XP:biological process xp chebi: Difference between revisions
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union_of: CHEBI:27529 ! P(1),P(2)-bis(5'-adenosyl) triphosphate | union_of: CHEBI:27529 ! P(1),P(2)-bis(5'-adenosyl) triphosphate | ||
</pre> | </pre> | ||
GO defines this as ''The chemical reactions and pathways involving diadenosine triphosphate, a derivative of the nucleoside adenosine with three phosphate groups attached'' | |||
CHEBI does not have a term '''diadenosine triphosphate''' | |||
=== Tracker Items === | === Tracker Items === |
Revision as of 04:54, 9 July 2008
bp_xp_chebi constructed by Mike Bada of UCDHSC
Augmented by obol results from CJM
Synopsis
Logical definitions for GO Biological Process and Molecular Function using CHEBI. The current set is maintained by Mike Bada in the Hunter Group at UCDHSC
Introduction
XPs defining GO terms in terms of chemical entities; example:
[Term] id: GO:0000273 name: lipoic acid metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_participant CHEBI:16494 ! lipoic acid
i.e. lipoic acid metabolic process =def a metabolic process that has_participant lipoic acid
Availability
Unlike the other GO cross-products, these are not housed in the go/scratch/xps directory. The primary copy is housed on sourceforge in the go_chebi_xp directory.
This xp file has been registered in the OBO xps metadata so it is available on the cross-product download page:
- downloads page
- imports.obo file (point oboedit at this)
- HTML
Missing Link Report
NOTE: This report is out of date w.r.t the latest xps, and there are a few problems with it.. check back later
Results
Relations used
The UCDHSC cross-products use a large set of relations; See:
Examples of use:
[Term] id: GO:0000316 name: sulfite transport intersection_of: GO:0006810 ! transport intersection_of: results_in_directed_movement_of CHEBI:17359 ! sulfite
[Term] id: GO:0051381 name: histamine binding intersection_of: GO:0005488 ! binding intersection_of: results_in_joining_of CHEBI:18295 ! histamine
The argument is that the relations are required for providing xp definitions that are necessary and sufficient (all definitions are by definition necessary and sufficient). For example, if we instead said:
[Term] id: GO:0000316 name: sulfite transport intersection_of: GO:0006810 ! transport intersection_of: has_participant CHEBI:17359 ! sulfite
This would be wrong as a definition. We need to indicate the role that sulfite plays in transport - i.e. it is the entity that is transported, as opposed to the location that it is transported too, or the entity that initiates the transport.
At the RO meeting some participants were not keen on having a large collection of hard to define relations in RO. Alan Ruttenberg showed an alternative way of defining biochemical processes using a minimal set of relations, OWL class expressions and an ontology of dispositions (i.e. to be a substrate). The approach needs concretized further to compare it with the Bada/UCDHSC method. In the meantime, it was decided that the UCDHSC relations and xps were useful today, so they would live in a separate RO called MACRO; these relations can be expanded to the longer Ruttenberg style expressions, when this has been fleshed out more.
CHEBI terms
On occasion there are entities referenced in GO processes that Mike identified as corresponding to the set-union of classes in CHEBI; for example:
[Term] id: GO:0015962 name: diadenosine triphosphate metabolic process intersection_of: GO:0008152 ! metabolism intersection_of: has_participant anon_chemical_16 [Term] id: anon_chemical_16 namespace: chebi_ontology is_anonymous: true union_of: CHEBI:27775 ! P(1),P(3)-bis(5'-adenosyl) triphosphate union_of: CHEBI:27529 ! P(1),P(2)-bis(5'-adenosyl) triphosphate
GO defines this as The chemical reactions and pathways involving diadenosine triphosphate, a derivative of the nucleoside adenosine with three phosphate groups attached
CHEBI does not have a term diadenosine triphosphate
Tracker Items
Chebi tracker:
Presentations
From 2007