InterPro2GO: GO:0019685 "dark reaction" read as "light-independent"

Back to the project page. Reproduce with
uv run python projects/CACAO/scripts/upstream_checks.py; raw query output in
data/interpro2go-GO0019685-2026-11-01.tsv
(the 3,731 annotation rows).

Found while reviewing the CACAO annotations on Rhodobacter capsulatus
bchF, whose own CACAO row was
sound. The defective row on that gene was not CACAO's.

The claim

GO:0019685 is the carbon-fixation grouping term. Its is_a children are
GO:0019253 reductive pentose-phosphate cycle (synonyms "Calvin cycle", "C3
photosynthesis"), GO:0009760 C4 photosynthesis and GO:0009761 CAM
photosynthesis, and its definition reads:

A complex cycle of enzyme-mediated reactions which catalyzes the reduction of
carbon dioxide to sugar. As well as carbon dioxide the cycle requires reducing
power in the form of reduced nicotinamide adenine dinucleotide phosphate
(NADP) and chemical energy in the form of adenosine triphosphate (ATP). The
reduced NADP (NADPH) and ATP are produced by the 'light' reactions.

Four InterPro entries map to it, and all four are light-independent
(bacterio)chlorophyll biosynthesis families:

The first three are the subunits of dark-operative protochlorophyllide
oxidoreductase (BchB/N/L, ChlB/N/L); the fourth is BchF. None of them fixes
carbon. The mapping is explicable only as reading the term's label — "dark
reaction" — as a synonym for "light-independent", which is what the entry names
say.

The error is invisible to any ancestor or descendant check, because the term is
neither too broad nor too narrow for these families. It is a different pathway.

Scale

GO:0019685 carries 3,731 GOA annotations, and every one of them is IEA from
GO_REF:0000002, assigned by InterPro — one reference, one assigning group.
The term has no use in GOA independent of this mapping. Every annotation GO
holds on carbon fixation's grouping term was produced by misreading its name.

Requested change

Delete the GO:0019685 line from all four entries. No replacement needs to
be chosen, because each entry already carries its correct terms beside the wrong
one:

IPR005969  GO:0016730 oxidoreductase activity, acting on iron-sulfur proteins as donors
IPR005969  GO:0015995 chlorophyll biosynthetic process
IPR005969  GO:0019685 photosynthesis, dark reaction            <-- remove
IPR005970  GO:0016730, GO:0015995                              (same pattern)
IPR005971  GO:0005524 ATP binding, GO:0016730, GO:0015995      (same pattern)
IPR009905  GO:0016836 hydro-lyase activity
IPR009905  GO:0030494 bacteriochlorophyll biosynthetic process
IPR009905  GO:0019685 photosynthesis, dark reaction            <-- remove

Deleting the four lines removes 3,731 wrong annotations and loses nothing.

Two optional refinements, lower priority and for a curator who knows the
families better than this review does:

• The three DPOR subunits could carry GO:0016630 protochlorophyllide
  reductase activity, which is exact for all three regardless of organism and
  avoids the chlorophyll/bacteriochlorophyll split that makes a single BP
  mapping imprecise (GO:0036068 light-independent chlorophyll biosynthetic
  process for ChlB/N/L against GO:0036070 light-independent
  bacteriochlorophyll biosynthetic process for BchB/N/L).
• IPR009905 is bacteriochlorophyll-specific, so GO:0036070 would be more
  precise than the GO:0030494 it already has. There is no MF term for the
  BchF reaction (EC 4.2.1.165); the bchF review files that as a separate
  proposed_new_terms request.

Separate request to GO, on the term itself

Two problems with GO:0019685 that this mapping exposes but does not cause.

The label is obsolete and actively misleading. "Dark reaction" was
abandoned in the field decades ago precisely because it suggests a reaction that
occurs in the dark rather than one that does not itself require light — and that
is exactly the misreading above. Suggest renaming to a carbon-fixation label and
keeping "photosynthesis, dark reaction" as an exact synonym, so that no future
pipeline can make the same inference from the primary name. The term dates to
2001-10-22 and its label has not been revisited since 2002-06-26.

The definition describes only one of its children. It is written as the
Calvin cycle specifically — CO2 to sugar via NADPH and ATP — while GO:0009760
C4 and GO:0009761 CAM photosynthesis are also is_a children. The definition
should be generalised to the grouping the term actually is, or the term should be
restructured. Note that GO:0019253, the proper Calvin cycle term, is the one
carrying the "Calvin cycle" synonym and the MetaCyc CALVIN-PWY and
UniProtKB-KW KW-0113 cross-references, and has 7,851 annotations of its own, so
there is no question of merging the two: GO:0019685 is the parent, not a
duplicate.

Status

• [ ] Report the four mapping deletions to InterPro.
• [ ] Report the label and definition problems to GO as a separate,
  lower-priority ontology request.