Difference between revisions of "RO:Main Page"

From NCBO Wiki
Jump to: navigation, search
m (Proposed new relations)
m (Proposed new relations)
Line 9: Line 9:
==Proposed new relations==
==Proposed new relations==
The lacks family of relations is being discussed
The lacks family of relations is being discussed: see: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]
See: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]
Next we will be examining:
Next we will be examining:

Revision as of 08:18, 2 May 2007

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 in this OBO file media:Hunter_Bada_OBO_relationship_proposal.zip. Each of our proposed relationships has a range over the GO biological process hierarchy, although with varying domains, mostly over continuants.

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 instances of these relationships among terms from the GO, ChEBI and CTO ontologies. For example, we identified 30 instances of a <GO Biological Process> results_in_change_in <ChEBI term>, 13 instances where <GO:BP> results_in_change_in <GO:CC> and 41 instances where <GO:BP> results_in_change_in <CTO term>. The more specific relationships are actually more prevalent: we propose 593 instances of <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