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=RO - OBO Relation Ontology=
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= Announcement =
  
The main RO page is located on sourceforge: [http://obo.sourceforge.net/relationship]
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OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro
  
You can browse the ontology and get e-mail list details there.
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Old material that was previously kept here has been moved to [[RO:Historic Material]]
 
 
=Open issues=
 
 
 
==Proposed new relations==
 
 
 
* inheres_in
 
* depends_on
 
* output_of
 
* has_input
 
* has_function
 
* has_quality
 
* realization_of
 
* lacks
 
 
 
The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]
 
 
 
The treatment of the derives_from relation has been criticised from an ontological point of view: [http://www.ifomis.uni-saarland.de/Home/DerivationBookVersion1-2.pdf]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original [http://genomebiology.com/2005/6/5/R46 RO paper] was (A) that the derives_from relation could be n-1 or 1-n (for n > 1) but also (B) that there are examples of 1-1 derives from relations (e.g. the relation between a living organism and a corpse). This thesis (B) has now been dropped. The relation between a corpse and the predecessor organism is one of transformation.
 
 
 
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
 
 
 
See also
 
 
 
[http://obofoundry.org/ro/#pending Pending]
 
 
 
==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 [http://compbio.uchsc.edu/Hunter_lab/Bada/extended_relationship.obo]. 
 
 
 
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
 

Latest revision as of 16:36, 1 November 2013

Announcement

OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro

Old material that was previously kept here has been moved to RO:Historic Material