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Community / AGENT SKILL
chemical-entity
0
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
Understand the trade-offs.
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The full skill.
Original instructions from the publisher’s SKILL.md
# When to use - Find ChEBI IDs for chemical entities to use in GO term definitions - Determine the correct protonation state for a chemical - Understand chemical classification and parent classes - Create biosynthetic process or metabolic process terms that reference chemicals - Verify chemical cross-references The general thing to keep in mind is that selecting the right CHEBI term is harder than it seems. Don't assume that the term with the most biologist-friendly label is the right one! CRITICAL: Protonation State Selection (pH 7.3 Canonicalization) **For GO term logical definitions, ALWAYS prefer the major species at physiological pH (approximately 7.3).** - for chemicals with different protonation states, the ph7.3 form must be used - for chemicals with different stereoisomers, the appropriate L or D form must be used (except in very rare cases where we want to be agnostic) ## Exemplar term ``` id: GO:0005290 name: L-histidine transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of L-histidine from one side of a membrane to the other. L-histidine is 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] synonym: "histidine/arginine/lysine/ornithine porter activity" NARROW [] synonym: "L-histidine transporter activity" BROAD [] is_a: GO:0015174 ! basic amino acid transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:57595 ! L-histidine zwitterion relationship: part_of GO:0089709 ! L-histidine transmembrane transport ``` Corresponds to `src/design_patterns/transmembrane_transport.yaml` design pattern. Note that even if the user requested `histidine` we would have interpreted that to mean the L-form. Note also that there is a CHEBI term with the label "L-histidine" (CHEBI:15971), but this is not the ph7.3 form, we instead use the ph7.3 form. However, we retain the biologist friendly label. ## Core Tool: OAK (Ontology Access Kit) ### Basic ChEBI Lookup The primary tool for ChEBI lookups is OAK with the sqlite adapter: ```bash # Search by name (exact match) runoak -i sqlite:obo:chebi info 'L-cysteine' # Search by fuzzy match (any match) runoak -i sqlite:obo:chebi info 'l~terpenoid' # Search by prefix (starts with) runoak -i sqlite:obo:chebi info 'l^glutam' # Finds terms starting with "glutam" ``` ## 7.3 mapping Here is how we would obtain the correct term for L-histidine ``` runoak -i sqlite:obo:chebi info L-histidine ``` ==> CHEBI:15971 Look this up ``` cd src/ontology && wget ftp://ftp.expasy.org/databases/rhea/tsv/chebi_pH7_3_mapping.tsv grep '^15971\t' chebi_pH7_3_mapping.tsv ``` yields ``` 15971 57595 computation ``` Check: ``` runoak -i sqlite:obo:chebi info CHEBI:57595 ``` ==> `CHEBI:57595 ! L-histidine zwitterion`