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For working with any terms in the catalytic activity branch; these often correspond to RHEA or EC terms
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Based on SOC occupation classification
For working with GO taxon constraints (TCs) using onlyin:/neverin: superclass assertions
Use whenever you run a Makefile target (e.g. `make travis_build`, `make test`, `make reasoned.ofn`) or any one-off ROBOT / owltools / dosdp-tools / scala-cli command derived from a Makefile recipe. These must run inside the pinned ODK Docker image, not against host tools. Covers validation, reasoning, imports, and release builds in src/ontology.
For handling the process around obsoleting GO terms. This is a complex process involving substantial analysis of impact, both on existing terms that reference to the to-be-obsoleted term, and on annotations
Use the /research skill when performing background research from the literature or the web to create a RESEARCH.md file; also covers use of `deep-research-client`
For working with any terms referencing chemical entities (CHEBI). CHEBI has some unusual properties that are counter-intuitive, so always use this skill to plan or check work that involves a chemical entity or CHEBI IDs, whether a new term, or significant alteration of existing terms
Use this skill when planning to create new ontology terms or modify existing ones to ensure proper design pattern compliance. This skill should be used proactively during issue planning to identify appropriate design patterns before term creation begins. No intersection_of tags should be added without using this skill.
| name | reaction |
| description | For working with any terms in the catalytic activity branch; these often correspond to RHEA or EC terms |
Reaction terms may have mappings that are qualified using skos (using source qualifiers), as in the following:
[Term]
id: GO:0000140
name: acylglycerone-phosphate reductase (NADP+) activity
namespace: molecular_function
def: "Catalysis of the reaction: 1-hexadecanoyl-sn-glycero-3-phosphate + NADP+ = 1-hexadecanoylglycerone 3-phosphate + H+ + NADPH." [RHEA:17341]
synonym: "1-acyldihydroxyacetone-phosphate reductase activity" EXACT []
synonym: "1-palmitoylglycerol-3-phosphate:NADP+ oxidoreductase activity" RELATED [EC:1.1.1.101]
synonym: "acyldihydroxyacetone phosphate reductase activity" RELATED [EC:1.1.1.101]
synonym: "palmitoyl dihydroxyacetone phosphate reductase activity" RELATED [EC:1.1.1.101]
synonym: "palmitoyl-dihydroxyacetone-phosphate reductase activity" RELATED [EC:1.1.1.101]
synonym: "palmitoyldihydroxyacetone-phosphate reductase activity" RELATED [EC:1.1.1.101]
xref: EC:1.1.1.101 {source="skos:exactMatch"}
xref: MetaCyc:ACYLGLYCERONE-PHOSPHATE-REDUCTASE-RXN {source="skos:exactMatch"}
xref: MetaCyc:RXN-15046 {source="skos:narrowMatch"}
xref: RHEA:17341 {source="skos:exactMatch"}
xref: RHEA:36175 {source="skos:narrowMatch"}
is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28070" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28526" xsd:anyURI
Ideally there is a single source of truth for a reaction terms, which should be specified in the def xref