedEntity (P450 polypeptide) and a NamedEntity (this "small" molecule). During the reaction it "transforms" into another complex of the same AccessionedEntity and a different NamedEntity (this is important, NamedEntities don't have modifications, "modified NamedEntities" is simply an independant NamedEntity. Think of ethanol <=> aldehyde <=> acetate).
2) If it is really protein modification then you can use AccessionedEntity's (P450) hasMOdifiedResidue attribute. However, I don't know yet the proper "syntax" for doing it in the text files. In this kind of situations Protege would really make life easier.
3) Not bother with the catalyst modifications. However, the threat there is that the catalyst for this reaction (P450) can one day be an output of another reaction or input to yet another reaction, i.e. someone actually describing what happens to P450. If this happens we won't be able to "make the ends meet". I think this is kind of a strategic decision that has to be taken hopefully collectively and with everybody's consent.
Rgds.,
i
Reported by: selewis
Original Ticket: "geneontology/ontology-requests/558":https://sourceforge.net/p/geneontology/ontology-requests/558