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Lisez SKILL.md et les fichiers associés affichés par SkillsMP avant de décider de l'installer.
Basé sur la classification professionnelle SOC
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Affichage de SKILL.md
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 reading, writing, debugging, or extending Soufflé Datalog (`.dl`) programs in this repo — the layered ontology QC program under `src/util/qc/`, the `basic-cycles.tsv` cycle check, taxon-constraint materialization, and the relation-diff CI report. Covers the RDF fact-file format these programs consume, this repo's Soufflé conventions, the check registry, and the required control-ontology self-test for any new or changed rule.
For reviewing a pull request against the GO ontology, whether from a local checkout or from the automated reviewer in CI. Covers what to check, how to grade severity, and how to report coverage honestly. Use whenever asked to review, critique, or check a PR or a diff to go-edit.obo.
| 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.