gocentral
commented
20 years ago Logged In: YES user_id=436423
> Problem: extracellular matrix (sensu magnoliophyta), > GO:0048196, is a child of extracellular matrix which is in- > turn a child of extracellular. It is also a child of external > encapsulating structure which is in-turn a child of cell. It > shouldn't be under both cell and extracellular since cell > and extracellular are mutual exclusive terms.
Good point.
> Should move extracellular matrix (sensu magnoliophyta), > in fact, the entire extracellular matrix node from > extracellular to cell? Extracellular matrix is considered > part of a cell.
This is true for plants, but not for animals, so we can't move the generic 'extracellular matrix' node to be a child of 'cell'.
> In addition, should make cell wall, GO:0005618, a child of > extracellular matrix? Currently plant primary cell wall and > secondary cell wall, GO:0009530 and GO:0009531, are > children terms of extracellular matrix (sensu > magnoliophyta). Should apply the same ontology to the > entire cell wall node?
No; this would not work for yeast or bacteria, which don't have anything called 'extracellular matrix' at all.
To solve the problem with GO:0048196, I think all we have to do is remove the relationship between 'extracellular matrix (sensu magnoliophyta)' and the generic 'extracellular matrix' (GO:0005578). I suspect the relationship was made only because of the similarity in text strings; the definition of GO:0005578 makes it clear that it's not a suitable parent for GO:0048196.
We could also add 'sensu Animalia' to the string for GO:0005578, which would be consistent with its definition and parentage, and create a new generic 'extracellular matrix' term that could be a direct child of 'cellular component', and a parent of GO:0005578 and GO:0048196.
midori
Original comment by: mah11
Problem: extracellular matrix (sensu magnoliophyta), GO:0048196, is a child of extracellular matrix which is in- turn a child of extracellular. It is also a child of external encapsulating structure which is in-turn a child of cell. It shouldn't be under both cell and extracellular since cell and extracellular are mutual exclusive terms.
Should move extracellular matrix (sensu magnoliophyta), in fact, the entire extracellular matrix node from extracellular to cell? Extracellular matrix is considered part of a cell.
In addition, should make cell wall, GO:0005618, a child of extracellular matrix? Currently plant primary cell wall and secondary cell wall, GO:0009530 and GO:0009531, are children terms of extracellular matrix (sensu magnoliophyta). Should apply the same ontology to the entire cell wall node?
Reported by: peifenz
Original Ticket: "geneontology/ontology-requests/1815":https://sourceforge.net/p/geneontology/ontology-requests/1815