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.