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OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro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

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-=RO - OBO Relation Ontology=
+= Announcement =
-The main RO page is located on sourceforge: [http://obo.sourceforge.net/relationship]
+OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro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.
+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

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Latest revision as of 16:36, 1 November 2013

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