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.
Use this to search for relevant terms in external ontologies. NEVER guess ontology terms or term IDs, always confirm using this skill. The general methodology is to use `obo-grep.pl`
For working with any terms in the catalytic activity branch; these often correspond to RHEA or EC terms
For working with GO taxon constraints (TCs), i.e never_in_taxon and only_in_taxon relationships
| name | mapping |
| description | For working with mappings (dbxrefs) in GO. |
Mappings in GO have been historically represented as xrefs
xref: EC:2.5.1.30
Mappings are always represented at the term level. Mappings should not be confused with definition provance, although there may be some duplication here, this is OK. Mappings should not be confused with external logical definition (we never map to CHEBI or UBERON for example, but we may have relationships or logical definitions pointing there).
More recently in GO we have been concerned with the meaning of a mapping and newer mappings always have a skos predicate for the mapping indicated as a trailing qualifier.
id: GO:0000031
name: mannosylphosphate transferase activity
xref: MetaCyc:RXN-22693 {source="skos:narrowMatch"}
means that the GO ID has a narrower concept in the MetaCyc ID
Example where the external term is narrower in meaning:
id: GO:0000031
name: mannosylphosphate transferase activity
namespace: molecular_function
def: "Catalysis of the reaction: GDP-alpha-D-mannose + n {[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]-alpha-D-Man-(1->6)}60-(Man9GlcNAc2-[protein] = phosphorylated {[alpha-D-Man-(1->2)-alpha-D-Man-(1->2)]-alpha-D-Man-(1->6)}60-(Man9GlcNAc2-[protein] + n GMP + n H+ or GDP-alpha-D-mannose + alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-3-O-(Ser/Thr)-[protein] = alpha-D-Man-(1->3)-alpha-D-Man-(1->3)-[alpha-D-Man-6P-]-alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-3-O-(Ser/Thr)-[protein] + GMP + H+." [MetaCyc:RXN-22693, MetaCyc:RXN-22694]
xref: MetaCyc:RXN-22693 {source="skos:narrowMatch"}
xref: MetaCyc:RXN-22694 {source="skos:narrowMatch"}
is_a: GO:0016758 ! hexosyltransferase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28340" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28811" xsd:anyURI
Example where the RHEA ID is equivalent, we disambiguate two MetaCycs and the EC is broader
id: GO:0000121
name: sn-glycerol 1-phosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: H2O + sn-glycerol 1-phosphate = glycerol + phosphate." [RHEA:46084]
synonym: "alpha-glycerol phosphatase activity" RELATED [EC:3.1.3.21]
synonym: "alpha-glycerophosphatase activity" RELATED [EC:3.1.3.21]
synonym: "glycerol 3-phosphatase activity" RELATED [EC:3.1.3.21]
synonym: "glycerol 3-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.21]
synonym: "glycerol-1-phosphatase activity" BROAD [EC:3.1.3.21]
synonym: "glycerol-1-phosphate phosphohydrolase activity" RELATED [EC:3.1.3.21]
synonym: "glycerol-3-phosphate phosphatase activity" RELATED [EC:3.1.3.21]
xref: EC:3.1.3.21 {source="skos:broadMatch"}
xref: MetaCyc:GLYCEROL-1-PHOSPHATASE-RXN {source="skos:broadMatch"}
xref: MetaCyc:RXN-14964 {source="skos:exactMatch"}
xref: RHEA:46084 {source="skos:exactMatch"}
is_a: GO:0016791 ! phosphatase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27964" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI
Note that the GO def follows the RHEA definition precisely, and one of the participants is 1-phosphate; there is a similar reaction (RHEA:66372; sn-glycerol 3-phosphate + H2O = glycerol + phosphate) with a different participant. Both are mapped to the broader EC.
runoak -i sqlite:obo:eccode info EC:3.1.3.21
=> EC:3.1.3.21 ! glycerol-1-phosphatase
runoak -i sqlite:obo:rhea info RHEA:46084
=> RHEA:46084 ! sn-glycerol 1-phosphate + H2O = glycerol + phosphate
Always lookup these IDs.
Most mappings are in MF, and it is possible to be precise due to the fact that RHEA has precise participants. ALWAYS consider the reaction participants when mapping MFs.