NCBO Wiki - User contributions [en]

Evolutionary Biology and Ontologies 2009

2009-01-06T17:09:01Z

Pmidford:

This workshop will be held in conjunction with the Annual Meeting of the
Society for Integrative and Comparative Biology ([http://www.sicb.org/meetings/2009/index.php3 SICB]) in Boston, MA on January 5, 2009. It is cosponsored by the National Evolutionary Synthesis Center ([http://www.nescent.org NESCent]) and the National Center for Biomedical Ontologies ([http://bioontology.org NCBO]).

'''Organizers'''
Paula Mabee, Barry Smith, Todd Vision, Monte Westerfield.

'''Goals'''
The workshop is focused on the application of ontologies to studies in comparative biology, with a particular emphasis on morphological and behavioral phenotypes. The goal is to introduce what ontologies are, how they are built, what makes an ontology useful, how ontologies can help researchers collaborate across disciplines, and to highlight several applications of this approach to comparative biology.

'''Registration'''
Registration is open to attendees of the SICB 2009 conference at no additional cost.

'''Agenda'''

January 5, 2009

8:00: Todd Vision (University of North Carolina, NESCent) - Introduction

8:05: Barry Smith (University of Buffalo, NCBO) - An introduction to ontologies for evolutionary biologists

8:35: Monte Westerfield (Zebrafish Information Service, University of
Oregon) - Linking animal models and human diseases

9:00: Paula Mabee (University of South Dakota) - [http://phenoscape.org Phenoscape]: extending model organism ontologies for devo-studies of evolutionary phenotypes

9:20: Wasila Dahdul (University of South Dakota; National Evolutionary
Synthesis Center): The promises and pitfalls of multi-species anatomy
ontologies

9:40: James Balhoff (National Evolutionary Synthesis Center): Software and
database resources for curation and management of evolutionary phenotypes

10:00: BREAK

10:20: Andy Deans (North Carolina State University): Developing a
Hymenopteran ontology

10:50: Peter Midford (University of Kansas): Comparative Analysis of
behavior using ontologies

11:20: Anne Maglia (Missouri University of Science and Technology): Developing an amphibian ontology

11:50: Suzanna Lewis (Berkeley Bioinformatics and Ontology Project): Wrap-up

'''Download presentations'''

The Powerpoint files for each presentation is available from [http://phenoscape.org/wiki/Training_and_Workshops this page on the Phenoscape wiki]

'''Background Reading'''

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith B (2008) [http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf CARO - The common anatomy reference ontology] In: Anatomy
''Ontologies for Bioinformatics: Principles and Practice'', A. Burger, D.
Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall
C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics
and evolution. ''Trends in Ecology and Evolution'', 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology
for amphibians. ''Pacific Symposium on Biocomputing'', 12: 367-378.

Midford PE (2004) Ontologies for behavior. ''Bioinformatics'', 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) Text linking of digital images to phylogenetic data matrices using a
morphological ontology. ''Systematic Biology'', 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. (2007) [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration]. ''Nature Biotechnology'', 25, 1251-1255.

Smith B, Ceusters W, Klagges B, et al. (2005) [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies]. ''Genome Biology'', 6 (5), R46.

Evolutionary Biology and Ontologies 2009

2009-01-06T16:48:02Z

Pmidford:

This workshop will be held in conjunction with the Annual Meeting of the
Society for Integrative and Comparative Biology ([http://www.sicb.org/meetings/2009/index.php3 SICB]) in Boston, MA on January 5, 2009. It is cosponsored by the National Evolutionary Synthesis Center ([http://www.nescent.org NESCent]) and the National Center for Biomedical Ontologies ([http://bioontology.org NCBO]).

'''Organizers'''
Paula Mabee, Barry Smith, Todd Vision, Monte Westerfield.

'''Goals'''
The workshop is focused on the application of ontologies to studies in comparative biology, with a particular emphasis on morphological and behavioral phenotypes. The goal is to introduce what ontologies are, how they are built, what makes an ontology useful, how ontologies can help researchers collaborate across disciplines, and to highlight several applications of this approach to comparative biology.

'''Registration'''
Registration is open to attendees of the SICB 2009 conference at no additional cost.

'''Agenda'''

January 5, 2009

8:00: Todd Vision (University of North Carolina, NESCent) - Introduction

8:05: Barry Smith (University of Buffalo, NCBO) - An introduction to ontologies for evolutionary biologists

8:35: Monte Westerfield (Zebrafish Information Service, University of
Oregon) - Linking animal models and human diseases

9:00: Paula Mabee (University of South Dakota) - [http://phenoscape.org Phenoscape]: extending model organism ontologies for devo-studies of evolutionary phenotypes

9:20: Wasila Dahdul (University of South Dakota; National Evolutionary
Synthesis Center): The promises and pitfalls of multi-species anatomy
ontologies

9:40: James Balhoff (National Evolutionary Synthesis Center): Software and
database resources for curation and management of evolutionary phenotypes

10:00: BREAK

10:20: Andy Deans (North Carolina State University): Developing a
Hymenopteran ontology

10:50: Peter Midford (University of Kansas): Comparative Analysis of
behavior using ontologies

11:20: Anne Maglia (Missouri University of Science and Technology): Developing an amphibian ontology

11:50: Suzanna Lewis (Berkeley Bioinformatics and Ontology Project): Wrap-up

'''Download presentations'''

The Powerpoint files for each presentation is available from [http://www.nescent.org/phenoscape/Training_and_Workshops this page on the Phenoscape wiki]

'''Background Reading'''

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith B (2008) [http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf CARO - The common anatomy reference ontology] In: Anatomy
''Ontologies for Bioinformatics: Principles and Practice'', A. Burger, D.
Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall
C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics
and evolution. ''Trends in Ecology and Evolution'', 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology
for amphibians. ''Pacific Symposium on Biocomputing'', 12: 367-378.

Midford PE (2004) Ontologies for behavior. ''Bioinformatics'', 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) Text linking of digital images to phylogenetic data matrices using a
morphological ontology. ''Systematic Biology'', 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. (2007) [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration]. ''Nature Biotechnology'', 25, 1251-1255.

Smith B, Ceusters W, Klagges B, et al. (2005) [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies]. ''Genome Biology'', 6 (5), R46.

Evolutionary Biology and Ontologies 2009

2009-01-06T16:46:47Z

Pmidford:

This workshop will be held in conjunction with the Annual Meeting of the
Society for Integrative and Comparative Biology ([http://www.sicb.org/meetings/2009/index.php3 SICB]) in Boston, MA on January 5, 2009. It is cosponsored by the National Evolutionary Synthesis Center ([http://www.nescent.org NESCent]) and the National Center for Biomedical Ontologies ([http://bioontology.org NCBO]).

'''Organizers'''
Paula Mabee, Barry Smith, Todd Vision, Monte Westerfield.

'''Goals'''
The workshop is focused on the application of ontologies to studies in comparative biology, with a particular emphasis on morphological and behavioral phenotypes. The goal is to introduce what ontologies are, how they are built, what makes an ontology useful, how ontologies can help researchers collaborate across disciplines, and to highlight several applications of this approach to comparative biology.

'''Registration'''
Registration is open to attendees of the SICB 2009 conference at no additional cost.

'''Agenda'''

January 5, 2009

8:00: Todd Vision (University of North Carolina, NESCent) - Introduction

8:05: Barry Smith (University of Buffalo, NCBO) - An introduction to ontologies for evolutionary biologists

8:35: Monte Westerfield (Zebrafish Information Service, University of
Oregon) - Linking animal models and human diseases

9:00: Paula Mabee (University of South Dakota) - [http://phenoscape.org Phenoscape]: extending model organism ontologies for devo-studies of evolutionary phenotypes

9:20: Wasila Dahdul (University of South Dakota; National Evolutionary
Synthesis Center): The promises and pitfalls of multi-species anatomy
ontologies

9:40: James Balhoff (National Evolutionary Synthesis Center): Software and
database resources for curation and management of evolutionary phenotypes

10:00: BREAK

10:20: Andy Deans (North Carolina State University): Developing a
Hymenopteran ontology

10:50: Peter Midford (University of Kansas): Comparative Analysis of
behavior using ontologies

11:20: Anne Maglia (Missouri University of Science and Technology): Developing an amphibian ontology

11:50: Suzanna Lewis (Berkeley Bioinformatics and Ontology Project): Wrap-up

'''Download presentations'''

The Powerpoint files for each presentation is available from [https://www.nescent.org/phenoscape/Training_and_Workshops this page on the Phenoscape wiki]

'''Background Reading'''

Haendel MA, Neuhaus F, Osumi-Sutherland D, Mabee PM, Mejino JLV, Mungall CJ, Smith B (2008) [http://www.bioontology.org/wiki/images/0/0d/CAROchapter.pdf CARO - The common anatomy reference ontology] In: Anatomy
''Ontologies for Bioinformatics: Principles and Practice'', A. Burger, D.
Davidson and R. Baldock (eds).

Mabee PM, Ashburner M, Cronk Q, Gkoutos GV, Haendel M, Segerdell E, Mungall
C, Westerfield M (2007) Phenotype ontologies: the bridge between genomics
and evolution. ''Trends in Ecology and Evolution'', 22, 345-50.

Maglia AM, Leopold JL, Pugener, LA, Gauch S (2007) An anatomical ontology
for amphibians. ''Pacific Symposium on Biocomputing'', 12: 367-378.

Midford PE (2004) Ontologies for behavior. ''Bioinformatics'', 20, 3700-1.

Ramirez MJ, Coddington JA, Maddison WP, Midford PE, Prendini L, Miller J,
Griswold CE, Hormiga G, Sierwald P, Scharff N, Benjamin SP, Wheeler WC
(2007) Text linking of digital images to phylogenetic data matrices using a
morphological ontology. ''Systematic Biology'', 56, 283-94.

Smith B, Ashburner M, Rosse C, et al. (2007) [http://www.nature.com/nbt/journal/v25/n11/pdf/nbt1346.pdf The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration]. ''Nature Biotechnology'', 25, 1251-1255.

Smith B, Ceusters W, Klagges B, et al. (2005) [http://genomebiology.com/2005/6/5/R46 Relations in biomedical ontologies]. ''Genome Biology'', 6 (5), R46.

RO:Main Page

2008-06-09T22:31:07Z

Pmidford: /* Proposed homologous_to relation */

=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]

Mike And Chris' Relation Ontology Proposed (MACROP), a list targets relations is [[MACROP]]

==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==

x1 '''directly_descends_from''' x2 iff there are y1, y2 such that:

- y1 is an organism

- x1 is an anatomical structure

- x1 '''part_of''' y1

- y2 is an organism

- x2 is an anatomical structure

- x2 '''part_of''' y2

- y2 is a parent of y1

- the genetic sequence that determined the morphology of x1 is partially a copy of the genetic sequence that determined the morphology of x2.*

'''descends_from''' is the instance level relation which is the transitive closure over '''directly_descends_from'''

[* This clause still needs some work]

[* On the Phenoscape project list, Jim Balhoff added the following critique of this:

Something that jumps out at me in the definition of directly_descends_from:

I would not say that genetic sequences "determine" any morphology. I would prefer something like "participates in the development of" the morphology of x1. Anyway, I don't see genetic sequences as an absolutely necessary component of homology (although they would very often be an important component).]

A in B ''descends_from'' C in D :

For all A(a) -> exists b, d, c: B(b) & C(c) & D(d)

a '''part_of''' b

a '''descends_from''' c

c '''part_of''' d

(Note – B must be a subclade of the clade descending* from D)

A1 in B1 ''homologous_to A2'' in B2

iff

exists A3, B3:

A1 in B1 ''descends_from A3'' in B3

&

A2 in B2 ''descends_from'' A3 in B3

(Note B1 and B2 must both be subclades of the clade descending (in the genealogical sense) from D)

Note: Do we need to include time (exists & existed)?

FN – just to be on the safe side we can include time – it's not obviously useful but it could block some objections and won't affect the logic.

=== relation to what is in RO proposed ===

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

File:ROMeetingNotesPhenoscape.doc

2008-06-02T22:40:00Z

Pmidford:

OntologyRelations

2008-06-02T22:38:48Z

Pmidford: /* Minutes, Notes and Presentation */

'''Workshop on the Relationship Ontology'''

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

== Minutes, Notes and Presentation ==
* [[Media:May 2008 RO meeting minutes.doc]]
* [[OntologyRelationsMay19MeetingNotes]]
* [[Media:ROMeetingNotesPhenoscape.doc]]
* [[Media:relations_for_representing_developmental_anatomy.ppt]]
* [[Media:regulates.ppt]]
* [[Media:overlaps.ppt]]
* [[Media:RO-denver-cjm.ppt]]
* [[Media:dahdul-ROmeeting.ppt]]
* [[Media:Fabian developmental relations.pdf]]
* [[Media:Fabian develops_from.pdf]]
* [[Media:melissa development examples.ppt]]
* [[Media:Homology.ppt]]
* [[Media:Hunter Epistemic relations.ppt]]
* [[Media:Ruttenberg-ro.pdf]]

* [[OntologyRelationsMeetingNotesCompiled]]

== 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 too 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.

=== Attended (alphabetically) ===
# Mike Bada (host / Denver, CO)
# Tanya Berardini (TAIR / Stanford, 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)
# 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)
# Cornelius Rosse (FMA / Seattle, WA)
# Bill Bug (BIRN / San Diego, CA)

== 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

2008-06-02T22:33:03Z

Pmidford: /* Guidelines and Goals */

'''Workshop on the Relationship Ontology'''

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

== Minutes, Notes and Presentation ==
* [[Media:May 2008 RO meeting minutes.doc]]
* [[OntologyRelationsMay19MeetingNotes]]
* [[Media:relations_for_representing_developmental_anatomy.ppt]]
* [[Media:regulates.ppt]]
* [[Media:overlaps.ppt]]
* [[Media:RO-denver-cjm.ppt]]
* [[Media:dahdul-ROmeeting.ppt]]
* [[Media:Fabian developmental relations.pdf]]
* [[Media:Fabian develops_from.pdf]]
* [[Media:melissa development examples.ppt]]
* [[Media:Homology.ppt]]
* [[Media:Hunter Epistemic relations.ppt]]
* [[Media:Ruttenberg-ro.pdf]]

* [[OntologyRelationsMeetingNotesCompiled]]

== 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 too 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.

=== Attended (alphabetically) ===
# Mike Bada (host / Denver, CO)
# Tanya Berardini (TAIR / Stanford, 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)
# 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)
# Cornelius Rosse (FMA / Seattle, WA)
# Bill Bug (BIRN / San Diego, CA)

== 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]]

OntologyRelationsMeetingNotesCompiled

2008-06-02T22:29:32Z

Pmidford: /* Epistemic relations or how do we know what we know? */

== Introductions ==

* Barry Smith: NCOR, OBO Foundry
* Alan Ruttenberg: Science Commons, OBO Foundry
* Nigam Shah: how to use relations for reasoning over biol data
* Vinay Chaudhri: SRI, knowledge building based on textbooks
* David Osumi-Sutherland: FlyBase anatomy development, modeling developmental biology
* Larry Hunter: building systems that represent large scale biol knowledge, current represent
* Peter Midford: Phenoscape, evolutionary and spatial relationships, behavior ontologies
* Melissa Haendel: anatomy and phenotype ontologies, w/ Berkeley on db querying across species
* Mike Bada: bio NLP tasks and ontologies
* Darren Natale: Protein Info Resource, protein ontology
* Karin Verspoor: comp linguist, capturing relational info in text
* Chris Mungall: phenotype/genotype representation
* Wasila Dahdul: Phenoscape, anatomy curator
* Mary Dolan: MGI
* Fabian Neuhaus: NIST
* Suzi Lewis: GO/NCBO/OBO Foundry
* David Hill: ontology development and annotation

== Background ==

RO v.1.0 contained binary relations only. Relations are of 3 kinds: type-type (core RO relationships);
type-instance; instance-instance

Ontologies are representations of types (the general) and the goal of
the RO is to create a limited repertoire of relations linking types to
build these ontologies.

For example the GO contains types only, no instances. Only something
that holds for all A-s will be an assertion that holds of the type A.

'All' ontologies is not ALL ontologies, there is an understanding of
what the 'scope' of all is.

ACTION ITEM: scope of 'all’ needs to be addressed taking into account
that some ontologies (GO, FMA) are canonical, while others are not
(for example, PRO includes mutant proteins)

Larry: what role does time play in 'all'?

Response: for process type, it plays no role, because the processes
are the same regardless of time. However for continuants it does make
a difference, For example, a cell membrane, isolated and experimented
on, is used to draw conclusions about its role in the intact cell.

The need (and goal) is for a small suite of ontologies that describe
the exceptions that can be used with the reference ontologies that
represent the typical/normal.

=== Why keep RO small? ===

Some people are going to use the relations in RO in sloppy ways. The
smaller the number of options the less the possibility of misuse.
More per se is not bad, but if the relations are ill defined that
could be bad and would poison the well.

For example, “currency has_unit $” is WRONG because there are other
units of currency.

Likewise, if we have “adjacent_to” then we don't need
“adjacent_to_neuron/cytoplasm/organ”. There is inherently more
expressivity in the class realm than in the relation realm, thus we
shall pick the former vs. the latter. But there is a counter example
of a useful releation from the Cell Ontology meeting: is_expressed_on_surface_of (aka EOSO)
(CD4 receptor and cell type).

The solution may be:

* Compositional relations: could be broken down into several
ontologies: RO + GO cc + cell ontology

* Mix up UI with ontologies - show the mashed up relation even if it
doesn't exist in the RO. That is: what is visible to the
biologist/user is something interpretable/intuitive) and what goes
into RO is whatever is necessary to capture as the formal, minimal
relations)

In other words, don't just focus on one vs. the other. Further, any
proposed lists of compound relational expressions should be validated
by provision of definitions in terms of RO relations.

=== Spectrum of existing relations ===

One end is the English side, what appears in papers and the other side
are formal definitions

GOAL is to find a middle ground: Larry: these should be driving the
development of the minimal, formal ones. If 'expressed on surface of'
can be broken down into existing core ones, then good - relational
cross-products. In addition to the formal definitions, non-rigorous,
intuitive definitions are also good.

OPEN QUESTION: expressed_in implies located_in, what relationship does
expressed_in have to existing relations in RO?

Rather than creating EOSO, could also classify receptors as cell
surface receptors. Describe the same biology in different ways.
Instead of capturing the location in terms of the relation, capture it
in the GO/CO.

all-some relations

All the instances of A stand in R to some B. For example: NOT -
transforms_into, BUT YES - transformation_of. Or specifically, not
every child transforms_into adult (single instance, apparently not on
population scale), but every adult is a transformation of a child.

We (RO) don't want to become Tim Berners-Lee. No some-some relations.

Suzi: Are OBO_REL ids going to remain as the strings or will they
transition to the numericals?

ACTION ITEM: move to numerical ids

Larry: Doesn't want type-type only for RO. Too constrained.

Barry: type-type require instance-type definitions

ACTION ITEM: Define instance level relations as well. Clarity is
important. Relations need to be clarified whether they be used for
type_type/type_instance/instance_instance.

Well-defined relationships are the ideal; clear to us, easy to explain
to others

Chris: Should we split out part_of for instances from part_of for types? How would we do this?
# Drop type-level relations (DON"T LIKE THIS)
# Separate ids for instance and class level relations, different namespaces (THIS IS THE CHOICE, details not important right now)
# Clarify current 'punning' semantics, same id, means different thing in different contexts (however, sometimes it's hard to tell what the context is)
# not all type level relations can be defined in terms of instance level relations, need to work on both fronts

Long term proposal: Provide CommonLogic definition, port this to obo
and owl as necessary - Fabian has some basic work done, Alan can help
in translation but doesn't want to be the blocker. Have this in place
for the next release.

Are ternary relationships possible? Yes.

Cyc solution (SRI): Rule macro predicates: Relation 'all' exists.
Has_part A, B.

BFO (Basic Formal Ontology) is an upper ontology of entities, and the
RO is an upper ontology of relations. The ro_bfo_bridge has domain and
range constraints

e.g. id OBO_REL:has participant; the domain is span: Occurrent, and
the Range is snap:Continuant

This is good in that they are separate and independent, but it is very
awkward to maintain, BFO is primarily realized in owl, RO is in
obo. The solution is to use a common language

ACTION ITEM: RO should have a commitment to an upper ontology and it
shall be BFO.

RO tracker is located at http://sourceforge.net/tracker/?group_id=76834&atid=947684. Requests can be
requirements-oriented. E.g. I need a relation for this purpose, please
help me formalize it.

One solution to has_part: add the qualifiers into it: all_has_part,
for example

== Representing Developmental Anatomy ==

Presenter: David Osumi-Sutherland

Current limitations: RO can't specify timing of transitions, can't use
existing part_of relations to apply to 'sometimes'. What is needed is
a system for capturing stage specific part relations.

What is developmental time?

In a developmental process, many events happen in an invariant order,
these events can be used as markers of developmental progress or time
(standard stage series). E.g. gastrulation is a process, which can be
arbitrarily divided into stages based on marker events

Stage = BFO, fiat part of process. In other words marker events:
birth, death, transformation of an anatomical structure/ beginning,
end, a key point in a developmental process

Timing relationships: before, simultaneous which can both be derived
from before_or_simultaneous_with

(Werner joins discussion at 11:05 am local time, during David's example of Drosophila oogenesis)

Question is: How to deal with relative processes? That is, X happens
during Y only during process Z?

Ternary relations? A before B during C? - but these are not supported
in OWL, so have to use binary relations.

Solution: for each type for which timing is to be captured, record a
reference occurrent (see slides for rest of detail). E.g. gastrulation
reference_occurrent embryogenesis. There is still an issue with
individual somite geneses - generalize to somitogenesis? (recurrent
process) - individual timing relationships

ACTION ITEM: Add new timing relationships: begins_at_end_of,
begins_during, ends_during, begins_before, ends_after,
simultaneous_with, happens_during

In the future we hope to use ternary relationships. The solution for
right now (that will work with the existing tools) is to use binary
that can be mapped to ternary ones in the future. But David (and
others) wants to reason using these relationships NOW. Argument for
ternary relationship: can have multiple reference processes.

Larry's example: oocyte maturation, follicle maturation with regards
to oogenesis and with regards to life of the organism.

(From Larry)

Here is my example of why a single reference occurrence doesn't work
(and we need a ternary relation in order to capture the reference
occurrent for a particular temporal relation):

* Oocyte fate determination <before> oocyte maturation [reference occurrent oogenesis]
* oocyte maturation <before> follicle maturation [reference occurrent lifespan]

First, note that oocyte maturation needs to have both reference
occurrents in order to be able to assert these two things. These are
different in that there are a bunch of oogenesis occurents (so we need
the reference occurrent), but they all end before the first follicle
maturation (so we need the other reference occurrent). Incidentally,
we should be able to infer Oocyte fate determination <before> follicle
maturation on something like the basis that oogenesis <part-of>
lifespan.

ACTION ITEM: fix phrasing to timing relationships (first_exists_during
vs. begin_to_exist) to be consistent.

Fabian demonstrated an example of a reasoner that uses David/Fabian's
new temporal relations. Reasoning at instance level breaks, is too
slow, but reasoning at type level works.

Define: what is the same and what is new? E.g. Neuroblast vs. neuron

Alan: does NOT like succeeds, doesn't like the generalization, either
have specifics or general, not both.

LUNCH BREAK occurred as a way to interrupt the escalating discussion/argument.

== derives_from vs. transformation_of ==

Presenter: Melissa Haendel

Gave specific examples of develops_from and why this needs to be
transitive: heart development. But the problem is that this is not the
definition of develops_from. Do we care about identity? If not, get
rid of transformation_of and keep develops_from.

develops_from
--derives_from
--transformation_of

Darren example: A -> A-PO4, is this transformation or derivation?

Define identity function first, then can decide what is transformation
and what is not. Views on what identity is, is the hard part -
complicated, context-dependent. For example, consider:

A -> B -> C -> D -> E

Where B derives from A, C transformation of B, C derives from D, and E buds from D

What is the relation of A to E? Is it develops from, needed from
transitive closure, good for querying

Alan's issue: if there's any lack of clarity of when to use
derives_from vs. transformation_of, then the system breaks down

SOLVE THE IDENTITY PROBLEM!!!!! (and solve it now)

Cell division and budding are pretty clear: division: A -> B + C
whereas budding: A -> A + B

What are the examples that are clearly transformation? Rule is to stay
at same level of granularity, anatomical parts down to the cellular
level (NOT molecular level) - id1 => id1

* caterpillar -> pupa -> butterfly
* neural plate transformation of neural tube
* neuron -> mature neuron
* mature leaf -> senescent leaf
* What are the examples that are clearly derives from? id1 => id2
* [mandible derives from cranial neural crest] - a bit controversial because of the 'scaffolding' involved in bone formation
* U2 neuron derives from GMC71B
* leaf primordium derives from shoot apical meristem
* neural crest derives from neural tube

Alan: Is identity reality or perspective?

If develops_from is used in cases where we don't know what to say ------ leads to a lazy way of usage.

Biologists: we KNOW it's develops from, we don't know whether it's
derives from or transformation of. A process needs to have a beginning
and the end, The thing that develops does not have to be there at the
beginning of the process but it needs to be there at some point during
the process

ACTION ITEM: make a biological definition of develops_from, test at
all levels of granularity, provide cases of NOT develops_from Is
transformation maturation? Is that the key? Not the single
criterion. Definitely not at the RNA level. Maybe just at the
organismal level. Can one have maturation independent of some
process? No.

COFFEE BREAK

== Spatial Relations, Coming From Rcc8 ==

* disconnected
* externally connected - adjacent?
* equal
* partially overlapping
* tangential proper part - contained in and adjacent to
* tangential proper part inverse
* non-tangential proper part
* non-tangential proper part inverse

Don't want to make projections of 3D onto 2D.

If we want to use RCC keep the dimensions the same at the instance
level. We should look at geospatial ontologies/descriptions for car
(?) part manufacturing?

What is the difference between R and R' where: “town R county” and
“island R' lake”? Or for a biological example: urine R bladder
(contains? located?)

ACTION ITEM: have v. small meeting with spatial ontology (CAD,
connectivity, etc.) experts + some biologists to adapt existing
spatial relations to RO, who to invite? Tony Cohn. Thomas
Bittner. Karen Pittman, Cycorp. Xenia Fiorentini, NIST. GOAL of this
meeting: get spatial relations into RO

=== Spatial use cases ===
Presenter: Wasila Dahdul

teeth R bone: What is this? attached_to? connected_to? When would you use one over the other?

bona fide boundary vs. fiat boundary Does it matter? When does it
matter? It is sufficient to share a boundary? Does it have to be a
bona fide boundary? Connected_to is currently a fiat boundary as in
the FMA: x is connected to y if X and y share a fiat (somewhat
arbitrary) boundary (doesn't reflect any physical discontinuity)

Vinay: connectedness: A is connected to B means that B will move if A
moves. It is grounded in physical actions/movement

Attached_to is a connected relationship where there is a large
disparity between the size of the two objects. E.g. muscle attached_to
bone, tooth attached_to bone, arm attached_to body, NOT body
attached_to arm,

In the case of ball and socket joint they are connected via fluid. The
thought experiment is whether there are more kinds of 'connected' for
things, force exerted, force connectedness? fiat connectedness?

Fabian: what kind of reasoning do you want to get out of this/support
with these relationship types? Both approaches have their merits.
What is the purpose? What would be useful?

He suggests, just have a single relationship called 'connected' which
covers both.

Barry's motion: add attachment, connected, synaptic connection, get
definitions from FMA which need improvement, improve them, submit to
biologists for review with examples, find out why FMA used them that
way. It looks like discussions on the RO list led to use of these
proposed types (with same names) in the opposite direction. Is there
really confusion or not? Not.

=== Overlaps relationship ===

Peter Midford

Overlaps means two things share parts, for example: synovial joint
* A part of Bone 1
* A part_of Synovial Joint 1
* Therefore Bone 1 overlaps Synovial Joint 1

Logically, everything overlaps with its parts. Are these symmetric on
the instance level but not on the type level? This seems the case for
the joint example. However uterine tract overlaps urogenital system
but NOT urogenital system overlaps uterine tracts

ACTION ITEM: Add symmetric_overlaps/mutally_overlaps, modify the
proposed definition.

If the femur overlaps knee joint then the reverse is knee joint
overlaps femur. Are both true? Is it important to capture that this
is a symmetric overlap?

Wasila notes that in the spatial ontology top level contains both
dependent and independent continuants: anatomical axis, anatomical
axis direction, anatomical compartment, anatomical compartment
boundary, anatomical gradient, anatomical region - included margins,
anatomical section, anatomical surface

=== Character, Character State ===
What is a character description? Characters from a phylogenetic
perspective, cover the variation in a single bone, how is it shaped
differently across different species. Sample character: shape of
posterior margin of lateral ethmoid has one phenotype in one species
and another phenotype in another species. Of another example: the
Character is the presence or absence of bone X. Or the position of
bone X with regard to bone Y, where bone X may be posterior to Bone Y
or Bone X may be anterior to Bone Y.

* ACTION ITEM: make GO spatial-related process definitions consistent with spatial ontology
* ACTION ITEM: add more axis-related terms to spatial list (adaxial/abaxial, apical/basical, caudal-cephalic)
* ACTION ITEM: take anything relational out of Spatial and move to RO, check out whether 'vicinity of' needs to stay
* ACTION ITEM: remove spatial stuff from FMA
* ACTION ITEM: decide what needs to stay in PATO and what needs to go into RO - punt to tomorrow
* ACTION ITEM: Define distal and proximal, ternary relationships?
* ACTION ITEM: Add medial and lateral?

== Agency ==

Chris: is_agent.

Is there really agency ? NO because of the absence of intent. But
still need something more specific than has_participant, e.g. heart
process has_participant heart

Alan : NO NEED FOR AGENT! (see his very complicated slide about how
one can get around this using roles and owl). The only role related
relation Alan thinks is necessary: realization_of

Fabian: participates in?

Is it one or is it a bunch? punt to tomorrow

== Regulates ==

David Hill

Fabian: can processes that regulate a process be a part of that process? Yes. Good.

Ignoring regulations of qualities for now? Yes. There are not targets in the GO that already exist.

Alan: so many things affect transcription, how do you distinguish some that regulate and some that don't

By restricting to occurrents, we avoid problems that could arise from
things like 'temperature' and 'nucleotide concentration' affecting the
'rate, frequency, extent.' I.e. RNA pol II does not regulate
transcription, it carries out transcription.

What about other parts of the transcription machinery? If they're
always there, they do transcription. If they're sometimes there, they
are regulating.

If it's static canonically, it does not regulate.

Alan has problems with the current definition: one that includes all
the things based on your intuition. cite the right entities. We
should have some procedure so that I can take two processes that are
happening in the vicinity of the other process that let's me tell
whether one is regulatory and the other is not. Right now, it's not
workable. Define rate. Who are the participants? What is the rate
of a process? Duration makes sense. What is frequency of a process?
His sense is that the current definition is completely lexically
driven. Define in terms of a continuant which feeds into the process
(did I catch this right?). In as many processes as possible.

There are participants in the BMP signaling pathway that directly do
the regulation of transcription. There are proximate processes that
affect transcription.

Suzi: it's the other way around. There is big effort in GO to use
regular syntax when naming things. These things got named this
because of what they did.

You can't change a canonically static process

The rate of a process is how many times does this get initiated?

Larry: Can Alan improve 'regulates' any further?

Qualities of occurrents? Can they exist?

Causation - regulation - How far back do you go? What is the scope?
Basic metabolic processes regulated EVERYTHING. Where is the
beginning and end? What is direct and indirect?

possible solution: use comparatives, why this instead of that? The
comparative approach helps us do science. All of experimentation is
comparative.

Why isn't the production of BMP part of this process? Probably yes,
but this figure was taken out of a paper.

Is regulates transitive? If A regulates B and B regulates C, does A regulate C?

ACTION ITEM: improve on the current 'regulates' definition referring
to continuants which interact and fulfill their functions, then see if
this definition works and can be applied to the use case/s that we
have

When known, the most proximal step to a process, should be the
regulator of that process. In the example, binding of SMAD4 complex
regulates transcription, all the previous stuff regulates
transcription by inference.

Do we need 'regulates' AND 'indirectly_regulates'? Not really.

Is regulation a mix of instructive and permissive signals?

Hh signaling regulates limb development? Melissa/David: yes David OS:
BS! -lots of argument, David H changes his mind, Hh signalling part
of limb development. In summary, instructive signals would be part of
the process

BMP signaling is required for dorsal/ventral patterning, it is
instructive, it needs to be a part of.

Darren: If all we know that BMP binding the receptor results in change
in tsc, then create BMP signaling pathway regulates transcription. As
we know more, add more information to the ontology, change the
annotation to something more specific.

Larry: why take away the more general and only keep the detail?

How many senses of 'regulates' are being lumped together in the
relationship 'regulates'?

END DAY ONE - GOING TO DINNER at 6:20 pm after beginning at 8:50 am

Day 2: starting at 9:13 am with tasks from last night

== Develops_from homework ==

Biologist, logicians to try to come up with definitions of
develops_from, discuss need for transformation_of, derives_from.

=== Biological ===

Melissa/David: Biological definition of develops_from (at the cellular level) and the continuity of cell lineage.

Darren: c develops from d iff there is a continuity of lineage extending from d to c, where:
# the existence of d preceds the existence of C
# some portion of the material of d is retained in the material of c
# one can trace the event or set of events linking d to c

What is 'material'?

Alan: still need and should have developmental specific definition,
build the specific definitions (developmental, protein) first, then
build the general one later

* cell1 parent_of cell 2 (single division process occurs)
* cell1 in_lineage_with cell2, if cell1 = cell2 or cell2 is some sequence of parent relationships to the cell2

(develops_from within a single organism) - gets around Larry's lung
developed from his grandmother's ovary

anatomical structure 1 develops from anatomical structure 2 iff some
cell in anatomical structure 2 in lineage with some cell in anatomical
structure 1.

Is there a problem with immaterial entities? Eg. blastocoel. Not
really, we don't care about them. What about secretions, things that
are built out of secreted structures? How do we extend to those? Use
'secretes'?)

This basic definition appears to apply on multiple levels: cellular,
biochemical, anatomical structures and organisms. We will try this
out.

Suzi: some events that result in something new, some events that
result in 'rearrangement of material'

Alan: we want at least the cell biological level defined, good logical
definition in the terms that biologists use and understand, build from
the cellular level up.

=== Logical ===

(2) ontologist's justification of why the two children terms are important ;

Biologists don't care explicitly, use it implicitly. Ignore the two children for now.

== Homology ==

Melissa: homology relation? 'descends_from'
homologous structures vs. analogous structures. For example, mouse limb homologous to human limb, but bird wing is analogous to bat wing
character = quality (shape of bone margin)
character state = variability in quality
Peter:
Review of tree building based on three characters, looking at the various character states independently reveals different things about the individual ancestral states. Comparing two trees derived from two different sets of characters reveals different phylogenetic relationships.
Homology evidence codes: (in use by Phenoscape using Phenote)
* inferred from morphological similarity
* inferred from positional similarity
* inferred from developmental similarity
* inferred from compositional similarity
* inferred from gene expression similarity
* inferred from phylogeny

Definition: (see RO meeting wiki but remove taxon reference and replace by 'population', remove the Instance 3-ary relation - Melissa editing now)

directly_descends_from = (definition, get rid of partially a copy, get rid of determination is instance_level

descends_from = ? in_lineage_with from the earlier discussion on develops_from

This looks good to Barry, fix italicization issue with definition

common ancestor forelimb
/ \
/ \ descends_from
/ \
/ \
bat wing human arm
bat wing <-homologous_to -> human arm

ACTION ITEM: Two relations: 'descends_from' (not the final string),
homologous_to both with definitions - generalize definition, work on
last bit of definition relating to genetic material and genetic
programs

What do you use to describe the relationship between a parent
anatomical structure and a child anatomical structure

Darren: current definition is restricted to anatomical structures,
huge problem for proteins/genes

Chris: structure of definition is fine, need to generalize homology to
apply to proteins/genes, anatomical structure could broadly refer to
character states

Melissa: need homologous_to NOW for anatomical structures

Note: Just because two anatomical structures are homologous, it does
not mean that its parts are homologous. Structures that are
homologous could use completely different programs.

David OS: transitive closure is important only between two 'generations'
* 1001
* 0001
* 0101
* 0110
* 0100

David OS: evolved_from relationship. The homologous_to relationship
does not involve time, can hold between simultaneously existing
entities: human arm and bat wing. In contrast, evolves_from does
involve time: human arm and 'ancestral forelimb'

Is evolves_from built from directly_descends_from? Yes. Figure out
strings to make them parallel.

BREAKTIME

Regulates discussion: not reopened to avoid non-constructive and never
ending discussion.

Action Item: David, Tanya and Chris will come up with a more rigorous
definition of 'regulates' and present that to the group for review.

== Epistemic relations or how do we know what we know? ==
Presenter: Larry Hunter

* supports
* is_supported_by (inverse)
* contradicts
* is_contradicted_by (inverse)

What is scientific evidence? (evidence that supports a hypothesis - 'citeable'?)
* peer review
* capable of being communicated
* secret information can't be scientific evidence

Making physical objects scientific evidence is a problem???
* "bug" with pins in it? scientific specimen: is this evidence?
* how about clones?

information entity - something that is communicated

GO gene_association file (GAF) use case

3 epistemic columns:

* DB:reference: <assertion> is_supported_by <DB:reference>
* NOT qualifier - flips evidence, not assertion: <assertion> is_contradicted_by <DB:reference>
* evidence code

How to handle one piece of evidence that supports two (or more) assertions in different ways.
I.e. sentence 1 provides info for IDA and IC, how do we capture these multiple roles?
# sub-relations: subclass binary supports, e.g. supports_by_direct_assay
# ternary relations: Make supports a ternary relation: supports <assertion> <evidence> <evidence type>
# PMID = ECO type
# represent the inference
[[Image:Inference_relations.jpg]]


* asserted sentences have a speaker
* asserted sentences = things we believe are true
* (When all fails, speak louder and/or faster.)
* partial constraints for supports?
* Barry: add to ROIL

== TAIR Relations ==

Tanya: has(function)

ACTION ITEM: table: map relationship_types to RO relations if known,
if not put?, also add range of things that go into term2, send to
group (obo-discuss, ro). For protein modification, use psi-mod
(potential target for)

== Biochemical relations ==

Presenter: Mike Bada

Built GO to CheBI cross products

Functions defined in terms of processes by which they can be realized:

kinase function = catalytic function THAT is_realized_in GO:kinase activity

Definitions are wrong!

THEY WANT: Catalytic processes and Catalytic activities defined in
terms of processes they are catalyzing:

GO:kinase activity = GO:molecular_function THAT results_in_catalysis_of GO:phosphorylation

This (Mike thinks) necessitates an ontology of types of (bio)chemical
reactions. GO lays out potential to do something vs. the doing
something. These both exist. We will not instantiate BOTH function
AND functioning. It is simpler to make links between functions and
processes.

Process(function) = realization of function, and Function (process) = realized_as process

Alan: automatic generation of one term when the other is made

DavidH: how about creating links between MF and BP and the relationship describes that link?

Discussion about Mike's definitions and how they could be improved.

David H: We will create a relationship describing that a gene product
has the potential to execute a molecular function (has disposition to
realize?). This way the MF ontology describes the realization
(execution) of a molecular function. These executions will then be
allowed to be part_of BPs. All MFs are part_of some type of BP.

=== TMRs, cross-products ===

ACTION ITEM: Larry will create and use too many relations (TMRs) Mike
has made now as 'macros' or shortcuts while the RO people write the
underlying framework that will support them. If some of them don't
break down properly, these will be fixed. Relations will be sent to
Alan together with Mike for training. Code named: Mike And Chris
Relations Ontology, or ROC, ROIL, MAC-RO, MAC-ROP

Chris: cross products, GO biological process and cell ontology

There are a bunch of different proposed relations: see ro_proposed:
aka Chris' macros (how many? 12, development, anatomy and cell, for
chemicals about 10)

ACTION ITEM: find an example of Chris' macro where there are two
relations that identify two participants to verify claim - source and
destination for a transport event

ACTION ITEM: again, find a way to translate the macros into a formal definition

Pattern: x results in A x2; A is term from another ontology

Alternate: for some y A(y); participant (x2,y) ^

(tried to transcribe the above from Fabian's writing on the board but missed some parts)

Necessary is easy, necessary and sufficient is hard

== Summary of Action Items ==

# Scope of 'all’ needs to be addressed taking into account that some ontologies (GO, FMA) are canonical, while others are not (for example, PRO includes mutant proteins)
# Move to numerical ids
# Define instance level relations as well. Clarity is important. Relations need to be clarified whether they be used for type_type/type_instance/instance_instance.
# RO should have a commitment to an upper ontology and it shall be BFO.
# Add new timing relationships: begins_at_end_of, begins_during, ends_during, begins_before, ends_after, simultaneous_with, happens_during
# Stages and temporal relations: are there cases where we do not need the reference process?
# Fix phrasing to timing relationships (first_exists_during vs. begin_to_exist) to be consistent.
# Make a biological definition of develops_from, test at all levels of granularity, provide cases of NOT develops_from
# Have v. small meeting with spatial ontology (CAD, connectivity, etc.) experts + some biologists to adapt existing spatial relations to RO, who to invite? Tony Cohn. Thomas Bittner. Karen Pittman, Cycorp. Xenia Fiorentini, NIST. GOAL of this meeting: get spatial relations into RO
# Spatial relations: add to ro attachment, connected, synaptic (use fma definitions, work on them, circulate to biologists to vet)
# Add symmetric_overlaps/mutally_overlaps, modify the proposed definition.
# Make GO spatial-related process definitions consistent with spatial ontology. Fix, harmonize, extract from appropriate places -- anything relational from spatial.obo to ro
# Add more axis-related terms to spatial list (adaxial/abaxial, apical/basical, caudal-cephalic). Make precise what is meant by medial, lateral -- dorsal, ventral -- proximal, distal -- anterior, posterior
# Take anything relational out of Spatial and move to RO, check out whether 'vicinity of' needs to stay
# Remove spatial stuff from FMA
# Decide what needs to stay in PATO and what needs to go into RO - punt to tomorrow
# Define distal and proximal, ternary relationships?
# Add medial and lateral?
# Improve on the current 'regulates' definition referring to continuants which interact and fulfill their functions, then see if this definition works and can be applied to the use case/s that we have
# Two relations: 'descends_from' (not the final string), homologous_to both with definitions - generalize definition, work on last bit of definition relating to genetic material and genetic programs. new relations descends_from (already used so need a different string!), homologous_to can be inferred.
# Evidence: add supports and contradicts relationships, small working group for domain and range
# David, Tanya and Chris will come up with a more rigorous definition of 'regulates' and present that to the group for review.
# Table: map relationship_types to RO relations if known, if not put? Also add range of things that go into term2, send to group (obo-discuss, ro). For protein modification, use psi-mod (potential target for)
# Tair: make table of tair relations, column for ro term if it exists, send to ro group make request for needed terms
# Larry will create and use too many relations (TMRs) Mike has made now as 'macros' or shortcuts while the RO people write the underlying framework that will support them. If some of them don't break down properly, these will be fixed. Relations will be sent to Alan together with Mike for training. Code named: Mike And Chris Relations Ontology, or ROC, ROIL, MAC-RO, MAC-ROP
# Find an example of Chris' macro where there are two relations that identify two participants to verify claim - source and destination for a transport event
# Again, find a way to translate the macros into a formal definition

File:Inference relations.jpg

2008-06-02T22:21:05Z

Pmidford: Cleaned up version of diagram Chris Mungall put up during Larry Hunter's presentation.

Cleaned up version of diagram Chris Mungall put up during Larry Hunter's presentation.

File:Homology.ppt

2008-05-20T22:03:03Z

Pmidford:

OntologyRelations

2008-05-20T22:01:55Z

Pmidford:

'''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:relations_for_representing_developmental_anatomy.ppt]]

[[Media:regulates.ppt]]

[[Media:overlaps.ppt]]

[[Media:RO-denver-cjm.ppt]]

[[Media:dahdul-ROmeeting.ppt]]

[[Media:Fabian developmental relations.pdf]]

[[Media:Fabian develops_from.pdf]]

[[Media:melissa development examples.ppt]]

[[Media:Homology.ppt]]

[[Image:Hunter Epistemic relations.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

2008-05-14T21:24:14Z

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

'''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.

== 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

== 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: 9:00AM-5:30PM Monday, May 19th 2008 ==

=== 9-10:30am" General (Barry/Chris) ===

* review of principles
** all-some(time) (Barry)
** desired level of granularity (Barry)
* 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 (Melissa)
* 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) ===

* Overview and RCC8 (Melissa)
* overlaps - bone + joint use case (Peter)
* connected_to - axon tracts and neuropil (fiat binary)
* attached_to - bone + bone use case (Wasila)
* bona fide vs fiat - when does it matter
* surrounded_by
* 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

2008-05-14T21:05:10Z

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

'''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.

== 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

== 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: 9:00AM-5:30PM Monday, May 19th 2008 ==

=== 9-10:30am" General (Barry/Chris) ===

* review of principles
** all-some(time) (Barry)
** desired level of granularity (Barry)
* 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 (Melissa)
* 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) ===

* overlaps - bone + joint use case (Peter)
* connected_to - axon tracts and neuropil (fiat binary)
* attached_to - bone + bone use case (Wasila)
* bona fide vs fiat - when does it matter
* RCC8 - can we just import directly?
* surrounded_by
* 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

2008-05-14T18:51:20Z

Pmidford: /* Proposed new type-level 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

* involved in
* functions as
* expressed in
* related to
* required for
* located in
* is subunit of
* constituent of
* regulates
* functions in
* represses
* is regulated by
* suppresses gene
* enhances gene
* partially enhances gene
* partially suppresses gene
* expressed during
* is downregulated by
* has function
* has protein-protein physical interaction with
* binds to cis-element of
* acts upstream of
* acts downstream of
* member of
* has protein-DNA interaction with
* has protein modification of type
* protein is modified by
* contributes to
* colocalizes with
* is upregulated 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

2008-05-14T18:49:29Z

Pmidford: /* Proposed new type-level 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 X overlaps all its parts.

==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

* involved in
* functions as
* expressed in
* related to
* required for
* located in
* is subunit of
* constituent of
* regulates
* functions in
* represses
* is regulated by
* suppresses gene
* enhances gene
* partially enhances gene
* partially suppresses gene
* expressed during
* is downregulated by
* has function
* has protein-protein physical interaction with
* binds to cis-element of
* acts upstream of
* acts downstream of
* member of
* has protein-DNA interaction with
* has protein modification of type
* protein is modified by
* contributes to
* colocalizes with
* is upregulated 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