XP:molecular function xp chebi
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Synopsis
Logical definitions for GO Molecular Function using CHEBI.
See also
Introduction
functions defined in terms of inputs/outputs:
[Term] id: GO:0003883 ! CTP synthase activity intersection_of: GO:0003674 ! molecular_function intersection_of: OBO_REL:has_input CHEBI:15422 ! ATP intersection_of: OBO_REL:has_input CHEBI:15713 ! UTP intersection_of: OBO_REL:has_input CHEBI:16134 ! ammonia intersection_of: OBO_REL:has_output CHEBI:16761 ! ADP intersection_of: OBO_REL:has_output CHEBI:35780 ! phosphate ion intersection_of: OBO_REL:has_output CHEBI:17677 ! CTP
cardinality used:
[Term] id: GO:0000293 ! ferric-chelate reductase activity intersection_of: GO:0003824 ! catalytic activity intersection_of: OBO_REL:has_input CHEBI:29033 {cardinality="2"} ! CHEBI:29033 ! iron(2+) intersection_of: OBO_REL:has_input CHEBI:15846 ! NAD(+) intersection_of: OBO_REL:has_output CHEBI:29034 {cardinality="2"} ! CHEBI:29034 ! iron(3+) intersection_of: OBO_REL:has_output CHEBI:16908 ! NADH intersection_of: OBO_REL:has_output CHEBI:15378 ! hydron def: "Catalysis of the reaction: 2 Fe2+ + NAD+ = 2 Fe3+ + NADH + H+." [EC:1.16.1.7]
todo: make cardinality of 1 explicit
Availability
Available in GO CVS:
Methods
For catalysis terms, Obol was used to parse text definitions of the form
Catalysis of the reaction: ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
For other terms, an Obol grammar was used to parse names
The xp defs were then partially vetted by CJM
The lack of EXACT synonyms in CHEBI hindered the automated process somewhat
Results
Reactome, Rhea and pathway db Alignment
in progress..
Chebi formulae
We have translated CHEBI formulae to cardinality-based definitions. See:
For example:
[Term] id: FORMULA:H3N namespace: formula intersection_of: CHEBI:24431 ! molecular structure intersection_of: has_part CHEBI:25555 {cardinality=1} ! nitrogen intersection_of: has_part CHEBI:49637 {cardinality=3} ! hydrogen
We then add is_a links from the CHEBI IDs to these formula expressions:
[Term] id: CHEBI:16134 name: ammonia namespace: chebi_ontology ... synonym: "AMMONIA" EXACT [MSDchem:NULL] synonym: "Ammonia" EXACT [KEGG_COMPOUND:NULL] synonym: "Ammoniak" RELATED [ChemIDplus:NULL] synonym: "H3N" RELATED FORMULA [KEGG_COMPOUND:NULL] synonym: "InChI=1/H3N/h1H3" RELATED InChI [ChEBI:NULL] synonym: "InChIKey=QGZKDVFQNNGYKY-UHFFFAOYAF" RELATED InChIKey [ChEBI:NULL] synonym: "NH(3)" RELATED [UniProt:NULL] synonym: "NH3" RELATED [IUPAC:NULL, KEGG_COMPOUND:NULL] synonym: "[H]N([H])[H]" RELATED SMILES [ChEBI:NULL] synonym: "[NH3]" RELATED [MolBase:NULL] synonym: "ammonia" EXACT IUPAC_NAME [IUPAC:NULL] synonym: "ammoniac" RELATED [ChEBI:NULL] synonym: "amoniaco" RELATED [ChEBI:NULL] synonym: "azane" EXACT IUPAC_NAME [IUPAC:NULL] synonym: "spirit of hartshorn" RELATED [ChemIDplus:NULL] xref: Beilstein:3587154 xref: ChemIDplus:7664-41-7 xref: Gmelin:79 xref: KEGG_COMPOUND:7664-41-7 xref: KEGG_COMPOUND:C00014 xref: MSDchem:NH3 xref: MolBase:930 xref: NIST_Chemistry_WebBook:7664-41-7 is_a: CHEBI:35107 ! azanes is_a: CHEBI:37176 ! mononuclear parent hydrides is_a: FORMULA:H3N relationship: is_conjugate_acid_of CHEBI:29337 ! azanide relationship: is_conjugate_base_of CHEBI:28938 ! ammonium
We can use this in reasoning. E.g. to check that equations are balanced.