RO:Main Page

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Revision as of 18:31, 5 July 2007 by Bada (talk | contribs) (Hunter/Bada Proposal for new relations)
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RO - OBO Relation Ontology

The main RO page is located on sourceforge: [1]

You can browse the ontology and get e-mail list details there.

Open issues

Proposed new relations

The lacks family of relations is being discussed: see: [2]

Next we will be examining:

inheres_in, has_function, has_quality, and relations that deal with creation, consumption and development

The treatment of the derives_from relation has been criticised from an ontological point of view: [3].

There is also the terminological problem that "derives_from" is used specifically for evolutionary relationships by some. We will report back on this after the september NCBO anatomy meeting. We may create a "develops_from" parent for transformation_of corresponding to how that relation is currently used in MOD AOs

Hunter/Bada Proposal for new relations

We propose the addition of nine new relationships (and nine additional inverse relationships) to the RO. The relationship are defined and linked to the existing relationships at [4].

Perhaps the most basic of these is intended to capture the idea of a process leading to a change in a continuant: <process> results_in_change_in <continuant> (see the above linked OBO file for formal definitions). We also propose two more specific versions of this when the continuant is either the thing changed (results_in_change_from) or the thing that results from the change (results_in_change_to).

In addition, we propose well over 1000 assertions using these relationships among terms from the GO, ChEBI and CL ontologies. In a first draft, we've identified 30 assertions in which <GO Biological Process> results_in_change_in <ChEBI term>, 13 assertions in which <GO:BP> results_in_change_in <GO:CC> and 41 assertions in which <GO:BP> results_in_change_in <CL term>. The more specific relationships are actually more prevalent: We've identified an initial 641 assertions in which <GO:BP> results_in_change_to <ChEBI term>.

The other relationships we propose are:

  • results_in_capability_to_change_to
  • results_in_directed_movement_of
  • results_in_division_of
  • results_in_joining_of
  • results_in_perception_of
  • results_in_regulation_of

Definitions of each and positions in the RO hierarchy are in the OBO file.

We've posted a message with the subject "Hunter/Bada Proposal for New Relations" on the relationship-ontology mailing list describing our rationales for these in more detail.

OWL Conversion

The standard GO obo->owl conversion is used. See OboInOwl:Main_Page for details

obo1.2 defines "builtin" tags for relations that are hardwired into the obo semantics - is_a and instance_of are tagged builtin. These are not exported in OWL, as these are also part of the OWL language