From OBO to OWL and back

2011-07-12T09:14:27Z

Djs93:

From OBO to OWL and back

2011-07-12T09:13:41Z

Djs93:

From OBO to OWL and back

2011-07-12T09:13:19Z

Djs93: Created page with "This page is the location for downloads and instructions for the ICBO 2011 tutorial "From OBO to OWL and back again" to be held on July 27th. It will include details of the soft..."

RO:Main Page

2009-07-24T20:02:43Z

Djs93: /* 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=

An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.

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]]

==Proposal regarding defined classes==

We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.

extension =def. the class [collection, totality, set] of all instances of a type

defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.

Example: all people holding violins in the La Scala Opera House at a certain time.

composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'

Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.

==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.

On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].

==Proposed new type-level relations (posted by Melanie Courtot) ==

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]

Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.

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_relations_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]

==Need for Specific Role Relations (BS)==

x has a role => x is assigned the role e.g. in the protocol
x realizes the role => x has the role
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it

Someone who has a role can also play it
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.

==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==

Note, the term 'homology' has had many uses. This is an attempt to formally define 'cladistic homology'. One possible informal way to define this: "similarity due to unbroken descent from a common ancestor" ('Developmental Plasticity and Evolution', Mary West-Eberhard (2003))

x1 '''derived_by_direct_descent_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 y2. *(see notes below)

'''derived_by_descent_from''' is the instance level relation which is the transitive closure over '''derived_by_direct_descent_from'''

From this we can define a type level relation:

A in B ''derived_by_descent_from'' C in D :

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

a '''part_of''' b

a '''derived_by_descent_from''' c

c '''part_of''' d

(Note – B must be a subclade of the clade genealogically descended from D)

A1 in B1 ''homologous_to A2'' in B2

iff

exists A3, B3:

A1 in B1 ''derived_by_descent_from'' A3 in B3

&

A2 in B2 ''derived_by_descent_from'' A3 in B3

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

[* 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 derived_by_direct_descent_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).]

[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.
]

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 derived_by_descent_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

== Measurements ==

At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation
called is_measurement_of to relate a measurement to some entity. (I
can't remember if these were the exact names we used).
is_measurement_of is subpropertyOf is_about

In the following we are discussing instance level relationships.

* measurement_datum:
** has_value:
** in_units:
** of_dimension:

m1 type measurement:

* m1 has_value 30^^xsd:float
* m1 in_units_of degree_celsius (UO:0000027)
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)

(Unresolved: latter two are classes. I guess that means that
in_units_of and of_dimension are annotation properties, which is a
shame. Either that or degree_celsius and temperature_dimension are
instances of some sort. Barry?)

* room1 type site
* room1 has_quality t1
* t1 instance_of temperature (PATO:0000146)

* m1 is_measurement_of t1

It was left open exactly how to represent uncertainty in the
measurement, but this was thought to be perhaps something associated
with the instrument or with a collection of measurements, rather than
what was associated with the individual measurement.

Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z

== Realization_of and Associated Relations ==

For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.

In its terms we might define, for example,

x deviation_from y

=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y

== derivation-like relations ==

From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf

We need relations that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Motivating examples are cases where entities retain identity as they become and cease to be part of something else (wheel/car, protein/protein complex).

Here's an attempt, following the language in the relations paper.

'''c assembled_from c1, c2, .. cn'''

assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t

'''c gains_part c1'''

gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.

'''c loses_part c1'''

loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.

'''c disassembles_into c1, c2,..., cn'''

disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.

In terms of the "16 days" paper, assembly = unification, disassembly = separation.

Another way to highlight the differences between the relations is this summary, in short
hand. -> marks the temporal divide. If you don't see a variable on one
side, the entity it denotes doesn't exist at that time.
The {} is a kind of signature, even shorter version to emphasize the
changes in existence. "," marks the temporal divide. "-" means
something ceases to exist. "*-" means all denoted entities ceases to
exist. "+" means something comes into existence.

'''derivation''' {*-,+} 
a -> b c ''aka fission'' 
b c -> a ''aka fusion''

'''transformation''' {,} 
a,C(a) -> a,C'(a)

'''gains part''' {,} 
a,b, not has_part(a,b) -> a,b, has_part(a,b)

'''loses part''' {,} 
a,b, has_part(a,b) -> a,b, not has_part(a,b)

'''unification/assembly''' {,+} 
a,b -> c, has_part(c,a),has_part(c,b)

'''separation/disassembly''' {-,} 
c, has_part(c,a),has_part(c,b) -> a,b

Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations

* derives_from
** fused_from
** fissioned_from ''yes, lousy name''
** assembled_from
** disassembled_from

gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.

=Background Material=

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

[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]

RO:Main Page

2009-07-24T19:35:28Z

Djs93: /* 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=

An RO expert meeting took place in May, 2008. See [[OntologyRelations]] for notes and presentations.

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]]

==Proposal regarding defined classes==

We take 'type' as primitive; types are children of BFO categories, which are themselves types. In the definitions that follow we ignore the factor of time, which should however be made explicit according to the practices established in RO.

extension =def. the class [collection, totality, set] of all instances of a type

defined class =def. a class all of whose members instantiate the same type T, that is (1) not itself the extension of any type, (2) defined by means of a statement of necessary and sufficient conditions of the form 'A ... is a T which ...'.

Example: all people holding violins in the La Scala Opera House at a certain time.

composite class =def. a class all of whose members instantiate one or other of a number of types, T1, ... Tn, that is (1) not itself the extension of any type, (2) defined by means of a disjunction of statements giving necessary and sufficient conditions of the form 'A ... is either a T1 which ... or a Tn which ...'

Example: all people or bacteria in the La Scala Opera House at a certain time; the pattern '...' exemplified by graphical instances and by morse code beeps.

==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.

On the logic of instance-level relations see also Bittner's paper [http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner_AO_07-60_printed.pdf here].

==Proposed new type-level relations (posted by Melanie Courtot) ==

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]

Some of those are described in the [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/OBO_REL/ro_proposed.obo RO proposed] file.

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_relations_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]

==Need for Specific Role Relations (BS)==

x has a role => x is assigned the role e.g. in the protocol
x realizes the role => x has the role
x plays the role => x performs those actions which someone who has the role would perform if they were realizing it

Someone who has a role can also play it
But so also can someone who does not have the role, e.g. the doctor takes on the nurse role because the nurse is off sick.

==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==

Note, this is an attempt to define 'cladistic homology'. One possible informal way to define this: "Similarity due to direct descent from a common ancestor'.

x1 '''derived_by_direct_descent_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 y2. *(see notes below)

'''derived_by_descent_from''' is the instance level relation which is the transitive closure over '''derived_by_direct_descent_from'''

From this we can define a type level relation:

A in B ''derived_by_descent_from'' C in D :

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

a '''part_of''' b

a '''derived_by_descent_from''' c

c '''part_of''' d

(Note – B must be a subclade of the clade genealogically descended from D)

A1 in B1 ''homologous_to A2'' in B2

iff

exists A3, B3:

A1 in B1 ''derived_by_descent_from'' A3 in B3

&

A2 in B2 ''derived_by_descent_from'' A3 in B3

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

[* 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 derived_by_direct_descent_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).]

[* DS: comment - I agree that reference to genetic sequence is (probably) unnecessary. Anyway, it is clear that the current formulation doesn't work: The morphology of my leg is determined by a partial copy of the genetic sequence that determined morphology of my father's arm. One possible alternative, deliberately ignoring genetics: Of all the anatomical structures in y2, x2 is the most morphologically similar to x1.
]

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 derived_by_descent_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

== Measurements ==

At the [http://neurocommons.org/page/First_IEO_workshop IEO meeting] people seemed to agree that we use a relation
called is_measurement_of to relate a measurement to some entity. (I
can't remember if these were the exact names we used).
is_measurement_of is subpropertyOf is_about

In the following we are discussing instance level relationships.

* measurement_datum:
** has_value:
** in_units:
** of_dimension:

m1 type measurement:

* m1 has_value 30^^xsd:float
* m1 in_units_of degree_celsius (UO:0000027)
* m1 of_dimension temperature_dimension (PATO:0000146? -that's what's in UO, but need to think about that)

(Unresolved: latter two are classes. I guess that means that
in_units_of and of_dimension are annotation properties, which is a
shame. Either that or degree_celsius and temperature_dimension are
instances of some sort. Barry?)

* room1 type site
* room1 has_quality t1
* t1 instance_of temperature (PATO:0000146)

* m1 is_measurement_of t1

It was left open exactly how to represent uncertainty in the
measurement, but this was thought to be perhaps something associated
with the instrument or with a collection of measurements, rather than
what was associated with the individual measurement.

Inference rule on is_about: forall x, y, z, if x is_about y and y inheres_in z then x is_about z

== Realization_of and Associated Relations ==

For OBI purposes there is a need for an instance-level relation between a plan (for instance a protocol) and the occurrent which realizes this plan.

In its terms we might define, for example,

x deviation_from y

=def. x is an occurrent and y is a plan and there is an agent z who is the agent_of x and is attempting in performing x to realize y and it is not the case that x realization_of y

== derivation-like relations ==

From [http://groups.google.com/group/bfo-discuss/browse_thread/thread/7929d436f64b8f04/428b25c2f72c3d60?#428b25c2f72c3d60 this thread].
Related, section VI from http://ontology.buffalo.edu/smith/articles/16Days.pdf

We need relations that parallel the definition of transformation and derivation, but for different configurations of identity and existence in time. Motivating examples are cases where entities retain identity as they become and cease to be part of something else (wheel/car, protein/protein complex).

Here's an attempt, following the language in the relations paper.

'''c assembled_from c1, c2, .. cn'''

assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t

'''c gains_part c1'''

gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.

'''c loses_part c1'''

loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.

'''c disassembles_into c1, c2,..., cn'''

disassembles_into holds between material continuants when one ceases to exist at a certain time and some of its parts come to be self standing. Thus we will have axioms to the effect that from c disassembles_into c1 and c2 we can infer that c1 part_of c just before t, c2 part_of c just before t, etc, that the spatial region occupied by c contains the spatial regions of c1.. cn just before t, that c does not exist after t, and c1, c2.. exist at t.

In terms of the "16 days" paper, assembly = unification, disassembly = separation.

Another way to highlight the differences between the relations is this summary, in short
hand. -> marks the temporal divide. If you don't see a variable on one
side, the entity it denotes doesn't exist at that time.
The {} is a kind of signature, even shorter version to emphasize the
changes in existence. "," marks the temporal divide. "-" means
something ceases to exist. "*-" means all denoted entities ceases to
exist. "+" means something comes into existence.

'''derivation''' {*-,+} 
a -> b c ''aka fission'' 
b c -> a ''aka fusion''

'''transformation''' {,} 
a,C(a) -> a,C'(a)

'''gains part''' {,} 
a,b, not has_part(a,b) -> a,b, has_part(a,b)

'''loses part''' {,} 
a,b, has_part(a,b) -> a,b, not has_part(a,b)

'''unification/assembly''' {,+} 
a,b -> c, has_part(c,a),has_part(c,b)

'''separation/disassembly''' {-,} 
c, has_part(c,a),has_part(c,b) -> a,b

Note that Barry has suggested that derivation be revised so as to not imply that the entities that exist before the temporal divide cease to exist, but retaining that a new entity is created. If this comes to be, then we might imagine a hierarchy of relations

* derives_from
** fused_from
** fissioned_from ''yes, lousy name''
** assembled_from
** disassembled_from

gains_part and loses_part aren't derivation since no new entity is created. In that sense they are similar to transformation.

=Background Material=

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

[http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]

File:OE2-tutorial.ppt

2009-07-23T17:14:25Z

Djs93: uploaded a new version of "Image:OE2-tutorial.ppt"

OBO-Edit

2009-07-23T13:59:14Z

Djs93:

'''The OBO-Edit Ontology Developer's Environment: A Practical Introduction'''

Tutorial by David Osumi-Sutherland (FlyBase / Gene Ontology Consortium) organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology.]

Date: July 23, 2009 (Afternoon)

[http://oboedit.org/ OBO-Edit2], the new version of the popular ontology editing software, has many powerful new tools for ontology analysis and construction. This tutorial will provide an introduction to using OBO-Edit2 to build and maintain ontologies, with special emphasis on working with computable definitions.

''''The following topics will be covered'''

:''OBO basics''
:: The type/instance distinction [2]
:: Theory of OBO relations [2]
:: Necessary and sufficient definitions
:: Avoiding tangled hierarchies [1]
:''OBO-Edit2 basics''
:: Basic editing with the tree editor and the parent editor
:: Basic searching, filtering and rendering
:: Necessary and sufficient definitions and use of the reasoner
:: Declaring disjunction and finding contradictions
:''OBO-Edit2 advanced use''
:: Advanced searching and rendering
:: Using renders to track editing progress
:: Selective importation of foreign terms
:: Tracking redundancy
:: Graphing with OBO-Edit
:''Preparing OBO files for release''
:: Verification
:: Instantiating implied links and eliminating redundancy.

'''Faculty'''

David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for development of the Drosophila [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy anatomy] and [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development development] ontologies. He is a member of the OBO-Edit working group and the OBO Foundry Relations Ontology working group.

'''Slides'''
: [[media:OE2-tutorial.ppt]]

'''Tutorial ontology'''

[http://oboedit.org/ICBOtutorialData/tutorial.obo tutorial.obo]

'''References'''

[1] Rector, A., 2003. [http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL.] Proc. K-CAP:ACM 2003, 121-129.

[2] Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies], Genome Biology, 2005, 6:R46.

[3] Smith B, et al., 2007 [http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration], Nature Biotechnology 25, 1251 - 1255.

OBO-Edit

2009-07-23T13:58:38Z

Djs93:

'''The OBO-Edit Ontology Developer's Environment: A Practical Introduction'''

Tutorial by David Osumi-Sutherland (FlyBase / Gene Ontology Consortium) organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology.]

Date: July 23, 2009 (Afternoon)

[http://oboedit.org/ OBO-Edit2], the new version of the popular ontology editing software, has many powerful new tools for ontology analysis and construction. This tutorial will provide an introduction to using OBO-Edit2 to build and maintain ontologies, with special emphasis on working with computable definitions.

''''The following topics will be covered'''

:''OBO basics''
:: The type/instance distinction [2]
:: Theory of OBO relations [2]
:: Necessary and sufficient definitions
:: Avoiding tangled hierarchies [1]
:''OBO-Edit2 basics''
:: Basic editing with the tree editor and the parent editor
:: Basic searching, filtering and rendering
:: Necessary and sufficient definitions and use of the reasoner
:: Declaring disjunction and finding contradictions
:''OBO-Edit2 advanced use''
:: Advanced searching and rendering
:: Using renders to track editing progress
:: Selective importation of foreign terms
:: Tracking redundancy
:: Graphing with OBO-Edit
:''Preparing OBO files for release''
:: Verification
:: Instantiating implied links and eliminating redundancy.

'''Faculty'''

David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for development of the Drosophila [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy anatomy] and [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development development] ontologies. He is a member of the OBO-Edit working group and the OBO Foundry Relations Ontology working group.

'''Slides'''
: [[media:OE2-tutorial.ppt]]

'''Tutorial ontology'''

[http://oboedit.org/ICBOtutorialData/tutorial.obo]

'''References'''

[1] Rector, A., 2003. [http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL.] Proc. K-CAP:ACM 2003, 121-129.

[2] Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies], Genome Biology, 2005, 6:R46.

[3] Smith B, et al., 2007 [http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration], Nature Biotechnology 25, 1251 - 1255.

OBO-Edit

2009-07-23T13:53:50Z

Djs93:

'''The OBO-Edit Ontology Developer's Environment: A Practical Introduction'''

Tutorial by David Osumi-Sutherland (FlyBase / Gene Ontology Consortium) organized in conjunction with the [http://icbo.buffalo.edu International Conference on Biomedical Ontology.]

Date: July 23, 2009 (Afternoon)

[http://oboedit.org/ OBO-Edit2], the new version of the popular ontology editing software, has many powerful new tools for ontology analysis and construction. This tutorial will provide an introduction to using OBO-Edit2 to build and maintain ontologies, with special emphasis on working with computable definitions.

''''The following topics will be covered'''

:''OBO basics''
:: The type/instance distinction [2]
:: Theory of OBO relations [2]
:: Necessary and sufficient definitions
:: Avoiding tangled hierarchies [1]
:''OBO-Edit2 basics''
:: Basic editing with the tree editor and the parent editor
:: Basic searching, filtering and rendering
:: Necessary and sufficient definitions and use of the reasoner
:: Declaring disjunction and finding contradictions
:''OBO-Edit2 advanced use''
:: Advanced searching and rendering
:: Using renders to track editing progress
:: Selective importation of foreign terms
:: Tracking redundancy
:: Graphing with OBO-Edit
:''Preparing OBO files for release''
:: Verification
:: Instantiating implied links and eliminating redundancy.

'''Faculty'''

David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for development of the Drosophila [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy anatomy] and [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development development] ontologies. He is a member of the OBO-Edit working group and the OBO Foundry Relations Ontology working group.

'''Slides'''
: [[media:OE2-tutorial.ppt]]

'''References'''

[1] Rector, A., 2003. [http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL.] Proc. K-CAP:ACM 2003, 121-129.

[2] Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies], Genome Biology, 2005, 6:R46.

[3] Smith B, et al., 2007 [http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration], Nature Biotechnology 25, 1251 - 1255.

2008-11-10T11:56:18Z

Djs93: OBO-Edit2 Tutorial moved to A practical introduction to OBO-Edit2

== An introduction to OBO-Edit2 ==

'''Tutorial by David Osumi-Sustherland (FlyBase)'''

'''Date: ???'''

[http://oboedit.org/ OBO-Edit2], the new version of the popular ontology editing tool, has many powerful new tools for ontology analysis and construction. This tutorial will provide an introduction to the use of OBO-Edit2 to build and maintain OBO ontologies with special emphasis on working with necessary and sufficient definitions.

'''The following topics will be covered'''

:OBO basics
:: The type/instance distinction [2]
:: Theory of OBO relations [2]
:: Necessary and sufficient definitions
:: Avoiding tangled hierarchies [1]
:OBO-Edit2 basics
:: Basic editing with the tree editor and the parent editor
:: Basic searching, filtering and rendering
:: Necessary and sufficient definitions and use of the reasoner
:: Declaring disjunction and finding contradictions
:OBO-Edit2 advanced:
:: Advanced searching and rendering
:: Using renders to track editing progress
:: Selective importation of foreign terms
:: Tracking redundancy
:: Graphing with OBO-Edit
:Preparing OBO files for release:
:: Verification
:: Making implied links hard and stripping redundancy.

'''Faculty'''

David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for editing the Drosophila [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_anatomy anatomy] and [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fly_development development ontologies]. He is a member of the OBO-Edit working group and the OBO foundry relations ontology working group.

'''References'''

[1] Rector, A., 2003. [http://www.cs.man.ac.uk/~rector/papers/rector-modularisation-kcap-2003-distrib.pdf Modularisation of Domain Ontologies Implemented in Description Logics and related formalisms including OWL.] Proc. K-CAP:ACM 2003, 121-129.

[2] Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 "Relations in Biomedical Ontologies"], Genome Biology, 2005, 6:R46.

[3] Smith B, wt al., 2007 [http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration"], Nature Biotechnology 25, 1251 - 1255.

A practical introduction to OBO-Edit2

2008-11-10T11:55:15Z

Djs93: /* An introduction to OBO-Edit2 */

A practical introduction to OBO-Edit2

2008-11-10T11:35:42Z

Djs93:

== An introduction to OBO-Edit2 ==

'''Tutorial by David Osumi-Sustherland (FlyBase)'''

'''Date: ???'''

This tutorial will provide an introduction to the use of [http://*** OBO-Edit2] to build and maintain ontologies with special emphasis on working with necessary and sufficient definitions

Topics to be addressed will include:

OBO basics:
The type/instance distinction
Theory of OBO relations
Necessary and sufficient definitions
Avoiding tangled hierarchies
OBO-Edit2 basics
Basic editing with the tree editor and the parent editor
Basic searching, filtering and rendering
Necessary and sufficient definitions and use of the reasoner

Declaring disjunction and finding contradictions
OBO-Edit2 advanced:
Advanced searching and rendering
Useful renders for tracking editing progress
Selective importation of foreign terms
Tracking redundancy
Graphing with OBO-Edit
Preparing OBO files for release:
Verification
Making implied links hard and stripping redundancy.

'''Faculty'''

David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for editing the Drosophila [link anatomy] and [link development ontologies]. He is a member of the OBO-Edit working group and the OBO foundry relations ontology working group.

'''References'''

Smith B, et al., 2005 [http://genomebiology.com/2005/6/5/R46 "Relations in Biomedical Ontologies"], Genome Biology, 2005, 6:R46.
Smith B, wt al., 2007 [http://www.nature.com/nbt/journal/v25/n11/full/nbt1346.html "The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration"], Nature Biotechnology 25, 1251 - 1255.
Rector paper on disentangling

'''Links'''

[http:// *** download OBO-Edit2] (currently in beta - full release expected well before the data of this tutorial)
[http://*** OBO-edit manual]
[http:// ]

A practical introduction to OBO-Edit2

2008-11-10T00:04:12Z

Djs93: New page: == An introduction to OBO-Edit2 == '''Tutorial by David Osumi-Sutherland (FlyBase)''' '''Date: ???''' This tutorial will provide an introduction to the use of OBO-Edit2 to build and mai...

== An introduction to OBO-Edit2 ==

'''Tutorial by David Osumi-Sutherland (FlyBase)'''

'''Date: ???'''

This tutorial will provide an introduction to the use of OBO-Edit2 to build and maintain ontologies with special emphasis on working with logically defined terms.

Topics to be addressed will include:

'''Faculty'''

David Osumi-Sutherland is an ontologist and curator at [http://www.flybase.net FlyBase], where he is responsible for editing the Drosophila anatomy and development ontologies. He is a member of the OBO-Edit working group

'''References'''

Smith B, et al. [http://genomebiology.com/2005/6/5/R46 "Relations in Biomedical Ontologies"], Genome Biology, 2005, 6:R46.

'''Links'''

An Introduction to Chemistry Ontology

2008-11-09T21:08:33Z

Djs93:

'''Tutorial by Colin Batchelor (Royal Society of Chemistry)'''

'''Tuesday, July 21, 2009: 1-5p.m.'''

We provide an introduction to the development and use of chemistry ontology, with special focus on ChEBI (Chemical Entities of Biological Interest) and the Sequence Ontology.

Topics to be addressed will include:

:chemical entities as continuants
:the productivity of chemical nomenclature
:parts vs. structures vs. names
:the IUPAC nomenclature
:the past, present and future of the ChEBI ontology
:the Sequence Ontology
:reasoning with chemistry ontology
:extending ontology to chemical processes
:experimental methods in chemistry

'''Faculty'''

Colin Batchelor is team leader, Informatics Research and Development, at Royal Society of Chemistry Publishing in Cambridge, UK. He has a DPhil in physical and theoretical chemistry and is presently working on natural language processing and ontology development as applied to the chemical literature.

'''References'''

Kirill Degtyarenko, et al., "[http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D344 ChEBI: a database and ontology for chemical entities of biological interest]", Nucleic Acids Research, 2008, 36(Database issue), D344-D350, doi:10.1093/nar/gkm791

Peter Corbett, Colin Batchelor and Ann Copestake, "[http://www.lrec-conf.org/proceedings/lrec2008/workshops/W4_Proceedings.pdf Pyridines, Pyridine and Pyridine Rings: Disambiguating Chemical Named Entities]", Proceedings of Building and Evaluating Resources for Biomedical Text Mining at LREC 2008, Marrakech, Morocco.

Colin Batchelor, "[http://www.tantallon.org.uk/preprints/fois-upperchemistry.pdf An Upper-Level Ontology for Chemistry]", in 5th International Conference on Formal Ontology in Information Systems, Saarbrücken, Germany, October 31st to 3rd November 2008.

N. Villanueva-Rosales, M Dumontier, "[http://www.scs.carleton.ca/~nvillanu/papers/2007_OWLED_CFG.pdf Describing chemical functional groups in OWL-DL for the classification of chemical compounds]", OWL: Experiences and Directions (OWLED 2007), colocated with European Semantic Web Conference (ESWC2007), Innsbruck, Austria, 2007.

Smith B, et al. [http://genomebiology.com/2005/6/5/R46 "Relations in Biomedical Ontologies"], Genome Biology, 2005, 6:R46.

'''Links'''

[http://www.ebi.ac.uk/chebi/ ChEBI]

[http://www.sequenceontology.org/ Sequence Ontology]

[http://goldbook.iupac.org/ IUPAC Compendium of Chemical Terminology (Gold Book)/]

[http://www.ifomis.uni-saarland.de/bfo/ Basic Formal Ontology].

2008-05-29T12:21:06Z

Djs93: /* Proposed homologous_to relation */