Split out of #174.
interpro_groundings.py refuses non-PROTEIN components by design, and it is
right to: an InterPro family denotes a protein, and the MS ring is ~26 copies of
FliF. Tagging the ring with the FliF family would assert the ring is a protein.
InterPro grounding import refused: automatic InterPro review accepts only
PROTEIN components; GO:0009288#ms_ring is 'PROTEIN_COMPLEX'
That leaves 16 PROTEIN_COMPLEX components with no route to a grounding at
all — the flagellum's MS ring, C ring, stator, rod, LP rings and export
apparatus among them.
Complex Portal is the obvious candidate
It is already ADOPTED in the source queue and scripts/complex_portal.py
exists. A Complex Portal accession denotes exactly a defined multi-protein
complex, which is what these components are.
Worth checking first whether the flagellar sub-complexes actually have Complex
Portal entries — several may not, in which case a GO cellular-component term is
the fallback (GO:0009431 bacterial-type flagellum basal body, and similar).
A related modelling question
lp_rings combines FlgH and FlgI, and each has an exact InterPro family of its
own — IPR000527 (L-ring) and IPR001782 (P-ring) — while the combined
component has none. It is the one case in the flagellum where splitting the
component would make both halves groundable. Whether that is worth doing, or
whether the L and P rings are better kept as one component, is a curation
decision rather than a tooling one.
Split out of #174.
interpro_groundings.pyrefuses non-PROTEIN components by design, and it isright to: an InterPro family denotes a protein, and the MS ring is ~26 copies of
FliF. Tagging the ring with the FliF family would assert the ring is a protein.
That leaves 16
PROTEIN_COMPLEXcomponents with no route to a grounding atall — the flagellum's MS ring, C ring, stator, rod, LP rings and export
apparatus among them.
Complex Portal is the obvious candidate
It is already
ADOPTEDin the source queue andscripts/complex_portal.pyexists. A Complex Portal accession denotes exactly a defined multi-protein
complex, which is what these components are.
Worth checking first whether the flagellar sub-complexes actually have Complex
Portal entries — several may not, in which case a GO cellular-component term is
the fallback (
GO:0009431bacterial-type flagellum basal body, and similar).A related modelling question
lp_ringscombines FlgH and FlgI, and each has an exact InterPro family of itsown —
IPR000527(L-ring) andIPR001782(P-ring) — while the combinedcomponent has none. It is the one case in the flagellum where splitting the
component would make both halves groundable. Whether that is worth doing, or
whether the L and P rings are better kept as one component, is a curation
decision rather than a tooling one.