Draft go-ontology tickets

Draft go-ontology tickets

Drafts for the project owner to file on
geneontology/go-ontology.
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1. GO:0000750 replaced_by misplaces non-kinase participants

Title: GO:0000750 replaced_by GO:0071507 moves upstream regulators onto the MAPK cascade

Body:

GO:0000750 pheromone-dependent signal transduction involved in conjugation
with cellular fusion was obsoleted (go-ontology#31335) as a precomposed term to
be represented as a GO-CAM, with replaced_by: GO:0071507 pheromone response
MAPK cascade.

Because replaced_by is applied to existing annotations automatically, every
gene annotated to GO:0000750 is moved into the MAPK cascade itself. That is
correct for the cascade kinases, but not for participants acting upstream of
it. Example: S. cerevisiae Arr4/GET3 (IMP, PMID:18261907) is a non-receptor
guanine-nucleotide exchange factor for the G alpha subunit Gpa1. It "promotes G
protein-dependent cellular responses, including mitogen-activated protein
kinase (MAPK) phosphorylation, new-gene transcription, and mating", but it is
not a component of the cascade.

Requests:

  1. Re-map such upstream annotations to GO:0062038 positive regulation of
    pheromone response MAPK cascade    . This follows the pattern of the S. pombe
    pheromone GO-CAM gomodel:693b3c0900000536, where GEF activity positively
    regulates the cascade.
  2. Where no single term is true of every annotated gene, use consider rather
    than replaced_by for this term.

2. General: check replaced_by against all annotated participants

Title: Obsoleting precomposed "X involved in Y" terms: check replaced_by covers every annotated gene

Body:

A precomposed term asserts two things, X and part_of Y. A single-term
replaced_by keeps one half. When it is applied automatically, it is only
safe if that term is true of every gene annotated to the obsolete class.
Two cases from our review of these terms:

Suggestion: before obsoleting a precomposed term with replaced_by, list the
distinct molecular roles among its annotated genes. If they are not all
covered by the replacement, use consider.

3. Caspase-regulator terms are not under their genus

Title: GO:0043027 and GO:0008656 are not subclasses of GO:0004869 / GO:0140608

Body:

GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic
process is_a only GO:0043028 cysteine-type endopeptidase regulator activity
involved in apoptotic process. It is not a subclass of GO:0004869
cysteine-type endopeptidase inhibitor activity. Likewise, GO:0008656
cysteine-type endopeptidase activator activity involved in apoptotic process
is_a GO:0016505 and GO:0043028, but not GO:0140608 cysteine-type endopeptidase
activator activity. None of these terms has a logical definition, and
GO:0043028 has no part_of apoptotic process. As a result, genes annotated
only to the apoptosis-specific term (for example XIAP, DIAP1 and CED-4) are not
returned by a query for cysteine-type endopeptidase inhibitor or activator
activity.

Requests:

  1. Add is_a to the genus and an intersection_of logical definition
    (genus and part_of GO:0006915).
  2. Alternatively, given the obsoletion policy for precomposed terms, obsolete
    them with consider pointing at the genus. A single replaced_by is unsafe
    here: some annotated genes regulate the caspase only indirectly, and
    Drosophila Hid, for example, acts on DIAP1 rather than on a caspase.

4. Precomposed terms with no logical definition (to collect)

Placeholder. During the full pass we are collecting live "involved in" terms
that have no intersection_of but whose label splits into two GO terms (for
example GO:0043027 cysteine-type endopeptidase inhibitor activity involved in
apoptotic process). The candidate list is in data/go_terms.yaml
(pattern: ... (label split)), regenerated by scripts/inventory.py.

5. MOMP regulation terms: "involved in apoptotic signaling pathway" is label-only

Title: GO:1901028/GO:1901029/GO:1901030: the "involved in" context is not in the logical definition, but the synonyms treat it as narrowing

Body:

GO:1901030 positive regulation of mitochondrial outer membrane permeabilization
involved in apoptotic signaling pathway is defined as GO:0065007 and positively_regulates GO:0097345 mitochondrial outer membrane
permeabilization. GO:1901029 and GO:1901028 follow the same pattern. The
logical definitions have no part_of GO:0097190. The context comes from
GO:0097345 itself, which is defined as MOMP "as part of the apoptotic
signaling pathway" (part_of GO:0097190). The "involved in apoptotic
signaling pathway" in the three labels is therefore entailed, not added.

The synonyms disagree. "regulation of MOMP" is EXACT on GO:1901028, and
"positive regulation of MOMP" is EXACT on GO:1901030. But the spelled-out
"positive regulation of mitochondrial outer membrane permeabilization" is
BROAD on GO:1901030, and the same holds on GO:1901029. Under the logical
definition, the spelled-out phrase names exactly the defined class.

Requests (either is fine):

  1. Relabel the three terms to (positive / negative) regulation of
    mitochondrial outer membrane permeabilization    . Keep the current labels as
    EXACT synonyms, and change the BROAD synonyms to EXACT.
  2. Or, if a non-apoptotic MOMP is meant to exist (compare GO:1902686
    mitochondrial outer membrane permeabilization involved in programmed cell
    death    ), say so in
    GO:0097345's definition and adjust the logical definitions so they
    distinguish the two.

Why it matters: precomposed "X involved in Y" terms are being retired in
favour of GO-CAM. Labels like these look precomposed, but there is no Y to
move into a model and no broader term to replace them with. In our corpus,
56 reviewer-authored uses and 10 GOA rows were on these terms.

6. Two "involved in" terms that name a process: rename, don't obsolete

Both terms are the right grain for the genes that carry them, but their
labels put them in the "X involved in Y" set that is being retired. A rename
would take them out of it without moving any annotation.

GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity.
The definition ("Any process which detects an amino-acid acetylated tRNA is
charged with the correct amino acid, or removes incorrect amino acids from a
charged tRNA") is aminoacyl-tRNA editing. GO has no other term for it, and
GO:0002161 aminoacyl-tRNA deacylase activity is part_of it. There is no
logical definition: "aminoacyl-tRNA metabolism" is not a GO class, and the
nearest genus, GO:0006399 tRNA metabolic process, is far broader.

Requests:

  1. Relabel to aminoacyl-tRNA editing (or aminoacyl-tRNA proofreading),
    keeping the current label as an EXACT synonym.
  2. Fix the synonym typo "aminoacyl-tRNA editin" → "aminoacyl-tRNA editing",
    and consider making it EXACT.
  3. Fix "amino-acid acetylated tRNA" in the definition, which presumably means
    "aminoacylated tRNA".

GO:0006271 DNA strand elongation involved in DNA replication. The term
names the elongation stage of replication: its EXACT synonym is "DNA
replication elongation", it xrefs Reactome R-HSA-69190 "DNA strand
elongation", and GO:0006272 leading strand elongation and GO:0006273
lagging strand elongation are is_a it. Obsoleting it in favour of
GO:0022616 DNA strand elongation would leave those stages under a genus
that also covers strand extension outside replication.

Request: relabel to DNA replication elongation, keeping the current label
as an EXACT synonym. The logical definition (GO:0022616 and part_of GO:0006260) can stay.

In our corpus, 49 reviewer-authored uses and 41 GOA rows are on these two
terms.