XP:biological process xp chebi

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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 metabolic process THAT has_participant (some) 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:

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NOTE: This report is out of date w.r.t the latest xps, and there are a few problems with it..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 correspond to the set-union of classes in CHEBI; for example:

 [Term]
 id: GO:0000052
 name: citrulline metabolic process
 intersection_of: GO:0008152 ! metabolic process
 intersection_of: has_participant anon_chemical_1
 [Term]
 id: anon_chemical_1
 is_anonymous: true
 union_of: CHEBI:18211 ! citrulline
 union_of: CHEBI:16349 ! L-citrulline

Should CHEBI create the superclass of citrulline and L-citrulline?

Or should the xps just pick one?

Tracker Items

Chebi tracker:

Presentations

From 2007