addiehl
commented
1 week ago Most likely, David Dougall, who used to work with Richard Scheuermann a decade ago, provided the list of markers.
Also of note, the Gene Ontology Consortium has helpfully made the "GO_REF:0000031" obsolete, meaning that while Protege attempts to resolve the URL, it leads to a dead page.
However, the GO_REF:0000031 page still can be found through Google: https://geneontology.org/GO_REF/0000031.html
CL has 196 uses of GO_REF:0000031. Thanks GO for obsoleting an identifier in use by another resource!
@cmungall @pgaudet
dosumis
Alevolar macrophage would be a good test case for cleaning up cell surface marker assertions.
The basic term can, I think, be defined very simply - these are macrophages that reside on the luminal surface of alveoli. see https://github.com/obophenotype/cell-ontology/issues/2404. This is probably sufficient for the EC def.
The current EC def includes a large set of markers. Breakdown:
lacks_plasma_membrane_part some CX3C chemokine receptor 1 PR has plasma membrane part RO some integrin alpha-X PR has plasma membrane part RO some C-type lectin domain family 7 member A PR has plasma membrane part RO some adhesion G protein-coupled receptor E1 PR has plasma membrane part RO some sialoadhesin PR has plasma membrane part RO some macrosialin PR has plasma membrane part RO some macrophage mannose receptor 1 PR has low plasma membrane amount RO some integrin alpha-M PR
For all of these we need
(a) a uniprot mapping - see #2293 (b) a breakdown of markers into mouse vs human+ refs. Some info on this in the def (which unfortunately has no ref!). Experiment with LLMs + ref resolution (e.g Perplexity) for doing this. The Manchester Syntax expressions work pretty well for this. Could also try using refs on subclasses of alveolar macrophage as context for LLM.