Extensions/substance by role

Background

To define biological processes and functions such as

• toxin transporter activity
• hormone secretion
• response to fungicide

In the same way as we define other processes, we cannot use CHEBI roles directly. The inputs and outputs of a process are necessarily material entities. We therefore define a set of chemical entities by their roles. For example:

• substance with herbicide application :: any entity of a class that is used by humans as a herbicide
• substance with acid chemical property :: any entity that has an acid chemical role by virtue of its chemical structure

Solution

We create new URIs (in the GOCHE namespace) for every CHEBI role. These have the same numeric part as the CHEBI ID, but this is a convenience and not to be relied upon.

Example:

• GOCHE:'substance with antibiotic application' EquivalentTo CHEBI:'molecular entity' and has_application some CHEBI:antibiotic

Axes

The CHEBI role hierarchy currently mixes applications, biological contexts, chemical properties. We disambiguate these lexically and with differens relations.

• has_application
• has_biological_role (see below)
• has_chemical_role

For biological contexts, we are likely to always define this directly with a GO process. E.g. we do not classify dopamine metabolism as neurotransmitter metabolism, as some organisms metabolise dopamine even if they don't have a nervous system. Here we introduce an extra subclass "dopamine metabolism involved in neurotransmission" for the contextual case.

• TODO: provide stable URIs for relations
• TODO: Add links from CHEBI structures to substance-by-role structures. These will not all follow CHEBI:has_role, due to the aforementioned cases like dopamine.

DONE

• Fixed GO logical defs to use material entities not roles diff

Download

• http://purl.obolibrary.org/obo/go/extensions/substance_by_role.owl

This ontology imports other ontologies. You can check out the extensions SVN directory and use the catalog there

It is recommended you use Protege and view the inferred hierarchy, using Elk

The editors xp file:

• http://purl.obolibrary.org/obo/go/editors/gene_ontology_xp_write.obo

and the go-plus release

• http://purl.obolibrary.org/obo/go/extensions/go-plus.owl

all use these

E.g.

[Term]
id: GO:0004887 ! thyroid hormone receptor activity
intersection_of: GO:0004872 ! receptor activity
intersection_of: has_input GOCHE:60311 ! substance with thyroid hormone biological role

[Term]
id: GO:0004903 ! growth hormone receptor activity
intersection_of: GO:0004872 ! receptor activity
intersection_of: has_input GOCHE:37845 ! substance with growth hormone biological role