Difference between revisions of "RO:Main Page"
| Line 9: | Line 9: | ||
==Proposed new relations== | ==Proposed new relations== | ||
| − | inheres_in | + | * inheres_in |
| − | depends_on | + | * depends_on |
| − | output_of | + | * output_of |
| − | has_input | + | * has_input |
| − | has_function | + | * has_function |
| − | has_quality | + | * has_quality |
| − | realization_of | + | * realization_of |
| − | lacks | + | * lacks |
| − | + | The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf] | |
| − | [http:// | + | 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== | ==Hunter/Bada Proposal for new relations== | ||
Revision as of 09:41, 2 January 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
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: [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
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