Difference between revisions of "RO:Main Page"

From NCBO Wiki
Jump to: navigation, search
m (Open issues)
m (Instance-level relations)
Line 13: Line 13:
 
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:
 
The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:
  
1. '''instance_of''' holding between an instance and a type
+
*1. '''instance_of''' holding between an instance and a type
2. '''part_of''' holding between an instance and an instance
+
*2. '''part_of''' holding between an instance and an instance
3. ''part_of'' holding between a type and a type
+
*3. ''part_of'' holding between a type and a type
  
 
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.
 
We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.
Line 23: Line 23:
 
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:
 
In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:
  
c instance_of C at t - a primitive relation between a continuant instance and a class which it instantiates at a specific time
+
*c instance_of C at t - a primitive relation between a continuant instance and a class which it instantiates at a specific time
  
p instance_of P - a primitive relation between a process instance and a class which it instantiates holding independently of time
+
*p instance_of P - a primitive relation between a process instance and a class which it instantiates holding independently of time
  
c part_of c1 at t - a primitive relation between two continuant instances and a time at which the one is part of the other
+
*c part_of c1 at t - a primitive relation between two continuant instances and a time at which the one is part of the other
  
p part_of p1, r part_of r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)
+
*p part_of p1, r part_of r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)
  
c located_in r at t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time
+
*c located_in r at t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time
  
r adjacent_to r1 - a primitive relation of proximity between two disjoint continuants
+
*r adjacent_to r1 - a primitive relation of proximity between two disjoint continuants
  
t earlier t1 - a primitive relation between two times
+
*t earlier t1 - a primitive relation between two times
  
c derives_from c1 - a primitive relation involving two distinct material continuants c and c1
+
*c derives_from c1 - a primitive relation involving two distinct material continuants c and c1
  
p has_participant c at t - a primitive relation between a process, a continuant, and a time
+
*p has_participant c at t - a primitive relation between a process, a continuant, and a time
  
p has_agent c at t - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process
+
*p has_agent c at t - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process
 
 
In proposing new relations (both here and in the , please specify which of the three types your proposal is
 
  
 +
In proposing new relations (both on the and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify which of the three types your proposal is
  
 
==Proposed new relations==
 
==Proposed new relations==

Revision as of 06:27, 9 February 2008

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

There's an RO expert meeting happening in May, 2008. See OntologyRelations

Instance-level relations

The OBO Relation Ontology (aka the OBO Relationship Types Ontology) distinguished three families of relations, according to whether they hold between instances, types, or combinations thereof, for example:

  • 1. instance_of holding between an instance and a type
  • 2. part_of holding between an instance and an instance
  • 3. part_of holding between a type and a type

We use bold face to mark out those relational expressions used in ontologies such as GO to represent the relations between the types these ontologies represent.

In the original Genome Biology paper we focused primarily on defining relations of type 3. in terms of those of types 1. and 2. This was to meet the need among biologists for clear guidance as to what the relational expressions used in ontologies such as GO precisely mean.

In our treatment of relations of types 1. and 2. we focused primarily on picking out certain instance level relations which we fixed on as primitive -- meaning that they are so basic to the relational architecture of reality that they cannot be defined in terms of anything more basic. The primitive relations selected were as follows:

  • c instance_of C at t - a primitive relation between a continuant instance and a class which it instantiates at a specific time
  • p instance_of P - a primitive relation between a process instance and a class which it instantiates holding independently of time
  • c part_of c1 at t - a primitive relation between two continuant instances and a time at which the one is part of the other
  • p part_of p1, r part_of r1 - a primitive relation of parthood, holding independently of time, either between process instances (one a subprocess of the other), or between spatial regions (one a subregion of the other)
  • c located_in r at t - a primitive relation between a continuant instance, a spatial region which it occupies, and a time
  • r adjacent_to r1 - a primitive relation of proximity between two disjoint continuants
  • t earlier t1 - a primitive relation between two times
  • c derives_from c1 - a primitive relation involving two distinct material continuants c and c1
  • p has_participant c at t - a primitive relation between a process, a continuant, and a time
  • p has_agent c at t - a primitive relation between a process, a continuant and a time at which the continuant is causally active in the process

In proposing new relations (both on the and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify which of the three types your proposal is

Proposed new relations

relations between generically dependent continuants and specifically dependent continuants:

  • concretizes
  • is_concretized_by
  • about
  • inheres_in
  • depends_on
  • output_of
  • has_input
  • has_function
  • has_quality
  • realization_of
  • lacks

The lacks family of relations is discussed at: [2]

The treatment of the derives_from relation has been criticised from an ontological point of view: [3]. Transformation_of is always, by definition a 1-1 relation. The thesis in the original 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

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 [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