// 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 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`
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 mappings (dbxrefs) in GO.
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 | chemical-entity |
| description | 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 |
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).
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.
The primary tool for ChEBI lookups is OAK with the sqlite adapter:
# 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"
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