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| − | =RO - OBO Relation Ontology= | + | = Announcement = |
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| − | 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| + | OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro |
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| − | 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]] |
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| − | =Open issues=
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| − | ==Proposed new relations==
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| − | * inheres_in
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| − | * depends_on
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| − | * output_of
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| − | * has_input
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| − | * has_function
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| − | * has_quality
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| − | * realization_of
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| − | * lacks
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| − | The lacks family of relations is discussed at: [http://ontology.buffalo.edu/medo/NegativeFindings.pdf]
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| − | 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.
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| − | 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
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| − | See also
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| − | [http://obofoundry.org/ro/#pending Pending] | |
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| − | ==Hunter/Bada Proposal for new relations==
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| − | 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].
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| − | 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).
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| − | 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>
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| − | 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>.
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| − | The other relationships we propose are:
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| − | * results_in_capability_to_change_to
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| − | * results_in_directed_movement_of
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| − | * results_in_division_of
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| − | * results_in_joining_of
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| − | * results_in_perception_of
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| − | * results_in_regulation_of
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| − | Definitions of each and positions in the RO hierarchy are in the OBO file.
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| − | 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.
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| − | ==OWL Conversion==
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| − | The standard GO obo->owl conversion is used. See [[OboInOwl:Main_Page]] for details
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| − | 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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