Latest revision as of 15:36, 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OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro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

Difference between revisions of "RO:Main Page"

Latest revision as of 15:36, 1 November 2013

Announcement

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-=RO - OBO Relation Ontology=
+= Announcement =
-The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]
+OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro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=
-There's an RO expert meeting happening in May, 2008. See [[OntologyRelations]]
-Note that requests for new terms etc should go in the [http://sourceforge.net/tracker/?group_id=76834&atid=947684 RO tracker]
-==Three types of 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 [http://genomebiology.com/2005/6/5/R46 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 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 [http://www.bioontology.org/wiki/index.php/RO:Main_Page#Proposed_new_relations wiki] and in the http://sourceforge.net/tracker/?group_id=76834&atid=947684&func=browse Sourceforge Tracker], please specify to which of the three types your proposed relation belongs.
-*If it is an instance-level relation, please answer the following questions:
-**a. is it already on the list above?
-**b. is it primitive in the above-mentioned sense?
-*If the answer to both of these questions is no,
-**c. can it be defined in terms of the relations on the above list?
-*If yes, please supply a definition (an example is provided below)
-*If no, please propose also those primitive instance-level relations which would need to be added to the RO in order to define it.
-==How to Define an Instance-Level Relation==
-First, check whether your proposed relation needs a definition -- perhaps it is primitive (see above).
-All definitions specify necessary and sufficient conditions. Thus if we are defining what it is to be an A, then the definition might read, for example:
-x is an A =def. x has features F1, F2, F3.
-This definition would be correct if and only if everything which has features F1, F2, and F3 is an A, and everything which is an A has features F1, F2, and F3.
-For instance-level relations, the definition might read as follows:
-x stands in instance-level relation r to y =def. x has features F1, F2, y has features F3, F4, x stands in instance-level relations r1, r2 to y.
-For a specific example consider '''preceded_by''', a relation between occurrents (drawn from the RO paper).
-With the primitive relations '''has_participant''' and '''earlier''' at our disposal we first define the instance-level relation p '''occurring_at''' t as follows:
-p '''occurring_at''' t =def. for some c, p '''has_participant''' c '''at''' t.
-We can then define:
-c '''exists_at''' t =def. for some p, p '''has_participant''' c '''at''' t
-p '''preceded_by''' p1 =def. for all t, t1, if p '''occurring_at''' t and p1 '''occurring_at''' t1, then t1 '''earlier''' t
-:t '''first_instant''' p =def.
-::p '''occurring_at''' t, and
-::for all t1, if t1 '''earlier''' t, then not p '''occurring_at''' t1
-:t '''last_instant''' p =def.
-::p '''occurring_at''' t and
-::for all t1, if t '''earlier''' t1, then not p '''occurring_at''' t1
-:p '''immediately_preceded_by''' p1 =def.
-::for some t, t '''first_instant''' p and
-::t '''last_instant''' p1.
-In these terms we can also define the instance-level relation '''has_duration''' proposed by Liju:
-:p '''has_duration''' y =def.
-::p is an occurrent, and
-::for some t1, t1 '''first_instant''' p, and
-::for some t2, t2 '''last_instant''' p, and
-::for all t, t1 '''earlier''' t and t '''earlier t2''' implies p '''occurring_at''' t [this to ensure that p is continuous; has no gaps],
-;; y is the interval (t1,t2).
-Here a new functional operator 'the interval ( , )' has been introduced, which generates the name of an interval from a pair of names for times.
-==Proposed new type-level 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: [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]
-'''The relation of ''overlaps'''''
-X ''overlaps''  Y =def. for every t and every x, if x '''instance_of''' X at t, then there is some instance y of Y at t such that (x '''overlaps''' y at t)
-where
-x '''overlaps''' y at t =def there is some z such that z is '''part_of''' x '''at t''' and z  '''part_of''' y '''at t'''
-Note that it can be the case that X ''overlaps'' Y as thus defined, even though Y does not ''overlap'' X.
-Thus uterine tracts ''overlaps'' urinogenital sysem but not uriongenital system OVERLAPS uterine tract (because of male urinogenital systems)
-==Proposed Gene Ontology 'Regulates' Relations==
-[Typedef]
-id: OBO_REL:regulates
-name: regulates
-def: "A relation between a process and a process or quality. A regulates B
-if the unfolding of A affects the frequency, rate or extent of B. A is
-called the regulating process, B the regulates process" []
-transitive_over: OBO_REL:part_of
-[Typedef]
-id: OBO_REL:positively_regulates
-name: positively_regulates
-def: "A regulation relation in which the unfolding of the regulating
-process *increases* the frequency, rate or extent of the regulated process"
-[]
-is_a: OBO_REL:regulates
-transitive_over: OBO_REL:part_of
-[Typedef]
-id: OBO_REL:negatively_regulates
-name: negatively_regulates
-def: "A regulation relation in which the unfolding of the regulating
-process *decreases* the frequency, rate or extent of the regulated process"
-[]
-is_a: OBO_REL:regulates
-transitive_over: OBO_REL:part_of
-Example file:
-ftp://ftp.geneontology.org/pub/go/scratch/gene_ontology_with_regulates_rela
-tions_test.obo
-Some follow-up comments at the sourceforge tracker page [https://sourceforge.net/tracker/index.php? func=detail&aid=1874192&group_id=76834&atid=947684 here]:
-==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.
-==TAIR Relations==
-* involved in
-* functions as
-* expressed in
-* not involved in
-* not functions as
-* not expressed in
-* related to
-* not related to
-* required for
-* not required for
-* located in
-* not located in
-* is subunit of
-* constituent of
-* regulates
-* functions in
-* represses
-* IS_A
-* PART_OF
-* DEVELOPS_FROM
-* is regulated by
-* suppresses gene
-* enhances gene
-* matches
-* partially enhances gene
-* partially suppresses gene
-* expressed during
-* expressed only in
-* expressed only during
-* is downregulated by
-* has
-* has protein-protein physical interaction with
-* binds to cis-element of
-* none
-* acts upstream of
-* acts downstream of
-* member of
-* has protein-DNA interaction with
-* has protein modification of type
-* protein is modified by
-* does not have
-* contributes to
-* describes method
-* protocol2term
-* colocalizes with
-* does not function in
-* is upregulated by
-* is not regulated by
-* is not a constituent of
-* not expressed during
-==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