NCBO Wiki - User contributions [en]

File:Regulates.ppt

2008-05-19T17:31:48Z

TanyaB:

OntologyRelations

2008-05-19T17:30:22Z

TanyaB:

'''Workshop on the Relationship Ontology'''

The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.

[[OntologyRelationsMay19MeetingNotes]]

[[Media:david_sutherland.ppt]]

[[Media:regulates.ppt]]

== Guidelines and Goals ==

* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:
** simple, with well-thought out definitions
** example-driven, that is an instance-level definition must exist (see RO paper)
** expressed in a clear, consistent symbol-free syntax

* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:
** All outstanding items on the request tracking system are solved
** All relations in ro_proposed are "blessed" and move into RO proper
** A release of the cross-product (xp) files is generated
** We will produce a new release of the RO

''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''

== Preparation ==

* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO

== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==

=== 8:30-10:30am General (Barry/Chris/Mike) ===

* review of principles
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]
** desired level of granularity (Barry/Mike)
* review of website, tracker (Chris)
** process for adding terms
* review of current primary representation in .obo, .owl conversion (Chris)
* ID policy (BFO), ontology lifecycle issues etc
* cross-products

=== 10:30am-10:45am: Coffee ===

=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===

* stages and temporal relations
** DavidOS/Fabian
** Interval calculus
** ZFA stages use case: start, end
* develops_from
* relations from CARO paper (Fabian)
* review biological_process_xp_cell (Chris/MikeB)
* agent_in - is it valid? "heart process" example - DavidH/Chris

=== 12:00 noon - 12:30: Lunch ===

=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===

* lacks_part (Werner)
* inheres_in
** relational qualities
*** towards relation
*** relational qualities and relations - what's the difference. lacks_part example
* relations between qualities, comparisons and abnormality

=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===

* RCC8-can we reuse? (Chris)
* surrounded_by (Chris)
* overlaps - bone + joint use case (Peter)
* connected_to and attached_to (Wasila)
** bona fide vs fiat - when does it matter?
** Example: axon tracts and neuropil (fiat)
** Example: tooth attachment use case (bona fide)
* spatial.obo (Wasila)

=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===

* regulates, +, -
* composition of regulation relations
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]

=== 5:30pm: Transportation to dinner ===

== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==

=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) ===

* homologous_to & evo_derives_from
* ternary relations in RO: DavidS's use case (DavidOS/Chris)

=== 10:30am - noon Biochemical (Larry / Mike B) ===

* pathways (BioPAX-OBO, AlanR)
* review bp_xp_chebi (Bada)
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)

=== 12:30pm - 2pm Epistemic (Larry) ===

* supported_by et al

=== 2:15pm - 4pm Other issues, and follow ups ===

* the time issue. OWL representation (Alan)
* idiosyncratic relations in the FMA (Suzi/Nigam)

== Logistics ==

* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building].

* Fly in to the [http://www.flydenver.com/ Denver International Airport].

* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].

* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.

== Invited Participants ==
=== Confirmed (alphabetically) ===
# Mike Bada (host / Denver, CO)
# Tanya Berardini (TAIR / Stanford, CA)
# Bill Bug (BIRN / San Diego, CA)
# Vinay Chaudhri (SRI / Menlo Park, CA)
# Werner Ceusters (ORG / Buffalo, NY)
# Wasila Dahdul (Phenoscape/NESCENT)
# Mary Dolan (MGI / Bar Harbor, ME)
# Melissa Haendel (ZFIN / Eugene, OR)
# David Hill (MGI / Bar Harbor, ME)
# Larry Hunter (host / Denver, CO)
# Suzi Lewis (NCBO / Berkeley, CA)
# Peter Midford (Phenoscape/ NESCent)
# Chris Mungall (Flybase / Berkeley, CA)
# Darren Natale (PRO / Georgetown, Washington, DC)
# Fabian Neuhaus (NIST / Washington, DC)
# David Osumi-Sutherland (FlyBase / Cambridge, UK)
# Cornelius Rosse (FMA / Seattle, WA)
# Alan Ruttenberg (Science Commons / Cambridge, MA)
# Nigam Shah (NCBO / Stanford, CA)
# Barry Smith (NCBO / Buffalo, NY)
# Karin Verspoor (host / Denver, CO)

=== Invited ===
# Thomas Bittner (ORG / Buffalo, NY)
# Waclaw Kusnierczyk (Bergen, Norway)

== Background Material ==

[http://obofoundry.org/ro/ Relation Ontology Home ]

[[RO:Main_Page | Current Proposals for new relations ]]

[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]

White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]

OntologyRelations

2008-05-19T17:25:00Z

TanyaB:

'''Workshop on the Relationship Ontology'''

The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the relationship between terms (classes) in ontologies.

[[OntologyRelationsMay19MeetingNotes]]
[[Media:david_sutherland.ppt]]

== Guidelines and Goals ==

* Our over-arching guiding principle is to keep the Relations Ontology biology driven. This means that any relations proposed must be kept:
** simple, with well-thought out definitions
** example-driven, that is an instance-level definition must exist (see RO paper)
** expressed in a clear, consistent symbol-free syntax

* The goals of this workshop are to develop the content of the relationship ontology. By the end of the meeting we hope to complete all of the following:
** All outstanding items on the request tracking system are solved
** All relations in ro_proposed are "blessed" and move into RO proper
** A release of the cross-product (xp) files is generated
** We will produce a new release of the RO

''Note: At least Alan Ruttenberg has expressed that these goals are to much to achieve in the time we have''

== Preparation ==

* The leader of each session topic should be prepared to provide a summary of the issues involved and the available choices to be decided upon
* Leaders should recommend papers to read in preparation and send out PDFs for CS folks and biologistsd
* Nomi Harris and Chris Mungall are working to ensure that OBO-Edit2 will be fit to use during the workshop so that we can use it to immediately modify the RO

== Agenda: 8:30AM-5:30PM Monday, May 19th 2008 ==

=== 8:30-10:30am General (Barry/Chris/Mike) ===

* review of principles
** all-some(time) (Barry) [http://ontology.buffalo.edu/smith/ppt/BFO_RO/OBO_RO_May08.ppt Slides]
** desired level of granularity (Barry/Mike)
* review of website, tracker (Chris)
** process for adding terms
* review of current primary representation in .obo, .owl conversion (Chris)
* ID policy (BFO), ontology lifecycle issues etc
* cross-products

=== 10:30am-10:45am: Coffee ===

=== 10:45am - 12:00 noon: Development and anatomy (DavidOS) ===

* stages and temporal relations
** DavidOS/Fabian
** Interval calculus
** ZFA stages use case: start, end
* develops_from
* relations from CARO paper (Fabian)
* review biological_process_xp_cell (Chris/MikeB)
* agent_in - is it valid? "heart process" example - DavidH/Chris

=== 12:00 noon - 12:30: Lunch ===

=== 12:30 - 2:30pm: Biological qualities and phenotypes (Chris/Werner) ===

* lacks_part (Werner)
* inheres_in
** relational qualities
*** towards relation
*** relational qualities and relations - what's the difference. lacks_part example
* relations between qualities, comparisons and abnormality

=== 2:45 - 4pm: Spatial relations (Melissa/Suzi) ===

* RCC8-can we reuse? (Chris)
* surrounded_by (Chris)
* overlaps - bone + joint use case (Peter)
* connected_to and attached_to (Wasila)
** bona fide vs fiat - when does it matter?
** Example: axon tracts and neuropil (fiat)
** Example: tooth attachment use case (bona fide)
* spatial.obo (Wasila)

=== 4:15 - 5:30pm: Regulation (David/Tanya/Chris) ===

* regulates, +, -
* composition of regulation relations
* [http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684] [http://www.bioontology.org/wiki/index.php/RO:Main_Page#TAIR_Relations TAIR relations]

=== 5:30pm: Transportation to dinner ===

== Agenda: 9:00AM-4:00PM Tuesday, May 20th 2008 ==

=== 9:00-10:15am Evolutionary (Melissa, Wasila, Peter) ===

* homologous_to & evo_derives_from
* ternary relations in RO: DavidS's use case (DavidOS/Chris)

=== 10:30am - noon Biochemical (Larry / Mike B) ===

* pathways (BioPAX-OBO, AlanR)
* review bp_xp_chebi (Bada)
* Molecular interactions and the PSI-MI relation(esque) terms. (Larry)

=== 12:30pm - 2pm Epistemic (Larry) ===

* supported_by et al

=== 2:15pm - 4pm Other issues, and follow ups ===

* the time issue. OWL representation (Alan)
* idiosyncratic relations in the FMA (Suzi/Nigam)

== Logistics ==

* This meeting will take place on the [http://www.uchsc.edu/anschutzmedicalcampus/ Anschutz medical Campus of the University of Colorado at Denver], probably in room 204 of the [http://www.uchsc.edu/anschutzmedicalcampus/projects/nativehealth.htm Nighthorse Campbell building].

* Fly in to the [http://www.flydenver.com/ Denver International Airport].

* A good nearby hotel is the [http://www.druryhotels.com/properties/denvereast.cfm East Denver Drury Inn]. It's not walking distance, but it is the closest decent hotel and we will work to arrange carpools if necessary. If you are driving yourself, you will need [http://ucdhsc.edu/admin/facilities/parking/docs/AMC-UCD-VisitorParking.pdf visitor parking information].

* If you need advice or want to talk to someone regarding logistics, email [mailto:Kathy.R.Thomas@uchsc.edu Kathy Thomas] and mention the Relation Ontology expert meeting in May.

== Invited Participants ==
=== Confirmed (alphabetically) ===
# Mike Bada (host / Denver, CO)
# Tanya Berardini (TAIR / Stanford, CA)
# Bill Bug (BIRN / San Diego, CA)
# Vinay Chaudhri (SRI / Menlo Park, CA)
# Werner Ceusters (ORG / Buffalo, NY)
# Wasila Dahdul (Phenoscape/NESCENT)
# Mary Dolan (MGI / Bar Harbor, ME)
# Melissa Haendel (ZFIN / Eugene, OR)
# David Hill (MGI / Bar Harbor, ME)
# Larry Hunter (host / Denver, CO)
# Suzi Lewis (NCBO / Berkeley, CA)
# Peter Midford (Phenoscape/ NESCent)
# Chris Mungall (Flybase / Berkeley, CA)
# Darren Natale (PRO / Georgetown, Washington, DC)
# Fabian Neuhaus (NIST / Washington, DC)
# David Osumi-Sutherland (FlyBase / Cambridge, UK)
# Cornelius Rosse (FMA / Seattle, WA)
# Alan Ruttenberg (Science Commons / Cambridge, MA)
# Nigam Shah (NCBO / Stanford, CA)
# Barry Smith (NCBO / Buffalo, NY)
# Karin Verspoor (host / Denver, CO)

=== Invited ===
# Thomas Bittner (ORG / Buffalo, NY)
# Waclaw Kusnierczyk (Bergen, Norway)

== Background Material ==

[http://obofoundry.org/ro/ Relation Ontology Home ]

[[RO:Main_Page | Current Proposals for new relations ]]

[http://www.biomedcentral.com/content/pdf/1471-2105-7-S3-S5.pdf SMBM paper discussing the relations in the PASBio predicates]

White paper on the relations used in the AURA biology system [[media:AURA_relations.pdf]]

RO:Main Page

2008-05-19T03:39:56Z

TanyaB: /* TAIR Relations */

=RO - OBO Relation Ontology=

The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]

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]]

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)

Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.

==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==

GRANULARITY/SPECIFICITY

We assert that the level of granularity/specifity of the proposed
relations is a central issue that, once resolved, will provide useful
guidelines as to what is needed to capture a piece of knowledge by a
relational link. The examples in this proposal use process terms from
the Gene Ontology, but we believe that this issue applies to other OBOs
as well.

We assert that the addition of relations should be primarily guided by
the effort to link OBO terms with other OBO terms, as is being done in
the OBO cross-product project. A composite set of links from a given
more complex OBO terms to more atomic OBO terms will provide the
(hopefully complete) definition of the former. A given link from the
term being defined, employing an RO relation, must unambiguously capture
some piece of knowledge, some part of the definition, of this term. It
is this unambiguous representation of some part of the complete
definition of the term that should determine the specificity of the
relation. This may require the use of a specific relation, but we assert
that it is more important to avoid losing knowledge in the represented
definition than to exclusively use general relations.

It is ideal to use general, reusable relations in such definitions
without losing information, and we believe that this is sometimes
possible. For example, for the many GO process terms that use “during”
to specify a process that is taking place within the span of another
process (''e.g.'', “actin filament reorganization during cell cycle”), it is
acceptable to use a standard temporal relation, as no information is
lost by doing so. However, especially in the definitions of processes,
we assert that the unambiguous capture of roles of participants will
require relatively specific relations.

There have been efforts to use general relations to denote roles, but
they have been difficult to define (''e.g.'', has_agent, has_patient,
has_central_participant) and/or insufficient to specify the role
(''e.g.'', has_output_participant). If suitably precise general relations
cannot be defined, relatively specific relations are needed. Thus, for
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),
if a general relation to indicate what is growing cannot be suitably
defined, then a specific relation must be created to capture this,
either in the form of a lexically analogous relation (''e.g.'',
results_in_growth_of) or as one that incorporates the template
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,
since most of the growth terms are defined as the increase in size or
mass of an entity). These two approaches by themselves are
computationally synonymous but differ in terms of human comprehension.
The former, while not adding information for human users, can be
straightforwardly formed. The latter, while helpful for human users, can
get unwieldy in the case of complex definitions. For example, the
detection-of-stimulus terms are defined as the series of events in which
a stimulus is received by an entity and converted into a molecular
signal, and
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of
is clearly getting ridiculous.

It is also ideal for relations, especially relatively specific ones as
exemplified above, to be formally defined (''i.e.'', in a computationlly
procesable way) in terms of more atomic relations. However, it will be
very difficult to produce formal definitions in terms of more atomic
relations, especially for relatively specific relations. We assert that
the linking of OBO terms to generate cross-products should be a
priority, and this requires the specification of relations (as discussed
above) to link the terms. A requirement for any proposed relation to
have a formal decomposed definition in terms of more atomic relations
would be a significant bottleneck to this process. Just as there is no
requirement for an added OBO term to have a formal definition, there
should be no such requirement for an added OBO relation. We would like
to be clear that we believe it extremely beneficial to have such formal
definitions (and thus efforts should continually be put into creating
such definitions), but this should not be an obstacle to the introduction of
new relations.

LEXICAL FORM

We propose that each relation should canonically be in the form of a
verb phrase. We assert that this promotes usability in that it
emphasizes the fact that these are relationships between entities.

==TAIR Relations==

See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684

Relations between continuants and occurrents:

* has (function)
* involved in
* functions as
* required for
* functions in
* has protein modification of type
* contributes to
* is upregulated by
* is downregulated by

Relations between continuants:

* located in
* expressed in
* colocalizes with
* is subunit of
* constituent of
* has protein-protein physical interaction with
* has protein-DNA interaction with
* binds to cis-element of
* acts upstream of
* acts downstream of
* expressed during
* protein is modified by
* is regulated by
* represses

Relations between continuants and qualities (phenotypes in our case):

* suppresses gene
* enhances gene
* partially enhances gene
* partially suppresses gene

==Proposed homologous_to relation==

Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:

All instances of continuant X part_of some organism which is part of taxon A

All instances of continuant Y part_of some organism which is part of taxon B

All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B.

X is homologous_to Y

IF (and only if)

All instances of X descended_from some instance of Z

AND

All instances of Y descended_from some instance of Z.

===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===

Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.

Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S pertaining to continuant E, to species R which is sufficient to generate continuant D.

Where:

All instances of continuant X part_of some organism which is part of taxon A

All instances of continuant Y part_of some organism which is part of taxon B

All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B.

All instances of continuant D part_of some organism which is part of species R

All instances of continuant E part_of some organism which is part of species S

X is homologous_to Y

IF (and only if)

All instances of X descended_from some instance of Z

AND

All instances of Y descended_from some instance of Z

Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:

id: OBO_REL:evolutionarily_derived_from

name: evolutionarily_derived_from

def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []

synonym: "derived_from" RELATED []

synonym: "descended_from" RELATED []

synonym: "evolved_from" RELATED []

is_transitive: true

==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

RO:Main Page

2008-05-19T03:39:18Z

TanyaB: /* TAIR Relations */

=RO - OBO Relation Ontology=

The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]

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]]

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)

Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.

==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==

GRANULARITY/SPECIFICITY

We assert that the level of granularity/specifity of the proposed
relations is a central issue that, once resolved, will provide useful
guidelines as to what is needed to capture a piece of knowledge by a
relational link. The examples in this proposal use process terms from
the Gene Ontology, but we believe that this issue applies to other OBOs
as well.

We assert that the addition of relations should be primarily guided by
the effort to link OBO terms with other OBO terms, as is being done in
the OBO cross-product project. A composite set of links from a given
more complex OBO terms to more atomic OBO terms will provide the
(hopefully complete) definition of the former. A given link from the
term being defined, employing an RO relation, must unambiguously capture
some piece of knowledge, some part of the definition, of this term. It
is this unambiguous representation of some part of the complete
definition of the term that should determine the specificity of the
relation. This may require the use of a specific relation, but we assert
that it is more important to avoid losing knowledge in the represented
definition than to exclusively use general relations.

It is ideal to use general, reusable relations in such definitions
without losing information, and we believe that this is sometimes
possible. For example, for the many GO process terms that use “during”
to specify a process that is taking place within the span of another
process (''e.g.'', “actin filament reorganization during cell cycle”), it is
acceptable to use a standard temporal relation, as no information is
lost by doing so. However, especially in the definitions of processes,
we assert that the unambiguous capture of roles of participants will
require relatively specific relations.

There have been efforts to use general relations to denote roles, but
they have been difficult to define (''e.g.'', has_agent, has_patient,
has_central_participant) and/or insufficient to specify the role
(''e.g.'', has_output_participant). If suitably precise general relations
cannot be defined, relatively specific relations are needed. Thus, for
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),
if a general relation to indicate what is growing cannot be suitably
defined, then a specific relation must be created to capture this,
either in the form of a lexically analogous relation (''e.g.'',
results_in_growth_of) or as one that incorporates the template
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,
since most of the growth terms are defined as the increase in size or
mass of an entity). These two approaches by themselves are
computationally synonymous but differ in terms of human comprehension.
The former, while not adding information for human users, can be
straightforwardly formed. The latter, while helpful for human users, can
get unwieldy in the case of complex definitions. For example, the
detection-of-stimulus terms are defined as the series of events in which
a stimulus is received by an entity and converted into a molecular
signal, and
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of
is clearly getting ridiculous.

It is also ideal for relations, especially relatively specific ones as
exemplified above, to be formally defined (''i.e.'', in a computationlly
procesable way) in terms of more atomic relations. However, it will be
very difficult to produce formal definitions in terms of more atomic
relations, especially for relatively specific relations. We assert that
the linking of OBO terms to generate cross-products should be a
priority, and this requires the specification of relations (as discussed
above) to link the terms. A requirement for any proposed relation to
have a formal decomposed definition in terms of more atomic relations
would be a significant bottleneck to this process. Just as there is no
requirement for an added OBO term to have a formal definition, there
should be no such requirement for an added OBO relation. We would like
to be clear that we believe it extremely beneficial to have such formal
definitions (and thus efforts should continually be put into creating
such definitions), but this should not be an obstacle to the introduction of
new relations.

LEXICAL FORM

We propose that each relation should canonically be in the form of a
verb phrase. We assert that this promotes usability in that it
emphasizes the fact that these are relationships between entities.

==TAIR Relations==

See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684

Relations between continuants and occurrents:

* has function
* involved in
* functions as
* required for
* functions in
* has protein modification of type
* contributes to
* is upregulated by
* is downregulated by

Relations between continuants:

* located in
* expressed in
* colocalizes with
* is subunit of
* constituent of
* has protein-protein physical interaction with
* has protein-DNA interaction with
* binds to cis-element of
* acts upstream of
* acts downstream of
* expressed during
* protein is modified by
* is regulated by
* represses

Relations between continuants and qualities (phenotypes in our case):

* suppresses gene
* enhances gene
* partially enhances gene
* partially suppresses gene

==Proposed homologous_to relation==

Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:

All instances of continuant X part_of some organism which is part of taxon A

All instances of continuant Y part_of some organism which is part of taxon B

All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B.

X is homologous_to Y

IF (and only if)

All instances of X descended_from some instance of Z

AND

All instances of Y descended_from some instance of Z.

===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===

Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.

Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S pertaining to continuant E, to species R which is sufficient to generate continuant D.

Where:

All instances of continuant X part_of some organism which is part of taxon A

All instances of continuant Y part_of some organism which is part of taxon B

All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B.

All instances of continuant D part_of some organism which is part of species R

All instances of continuant E part_of some organism which is part of species S

X is homologous_to Y

IF (and only if)

All instances of X descended_from some instance of Z

AND

All instances of Y descended_from some instance of Z

Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:

id: OBO_REL:evolutionarily_derived_from

name: evolutionarily_derived_from

def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []

synonym: "derived_from" RELATED []

synonym: "descended_from" RELATED []

synonym: "evolved_from" RELATED []

is_transitive: true

==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

RO:Main Page

2008-05-15T23:04:33Z

TanyaB: /* TAIR Relations */

=RO - OBO Relation Ontology=

The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]

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]]

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)

Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.

==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==

GRANULARITY/SPECIFICITY

We assert that the level of granularity/specifity of the proposed
relations is a central issue that, once resolved, will provide useful
guidelines as to what is needed to capture a piece of knowledge by a
relational link. The examples in this proposal use process terms from
the Gene Ontology, but we believe that this issue applies to other OBOs
as well.

We assert that the addition of relations should be primarily guided by
the effort to link OBO terms with other OBO terms, as is being done in
the OBO cross-product project. A composite set of links from a given
more complex OBO terms to more atomic OBO terms will provide the
(hopefully complete) definition of the former. A given link from the
term being defined, employing an RO relation, must unambiguously capture
some piece of knowledge, some part of the definition, of this term. It
is this unambiguous representation of some part of the complete
definition of the term that should determine the specificity of the
relation. This may require the use of a specific relation, but we assert
that it is more important to avoid losing knowledge in the represented
definition than to exclusively use general relations.

It is ideal to use general, reusable relations in such definitions
without losing information, and we believe that this is sometimes
possible. For example, for the many GO process terms that use “during”
to specify a process that is taking place within the span of another
process (''e.g.'', “actin filament reorganization during cell cycle”), it is
acceptable to use a standard temporal relation, as no information is
lost by doing so. However, especially in the definitions of processes,
we assert that the unambiguous capture of roles of participants will
require relatively specific relations.

There have been efforts to use general relations to denote roles, but
they have been difficult to define (''e.g.'', has_agent, has_patient,
has_central_participant) and/or insufficient to specify the role
(''e.g.'', has_output_participant). If suitably precise general relations
cannot be defined, relatively specific relations are needed. Thus, for
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),
if a general relation to indicate what is growing cannot be suitably
defined, then a specific relation must be created to capture this,
either in the form of a lexically analogous relation (''e.g.'',
results_in_growth_of) or as one that incorporates the template
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,
since most of the growth terms are defined as the increase in size or
mass of an entity). These two approaches by themselves are
computationally synonymous but differ in terms of human comprehension.
The former, while not adding information for human users, can be
straightforwardly formed. The latter, while helpful for human users, can
get unwieldy in the case of complex definitions. For example, the
detection-of-stimulus terms are defined as the series of events in which
a stimulus is received by an entity and converted into a molecular
signal, and
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of
is clearly getting ridiculous.

It is also ideal for relations, especially relatively specific ones as
exemplified above, to be formally defined (''i.e.'', in a computationlly
procesable way) in terms of more atomic relations. However, it will be
very difficult to produce formal definitions in terms of more atomic
relations, especially for relatively specific relations. We assert that
the linking of OBO terms to generate cross-products should be a
priority, and this requires the specification of relations (as discussed
above) to link the terms. A requirement for any proposed relation to
have a formal decomposed definition in terms of more atomic relations
would be a significant bottleneck to this process. Just as there is no
requirement for an added OBO term to have a formal definition, there
should be no such requirement for an added OBO relation. We would like
to be clear that we believe it extremely beneficial to have such formal
definitions (and thus efforts should continually be put into creating
such definitions), but this should not be an obstacle to the introduction of
new relations.

LEXICAL FORM

We propose that each relation should canonically be in the form of a
verb phrase. We assert that this promotes usability in that it
emphasizes the fact that these are relationships between entities.

==TAIR Relations==

See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684

Relations between continuants and occurrents:

* has function
* involved in
* functions as
* required for
* functions in
* has protein modification of type
* contributes to
* is upregulated by
* is downregulated by

Relations between continuants:

* located in
* expressed in
* colocalizes with
* is subunit of
* constituent of
* has protein-protein physical interaction with
* has protein-DNA interaction with
* binds to cis-element of
* acts upstream of
* acts downstream of
* expressed during
* protein is modified by
* is regulated by

Relations between continuants and qualities (phenotypes in our case):

* represses
* suppresses gene
* enhances gene
* partially enhances gene
* partially suppresses gene

==Proposed homologous_to relation==

Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:

All instances of continuant X part_of some organism which is part of taxon A

All instances of continuant Y part_of some organism which is part of taxon B

All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B.

X is homologous_to Y

IF (and only if)

All instances of X descended_from some instance of Z

AND

All instances of Y descended_from some instance of Z.

===Since this definition includes 'descended_from', we've been discussing the following more extensive definition:===

Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most common ancestor.

Continuant D in species R is genealogically descended from continuant E in species S when there is passage of genetic information from species S pertaining to continuant E, to species R which is sufficient to generate continuant D.

Where:

All instances of continuant X part_of some organism which is part of taxon A

All instances of continuant Y part_of some organism which is part of taxon B

All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B.

All instances of continuant D part_of some organism which is part of species R

All instances of continuant E part_of some organism which is part of species S

X is homologous_to Y

IF (and only if)

All instances of X descended_from some instance of Z

AND

All instances of Y descended_from some instance of Z

Note that there are a number of synonyms for descended_from, including 'evolutionarily_derived_from' which is currently in ROproposed as follows:

id: OBO_REL:evolutionarily_derived_from

name: evolutionarily_derived_from

def: "Instance 3-ary relation: x edf y as T iff x specified_by gx and gx ancestral_copy_of gy and gy specifies y" []

synonym: "derived_from" RELATED []

synonym: "descended_from" RELATED []

synonym: "evolved_from" RELATED []

is_transitive: true

==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

RO:Main Page

2008-05-14T20:42:09Z

TanyaB: /* TAIR Relations */

=RO - OBO Relation Ontology=

The main RO page is located on [http://obofoundry.org/ro The OBO Foundry Website]

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]]

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)

Actually uterine tract is part_of urinogenital system, which raises the question of whether each of X's parts overlaps X.

==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==

GRANULARITY/SPECIFICITY

We assert that the level of granularity/specifity of the proposed
relations is a central issue that, once resolved, will provide useful
guidelines as to what is needed to capture a piece of knowledge by a
relational link. The examples in this proposal use process terms from
the Gene Ontology, but we believe that this issue applies to other OBOs
as well.

We assert that the addition of relations should be primarily guided by
the effort to link OBO terms with other OBO terms, as is being done in
the OBO cross-product project. A composite set of links from a given
more complex OBO terms to more atomic OBO terms will provide the
(hopefully complete) definition of the former. A given link from the
term being defined, employing an RO relation, must unambiguously capture
some piece of knowledge, some part of the definition, of this term. It
is this unambiguous representation of some part of the complete
definition of the term that should determine the specificity of the
relation. This may require the use of a specific relation, but we assert
that it is more important to avoid losing knowledge in the represented
definition than to exclusively use general relations.

It is ideal to use general, reusable relations in such definitions
without losing information, and we believe that this is sometimes
possible. For example, for the many GO process terms that use “during”
to specify a process that is taking place within the span of another
process (''e.g.'', “actin filament reorganization during cell cycle”), it is
acceptable to use a standard temporal relation, as no information is
lost by doing so. However, especially in the definitions of processes,
we assert that the unambiguous capture of roles of participants will
require relatively specific relations.

There have been efforts to use general relations to denote roles, but
they have been difficult to define (''e.g.'', has_agent, has_patient,
has_central_participant) and/or insufficient to specify the role
(''e.g.'', has_output_participant). If suitably precise general relations
cannot be defined, relatively specific relations are needed. Thus, for
all of the growth terms (''e.g.'', “organ growth”, “filamentous growth”),
if a general relation to indicate what is growing cannot be suitably
defined, then a specific relation must be created to capture this,
either in the form of a lexically analogous relation (''e.g.'',
results_in_growth_of) or as one that incorporates the template
definitions of the term (''e.g.'', results_in_increase_in_size_or_mass_of,
since most of the growth terms are defined as the increase in size or
mass of an entity). These two approaches by themselves are
computationally synonymous but differ in terms of human comprehension.
The former, while not adding information for human users, can be
straightforwardly formed. The latter, while helpful for human users, can
get unwieldy in the case of complex definitions. For example, the
detection-of-stimulus terms are defined as the series of events in which
a stimulus is received by an entity and converted into a molecular
signal, and
results_in_reception_of_stimulus_and_conversion_into_molecular_signal_of
is clearly getting ridiculous.

It is also ideal for relations, especially relatively specific ones as
exemplified above, to be formally defined (''i.e.'', in a computationlly
procesable way) in terms of more atomic relations. However, it will be
very difficult to produce formal definitions in terms of more atomic
relations, especially for relatively specific relations. We assert that
the linking of OBO terms to generate cross-products should be a
priority, and this requires the specification of relations (as discussed
above) to link the terms. A requirement for any proposed relation to
have a formal decomposed definition in terms of more atomic relations
would be a significant bottleneck to this process. Just as there is no
requirement for an added OBO term to have a formal definition, there
should be no such requirement for an added OBO relation. We would like
to be clear that we believe it extremely beneficial to have such formal
definitions (and thus efforts should continually be put into creating
such definitions), but this should not be an obstacle to the introduction of
new relations.

LEXICAL FORM

We propose that each relation should canonically be in the form of a
verb phrase. We assert that this promotes usability in that it
emphasizes the fact that these are relationships between entities.

==TAIR Relations==

See http://sourceforge.net/tracker/index.php?func=detail&aid=1888149&group_id=76834&atid=947684

Relations between continuants and occurrents:

* has function
* involved in
* functions as
* required for
* functions in
* has protein modification of type
* contributes to

Relations between continuants:

* located in
* expressed in
* colocalizes with
* is subunit of
* constituent of
* related to
* represses
* is regulated by
* suppresses gene
* enhances gene
* partially enhances gene
* partially suppresses gene
* is upregulated by
* is downregulated by
* has protein-protein physical interaction with
* has protein-DNA interaction with
* binds to cis-element of
* acts upstream of
* acts downstream of
* expressed during
* protein is modified by

==Proposed homologous_to relation==

Symmetric; Instance 3-ary relation; Continuant X in taxon A is homologous to continuant Y in taxon B when both are genealogically descended from continuant Z in their most recent common ancestor. Where:

All instances of continuant X part_of some organism which is part of taxon A
All instances of continuant Y part_of some organism which is part of taxon B
All instances of continuant Z part_of some organism which is part of the most recent common ancestor of taxa A and B.

X is homologous_to Y
IF (and only if)
All instances of X descended_from some instance of Z

AND

All instances of Y descended_from some instance of Z.

==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

RO:Main Page

2008-04-11T20:38:00Z

TanyaB: /* TAIR Relations */

RO:Main Page

2008-04-11T20:37:23Z

TanyaB: /* TAIR Relations */ removing most obvious inappropriate relationships