NCBO Wiki - User contributions [en]

RO:Main Page

2013-11-01T23:36:26Z

Cjm: Replaced content with "= Announcement = OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro Old material that was previously kept here ..."

= Announcement =

OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro

Old material that was previously kept here has been moved to [[RO:Historic Material]]

RO:Historic Material

2013-11-01T23:35:50Z

Cjm: Created page with " This page contains historic material on the RO Note most of this is out of date and kept for archival purposes. '''For up to date documentation please see the RO homepage..."

This page contains historic material on the RO

Note most of this is out of date and kept for archival purposes.

'''For up to date documentation please see the RO homepage''': http://purl.obolibrary.org/obo/ro

=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.

=A formalization of instance-level relations in RO=

In [http://web.me.com/tbittner1/BittnerProfessional/Publications_files/Bittner_AO_07-60_printed.pdf "Logical properties of foundational mereogeometrical relations in bio-ontologies"] Tom Bittner provides axiomatization of the instance-level spatial relations in RO.

=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.

=Errata in Relations paper=

"C part_of C1 = [definition] for all c, t, if Cct then there is some c1 such that C1c1t and c part_of c1 at t.
Note the 'all-some' structure of this definition, a structure which will recur in almost all the relations treated here.
C part_of C1 defines a relational property of permanent parthood for Cs. It tells us that Cs, whenever they exist, exist as parts of C1s."

it's not right to say "permanent" or "whenever they exist". Since entities (e.g. embryos) can change type as they grow older, more like "entities, whenever then instantiate C, are parts of C1s"

Alan Ruttenberg

----

Page R46.7, Contained_in relationship:

The text says: "C1 overlap c2 at t =[definition] for some c, c part_of c1 at t and c part_of c2 at t."

The first C1 is in upper case letters; it should be lower case.

Barry Smith

=Background Material=

* [http://obofoundry.org/ro/ Relation Ontology Home]
* [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]
* [http://ontology.buffalo.edu/smith/articles/cornucopia.pdf The Cornucopia of Formal-Ontological Relations]
* [http://www.ifomis.org/bfo/ BFO Home page]

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= Announcement =

OBO_REL has been replaced by RO - the new website and wiki can be found at http://purl.obolibrary.org/obo/ro

=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.

=A formalization of instance-level relations in RO=

In [http://web.me.com/tbittner1/BittnerProfessional/Publications_files/Bittner_AO_07-60_printed.pdf "Logical properties of foundational mereogeometrical relations in bio-ontologies"] Tom Bittner provides axiomatization of the instance-level spatial relations in RO.

=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.

=Errata in Relations paper=

"C part_of C1 = [definition] for all c, t, if Cct then there is some c1 such that C1c1t and c part_of c1 at t.
Note the 'all-some' structure of this definition, a structure which will recur in almost all the relations treated here.
C part_of C1 defines a relational property of permanent parthood for Cs. It tells us that Cs, whenever they exist, exist as parts of C1s."

it's not right to say "permanent" or "whenever they exist". Since entities (e.g. embryos) can change type as they grow older, more like "entities, whenever then instantiate C, are parts of C1s"

Alan Ruttenberg

----

Page R46.7, Contained_in relationship:

The text says: "C1 overlap c2 at t =[definition] for some c, c part_of c1 at t and c part_of c2 at t."

The first C1 is in upper case letters; it should be lower case.

Barry Smith

=Background Material=

* [http://obofoundry.org/ro/ Relation Ontology Home]
* [http://genomebiology.com/2005/6/5/R46 Relations in Biomedical Ontologies]
* [http://ontology.buffalo.edu/smith/articles/cornucopia.pdf The Cornucopia of Formal-Ontological Relations]
* [http://www.ifomis.org/bfo/ BFO Home page]

From OBO to OWL and back

2011-07-27T17:04:42Z

Cjm:

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.

== Program ==

The program, including suggestions for preparatory reading, can be found here:

http://icbo.buffalo.edu/2011/TutorialF.pdf

== Slides ==

[http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.ppt draft slides ppt version] (may change slightly)

[http://caro2.googlecode.com/svn/trunk/scratch/tutorial_slides3.pdf draft slides PDF version] (may change slightly)

== Test ontology ==

[http://caro2.googlecode.com/svn/trunk/scratch/tutorial.obo tutorial.obo]

Right click and choose 'save link as'

== Software to install ==

=== OBO-Edit 2.1 ===

Please use [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/oboedit-2.1beta16/ OBO-Edit 2.1beta16].

Note - for (recent versions of?) Windows, the Java Virtual Machine is limited to 1G. If OBO-Edit fails to load in windows with the default memory settings, please re-install with memory set to 1024M.

=== OBO to OWL conversion tool ===

Download the latest version (0.3) of the Obo Ontology Release Tool GUI from here:

* http://code.google.com/p/owltools/downloads/list

Installers are available for mac, windows and unix. After installation, you will have two applications:

* The obo2owl converter
* [http://code.google.com/p/owltools/wiki/OBOReleaseManagerGUIDocumentation The Obo Ontology Release Tool]

=== Protege 4.1 ===

Please install [http://protege.stanford.edu/download/protege/4.1/installanywhere/Web_Installers/ Protege 4.1 release candidate 5 (build 235)].

This version of Protege should not need any configuring.

Previous version required configuring to ensure labels (OBO names) are displayed in all components instead of IDs. Try loading an OBO file to test this (it should load straight in, even though the dialog box asks you to choose and OWL file). If you can only see IDs in
the class hierarchy, then you should configure following the instructions here:

http://code.google.com/p/caro2/wiki/Getting_started

=== Optional ===

Kent's test ontology from the anatomy workshop:
[http://caro2.googlecode.com/svn/trunk/scratch/icbo-snomed-partonomy-test.owl icbo-snomed-partonomy-test.owl]

From OBO to OWL and back

2011-07-27T17:02:26Z

Cjm: /* Optional */

From OBO to OWL and back

2011-07-27T17:01:58Z

Cjm: /* Protege 4.1 */

From OBO to OWL and back

2011-07-25T18:46:02Z

Cjm: /* OBO to OWL conversion tool */

From OBO to OWL and back

2011-07-23T23:45:14Z

Cjm: /* OBO to OWL conversion tool */

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 software to install and their configuration along with test ontologies to download. Please check back closer to the session for details.

== Program ==

== Slides ==

== Test ontologies ==

== Software to install ==

=== OBO-Edit 2.1 ===

Please use [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/oboedit-2.1beta16/ OBO-Edit 2.1beta16].

=== OBO to OWL conversion tool ===

Download the latest version of the Obo Ontology Release Tool GUI from here:

* http://code.google.com/p/owltools/downloads/list

Installers are available for mac, windows and unix. After installation, you will have two applications:

* The obo2owl converter
* [http://code.google.com/p/owltools/wiki/OBOReleaseManagerGUIDocumentation The Obo Ontology Release Tool]

=== Protege 4.1 ===

==== Configuring Protege 4.1 ====

From OBO to OWL and back

2011-07-23T23:44:17Z

Cjm: /* OBO to OWL conversion tool */

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 software to install and their configuration along with test ontologies to download. Please check back closer to the session for details.

== Program ==

== Slides ==

== Test ontologies ==

== Software to install ==

=== OBO-Edit 2.1 ===

Please use [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/oboedit-2.1beta16/ OBO-Edit 2.1beta16].

=== OBO to OWL conversion tool ===

Download the latest version of the Obo Ontology Release Tool GUI from here:

* http://code.google.com/p/owltools/downloads/list

Installers are available for mac, windows and unix. After installation, you will have two applications:

* The obo2owl converter
* The Obo Ontology Release Tool

=== Protege 4.1 ===

==== Configuring Protege 4.1 ====

OMIM Annotation Standards

2010-01-15T19:43:28Z

Cjm: Replacing page with 'Moved to [http://www.obofoundry.org/wiki/index.php/PATO:OMIM_Annotation_Standards OMIM_Annotation_Standards]'

Moved to [http://www.obofoundry.org/wiki/index.php/PATO:OMIM_Annotation_Standards OMIM_Annotation_Standards]

Special:Badtitle/NS200:Absent

2009-10-20T23:28:04Z

Cjm: Replacing page with 'See http://www.obofoundry.org/wiki/index.php/PATO:Absent'

See http://www.obofoundry.org/wiki/index.php/PATO:Absent

Special:Badtitle/NS200:Pre vs Post Coordinating

2009-10-20T21:55:40Z

Cjm: Replacing page with 'See http://www.obofoundry.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating#LATEST_RESULTS for latest version'

See
http://www.obofoundry.org/wiki/index.php/PATO:Pre_vs_Post_Coordinating#LATEST_RESULTS

for latest version

Special:Badtitle/NS200:Revised 2008

2009-10-20T21:44:25Z

Cjm: Replacing page with 'moved to http://obofoundry.org/wiki/index.php/PATO:Revised_2008'

moved to http://obofoundry.org/wiki/index.php/PATO:Revised_2008

CL:Main Page

2009-06-08T16:05:00Z

Cjm:

=CL - OBO Cell Ontology=

=Resources=

==Ontology==

http://obofoundry.org/obo/CL

===Applications===

[[CL:Aligning species-specific anatomy ontologies with CL]]

[[Media:CLalign.biocuratorposter.final.ppt|CL_alignment_Biocurator07_poster]]

==Request tracker==

- [http://sourceforge.net/tracker/?group_id=76834&atid=925065 CL tracker]

You can also submit requests to the list.

==Mail Lists==

- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct OBO CrossProduct]

GO is pre-coordinating biological process terms that refer to cell types using CL IDs

==Cell ontology restructuring efforts==

The cell ontology is being restructured with the general goals of improving definitions, moving towards single inheritance and is_a completeness, and making the CL more interoperable with the GO and CARO. These discussions are occurring via chat, the histories of which will be posted here. Please email the OBO cell list if you would like to participate.

[[Media:cell_ontology_evaluation.doc|cell ontology evaluation.doc]]

[[Media:cellchat.2.12.07.doc|cellchat.2.12.07.doc]]

[[Media:cellchat.2.23.07.doc|cellchat.2.23.07.doc]]

[[Media:cellchat.2.27.07.doc|cellchat.2.27.07.doc]]

[[Media:cellchat.3.15.07.doc|cellchat.3.15.07.doc]]

[[Media:cellchat.6.1.07.doc|cellchat.6.1.07.doc]]

[[Media:cellchat.8-9-2007.doc|cellchat.8-9-2007]]

[[Media:cell_chat_8-24-2007.doc|cell_chat_8-24-2007]]

An initial rough draft can be found below in OBO format with the proposed new branch at the same level as 'cell'. Current tasks include moving cells over to the 'by structure' branch to test for compatibility and potential problems.

[[Media:CLRevised.obo|CL Revised.obo]]

Notes and action items from the cell ontology breakout session at the 2nd International Biocuration Meeting 2007.
[[Media:Cell_ontology_reorganization_working_group_notes.doc|Cell_ontology_reorganization_working_group_notes.doc]]

===NIAID Cell Ontology Workshop, May 13-14, 2008===

The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing on improving representation of immune cell types in the Cell Ontology. The participants in the workshop worked together to extend the current ontology in the area of immune cell types and to provide the necessary information for the upcoming restructuring of the Cell Ontology in single-inheritance form with genus-differentia definitions.

More information on the workshop can be found [[NIAID Cell Ontology Workshop May 2008|here]].

===Is_a Completeness for the current Cell Ontology===

As of May 30, 2008, 57 cell types in the Cell Ontology lack an is_a path to the root node '''cell'''. We would like to provide this is_a path in short order. The proposal is to provide these paths by June 15, 2008, either by providing an is_a parent of an appropriate superclass of cell, or by linking to the root. We are taking suggestions about what is_a parents to use. Please check out the page for [[May 2008 Is_a Orphans in the Cell Ontology]] and make some suggestions. All cells still without a valid suggestion for an is_a path to the root will be made direct is_a children of the root node after June 15, 2008.

== A list of useful differentia for defining cell-type terms==

has_part: <GO:cellular_compomnent>

has_function_from_process: <GO:biological_process>

has_quality: <PATO:quality/monadic quality of continuant>

develops_into: <CL:cell>

has_part: <CHEBI:chebi_ontology>

has_part: (<CHEBI:chebi_ontology>^part_of <GO:cellular_component>)

CL:Aligning species-specific anatomy ontologies with CL

2009-06-08T16:02:59Z

Cjm: Replacing page with 'http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL'

http://obofoundry.org/wiki/index.php/CL:Aligning_species-specific_anatomy_ontologies_with_CL

CL:Main Page

2009-06-08T16:02:14Z

Cjm: Replacing page with 'Redirected to http://obofoundry.org/wiki/index.php/CL:Main_Page'

Redirected to http://obofoundry.org/wiki/index.php/CL:Main_Page

UBERON:Main Page

2009-06-08T16:00:23Z

Cjm: Replacing page with 'http://obofoundry.org/wiki/index.php/UBERON:Main_Page'

http://obofoundry.org/wiki/index.php/UBERON:Main_Page

Special:Badtitle/NS200:Annotations

2009-06-08T15:57:31Z

Cjm: Replacing page with 'http://obofoundry.org/wiki/index.php/PATO:Annotations'

http://obofoundry.org/wiki/index.php/PATO:Annotations

Special:Badtitle/NS200:About

2009-06-08T15:55:40Z

Cjm: Replacing page with 'http://obofoundry.org/wiki/index.php/PATO:About'

http://obofoundry.org/wiki/index.php/PATO:About

Special:Badtitle/NS200:Main Page

2009-06-08T15:55:03Z

Cjm: Replacing page with 'Page moved: http://obofoundry.org/wiki/index.php/PATO:Main_Page'

Page moved: http://obofoundry.org/wiki/index.php/PATO:Main_Page

CL:Checklist

2009-02-17T20:16:53Z

Cjm: /* equatorial cone cell (sensu Endopterygota) */

= Name Changes =

== cell by organism ==

cell by organism [http://obofoundry.org/obo/CL:0000004 CL:0000004] becomes cell by phylum

* Alex: Y

== macrophage (sensu Diptera) ==

macrophage (sensu Diptera) [http://obofoundry.org/obo/CL:0000401 CL:0000401] becomes dipeteran macrophage

* Alex: Y

macrophage (CL:0000235) becomes vertebrate macrophage Y

== phagocyte (sensu Vertebrata) ==

phagocyte (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000518 CL:0000518] becomes vertebrate macrophage

* Alex: Y

phagocyte (sensu Nematoda and Protostomia) becomes invertebrate phagocyte Y
cardiac muscle cell (sensu Arthopoda) becomes cardioblast-derived cardiac muscle cell Y
epidermal cell (sensu Insecta)– becomess epidemioblast-derived epidermal cell Y

== podocyte (sensu Diptera) ==

podocyte (sensu Diptera) [http://obofoundry.org/obo/CL:0000391 CL:0000391] becomes Dipteran podocyte

* Alex: Y

== podocyte ==

podocyte [http://obofoundry.org/obo/CL:0000653 CL:0000653] becomes vertebrate podocyte

* Alex: Y

== glioblast (sensu Nematoda and Protostomia) ==

glioblast (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:? CL:?] becomes invertebrate glioblast

* Alex: Y

== glioblast (sensu Vertebrata) ==

glioblast (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000339 CL:0000339] becomes vertbrate glioblast

* Alex: Y

== glial cell (sensu Nematoda and Protostomia) ) ==

glial cell (sensu Nematoda and Protostomia) ) [http://obofoundry.org/obo/CL:? CL:?] becomes invertebrate glial cell

* Alex: Y

== glial cell (sensu Vertebrata) ) ==

glial cell (sensu Vertebrata) ) [http://obofoundry.org/obo/CL:? CL:?] becomes invertebrate glial cell

* Alex: Y

== neuron associated cell (sensu Nematoda and Protostomia) ) ==

neuron associated cell (sensu Nematoda and Protostomia) ) [http://obofoundry.org/obo/CL:? CL:?] becomes invertebrate NAS

* Alex: Y

== neuron associated cell (sensu Vertebrata) ) ==

neuron associated cell (sensu Vertebrata) ) [http://obofoundry.org/obo/CL:? CL:?] becomes vertebrate NAS

* Alex: Y

== extraembryonic cell/ germ line stem cell ) ==

extraembryonic cell/ germ line stem cell ) [http://obofoundry.org/obo/CL:? CL:?] replaced with EEC/primordial germ cell

* Alex: Y

= Obsoletions/Merges =

== cardioblast (sensu Arthropoda) ==

cardioblast (sensu Arthropoda) [http://obofoundry.org/obo/CL:0000465 CL:0000465]

* Alex: Y

== blood cell (sensu Nematoda and Protostomia) ==

blood cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000390 CL:0000390]

* Alex: Y

== hemocyte (sensu Nematoda and Protostomia) ==

hemocyte (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000387 CL:0000387]

* Alex: Y

== prohemocyte (sensu Nematoda and Protostomia) ==

prohemocyte (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000385 CL:0000385]

* Alex: Y

== chemotactic amoeboid cell (sensu Mycetozoa) ==

chemotactic amoeboid cell (sensu Mycetozoa) [http://obofoundry.org/obo/CL:0000289 CL:0000289]

* Alex: Y

== prohemocyte (sensu Nematoda and Protostomia) ==

prohemocyte (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000385 CL:0000385]

* Alex: Y

== chemotactic amoeboid cell (sensu Mycetozoa) ==

chemotactic amoeboid cell (sensu Mycetozoa) [http://obofoundry.org/obo/CL:0000289 CL:0000289]

* Alex: Y

== Distal tip cell (sensu nematoda) – ==

Distal tip cell (sensu nematoda) – [http://obofoundry.org/obo/CL:0000422 CL:0000422]

* Alex: Y

== pigment cell (sensu Nematoda and Protostomia) ==

pigment cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000341 CL:0000341]

* Alex: Y maybe, but it would be great to get a definition for pigment cell

== pigment cell (sensu Vertebrata) ==

pigment cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000342 CL:0000342]

* Alex: Y

== visual pigment cell (sensu Nematoda & Protostomia) ==

visual pigment cell (sensu Nematoda & Protostomia) [http://obofoundry.org/obo/CL:0001658 CL:0001658]

* Alex: Mycetozoa Y

== visual pigment cell (sensu Vertebrata) ==

visual pigment cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000343 CL:0000343]

* Alex: Y

== non-visual cell (sensu Vertebrata) ==

non-visual cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000344 CL:0000344]

* Alex: Y

== receptor cell (sensu Animalia) ==

receptor cell (sensu Animalia) [http://obofoundry.org/obo/CL:0000006 CL:0000006]

* Alex: Y

== sperm cell (sensu Viridiplantae) ==

sperm cell (sensu Viridiplantae) [http://obofoundry.org/obo/CL:0000366 CL:0000366]

* Alex: Y

== spore (sensu Mycetozoa) ==

spore (sensu Mycetozoa) [http://obofoundry.org/obo/CL:000029 CL:000029]

* Alex: N, see my email discussion

== vegetative cell ==

vegetative cell [http://obofoundry.org/obo/CL:0000296 CL:0000296]

* Alex: N, no true commonalities here

== vegetative cell (sensu Fungi) ==

vegetative cell (sensu Fungi) [http://obofoundry.org/obo/CL:0000334 CL:0000334]

* Alex: N, no true commonalities here

== vegetative cell (sensu Mycetozoa) ==

vegetative cell (sensu Mycetozoa) [http://obofoundry.org/obo/CL:0000263 CL:0000263]

* Alex: N, no true commonalities here

== CNS neuron (sensu Nematoda and Protostomia) ==

CNS neuron (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000028 CL:0000028]

* Alex: Y

== CNS neuron (sensu Vertebrata) ==

CNS neuron (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000117 CL:0000117]

* Alex: Y

neuroblast (sensu Nematoda and Protostomia) Y

== neuroblast (sensu Vertebrata) ==

neuroblast (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000337 CL:0000337]

* Alex: Y

== neuroglioblast (sensu Nematoda) ==

neuroglioblast (sensu Nematoda) [http://obofoundry.org/obo/CL:0000662 CL:0000662]

* Alex: Y

== support cell (sensu Nematoda and Protostomia) ==

support cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000378 CL:0000378]

* Alex: Y

== support cell (sensu Nematoda) ==

support cell (sensu Nematoda) [http://obofoundry.org/obo/CL:0000619 CL:0000619]

* Alex: Y

== female germ line stem cell (sensu Nematoda and Protostomia) ==

female germ line stem cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000088 CL:0000088]

* Alex: Y

== female germ line stem cell (sensu Vertebrata) ==

female germ line stem cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000090 CL:0000090]

* Alex: Y

== germ line stem cell (sensu Nematoda and Protostomia) ==

germ line stem cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000086 CL:0000086]

* Alex: Y

== germ line stem cell (sensu Vertebrata) ==

germ line stem cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000085 CL:0000085]

* Alex: Y

== male germ line stem cell (sensu Nematoda and Protostomia) ==

male germ line stem cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000087 CL:0000087]

* Alex: Y

== male germ line stem cell (sensu Vertebrata) ==

male germ line stem cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000089 CL:0000089]

* Alex: Y

== male germ line stem cell ==

male germ line stem cell [http://obofoundry.org/obo/CL:0000016 CL:0000016]

* Alex: Y

== Cone bipolar cells types 1-9 (sensu mouse) ) ==

Cone bipolar cells types 1-9 (sensu mouse) ) [http://obofoundry.org/obo/CL:? CL:?]

* Alex: Y

== cone cell (sensu Endopterygota) ==

cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000718 CL:0000718]

* Alex: Y

== anterior cone cell (sensu Endopterygota) ==

anterior cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000720 CL:0000720]

* Alex: Y

== posterior cone cell (sensu Endopterygota) ==

posterior cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000719 CL:0000719]

* Alex: Y

== equatorial cone cell (sensu Endopterygota) ==

equatorial cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000721 CL:0000721]

* Alex: Y

= Disjointness violations =

== Prok/Euk ==

Adding a disjoint_from axiom between prokaryotic cell and eukaryotic cell. Remove is_a parentage of all violators (eg spore)

* Chris: Y

CL:Checklist

2009-02-17T20:13:05Z

Cjm:

CL:Checklist

2009-02-17T20:04:02Z

Cjm:

== cardioblast (sensu Arthropoda) ==

cardioblast (sensu Arthropoda) [http://obofoundry.org/obo/CL:0000465 CL:0000465]

* Alex: Y

== blood cell (sensu Nematoda and Protostomia) ==

blood cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000390 CL:0000390]

* Alex: Y

== hemocyte (sensu Nematoda and Protostomia) ==

hemocyte (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000387 CL:0000387]

* Alex: Y

== prohemocyte (sensu Nematoda and Protostomia) ==

prohemocyte (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000385 CL:0000385]

* Alex: Y

== chemotactic amoeboid cell (sensu Mycetozoa) ==

chemotactic amoeboid cell (sensu Mycetozoa) [http://obofoundry.org/obo/CL:0000289 CL:0000289]

* Alex: Y

== prohemocyte (sensu Nematoda and Protostomia) ==

prohemocyte (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000385 CL:0000385]

* Alex: Y

== chemotactic amoeboid cell (sensu Mycetozoa) ==

chemotactic amoeboid cell (sensu Mycetozoa) [http://obofoundry.org/obo/CL:0000289 CL:0000289]

* Alex: Y

== Distal tip cell (sensu nematoda) – ==

Distal tip cell (sensu nematoda) – [http://obofoundry.org/obo/CL:0000422 CL:0000422]

* Alex: Y

== pigment cell (sensu Nematoda and Protostomia) ==

pigment cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000341 CL:0000341]

* Alex: Y maybe, but it would be great to get a definition for pigment cell

== pigment cell (sensu Vertebrata) ==

pigment cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000342 CL:0000342]

* Alex: Y

== visual pigment cell (sensu Nematoda & Protostomia) ==

visual pigment cell (sensu Nematoda & Protostomia) [http://obofoundry.org/obo/CL:0001658 CL:0001658]

* Alex: Mycetozoa Y

== visual pigment cell (sensu Vertebrata) ==

visual pigment cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000343 CL:0000343]

* Alex: Y

== non-visual cell (sensu Vertebrata) ==

non-visual cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000344 CL:0000344]

* Alex: Y

== receptor cell (sensu Animalia) ==

receptor cell (sensu Animalia) [http://obofoundry.org/obo/CL:0000006 CL:0000006]

* Alex: Y

== sperm cell (sensu Viridiplantae) ==

sperm cell (sensu Viridiplantae) [http://obofoundry.org/obo/CL:0000366 CL:0000366]

* Alex: = algae Y

== spore (sensu Mycetozoa) ==

spore (sensu Mycetozoa) [http://obofoundry.org/obo/CL:000029 CL:000029]

* Alex: N, see my email discussion

== vegetative cell ==

vegetative cell [http://obofoundry.org/obo/CL:0000296 CL:0000296]

* Alex: N, no true commonalities here

== vegetative cell (sensu Fungi) ==

vegetative cell (sensu Fungi) [http://obofoundry.org/obo/CL:0000334 CL:0000334]

* Alex: N, no true commonalities here

== vegetative cell (sensu Mycetozoa) ==

vegetative cell (sensu Mycetozoa) [http://obofoundry.org/obo/CL:0000263 CL:0000263]

* Alex: N, no true commonalities here

== CNS neuron (sensu Nematoda and Protostomia) ==

CNS neuron (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000028 CL:0000028]

* Alex: Y

== CNS neuron (sensu Vertebrata) ==

CNS neuron (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000117 CL:0000117]

* Alex: Y

neuroblast (sensu Nematoda and Protostomia) Y
== neuroblast (sensu Vertebrata) ==

neuroblast (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000337 CL:0000337]

* Alex: Y

== neuroglioblast (sensu Nematoda) ==

neuroglioblast (sensu Nematoda) [http://obofoundry.org/obo/CL:0000662 CL:0000662]

* Alex: Y

== support cell (sensu Nematoda and Protostomia) ==

support cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000378 CL:0000378]

* Alex: Y

== support cell (sensu Nematoda) ==

support cell (sensu Nematoda) [http://obofoundry.org/obo/CL:0000619 CL:0000619]

* Alex: Y

== female germ line stem cell (sensu Nematoda and Protostomia) ==

female germ line stem cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000088 CL:0000088]

* Alex: Y

== female germ line stem cell (sensu Vertebrata) ==

female germ line stem cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000090 CL:0000090]

* Alex: Y

== germ line stem cell (sensu Nematoda and Protostomia) ==

germ line stem cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000086 CL:0000086]

* Alex: Y

== germ line stem cell (sensu Vertebrata) ==

germ line stem cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000085 CL:0000085]

* Alex: Y

== male germ line stem cell (sensu Nematoda and Protostomia) ==

male germ line stem cell (sensu Nematoda and Protostomia) [http://obofoundry.org/obo/CL:0000087 CL:0000087]

* Alex: Y

== male germ line stem cell (sensu Vertebrata) ==

male germ line stem cell (sensu Vertebrata) [http://obofoundry.org/obo/CL:0000089 CL:0000089]

* Alex: Y

== male germ line stem cell ==

male germ line stem cell [http://obofoundry.org/obo/CL:0000016 CL:0000016]

* Alex: Y

Cone bipolar cells types 1-9 (sensu mouse) Y
== cone cell (sensu Endopterygota) ==

cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000718 CL:0000718]

* Alex: Y

== anterior cone cell (sensu Endopterygota) ==

anterior cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000720 CL:0000720]

* Alex: Y

== posterior cone cell (sensu Endopterygota) ==

posterior cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000719 CL:0000719]

* Alex: Y

== equatorial cone cell (sensu Endopterygota) ==

equatorial cone cell (sensu Endopterygota) [http://obofoundry.org/obo/CL:0000721 CL:0000721]

* Alex: Y

CL:Checklist

2009-02-17T20:02:42Z

Cjm: New page: == cardioblast (sensu Arthropoda) == cardioblast (sensu Arthropoda) [http://obofoundry.org/obo/CL:0000465 CL:0000465] * Alex: Y == blood cell (sensu Nematoda and Protostomia) == blo...

UBERON:Main Page

2009-01-23T19:29:25Z

Cjm: /* Relationship to other ontologies */

Uberon is a multi-species anatomy ontology created to facilitate comparison of phenotypes across multiple species and to use in definition GO biological process terms.

The first iteration of Uberon was generated semi-automatically from the union of existing species-centric anatomy ontologies. As such, it contained many errors and biological falsehoods. The guiding principles deliberately err on the side of generating false positives in query results.

In addition, there has been a fairly light amount of curation of Uberon. New versions of species-centric AOs are periodically aligned against Uberon and incorporated.

== Status and Availability ==

* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=uberon OBO Foundry Page]
* [http://www.obofoundry.org/obo/UBERON Browse term list]

This is an alpha release, Uberon still contains many mistakes

== Continued Development ==

We hope that there will eventually be resources for a biologically sound multi-species anatomy ontology - when this arrives Uberon will have served its purpose and can disappear into the night.

In the intermediate time, Uberon can serve as a strawman ontology, and a useful source of empirical results illustrating the need for a properly curated multi-species anatomy ontology with highly specific classes.

== Relationship to other ontologies ==

Uberon contains xref tags pointing to other ontology terms. These can be interpreted as reverse is_a links.

=== MIAA ===

MIAA is undoubtedly better than Uberon in that it is manually curated. However, Uberon has more specific and granular classes than MIAA (Uberon has 2000, MIAA 400). Uberon also attempts to employ is_a, part_of and developmental relations in the same manner as species specific ontologies (sometimes wrongly) - it attempts (not entirely successfully) to be an ontology. MIAA is more of a terminology.

Uberon subsumes MIAA (MIAA was one of the inputs), and includes xrefs to MIAA IDs.

=== CARO ===

CARO represents very general upper level types. Uberon extends CARO

=== species-centric anatomy ontologies ===

Uberon links to these via xrefs. In addition, there is a separate mapping file that provides is_a links between ssAO IDs and Uberon IDs. This is to facilitate subsumption based reasoning (eg queries for uberon:lower_jaw should return ma:lower_jaw)

== Relationship to Wikipedia ==

Many terms in wikipedia have either definitions sourced from wikipedia (where no defs were available in the source ontologies), or are linked to wikipedia pages.

For example: [http://www.obofoundry.org/obo/UBERON:FMA_67325-MA_0000913-ZFA_0001414 Occipital lobe]

== Homology ==

Uberon was constructed around analogy rather than homology, purely as a matter of expediency. In fact Uberon may even contain classes that represent groupings that are not even analagous (these are errors and should be remobed).

uberon has utility despite not having formal phylogenetic representation. Here is why:

What uberon does do that is really important is that it allows biologists
to search for analogy too. A lot of things that are considered analogous
are really homologous, just in ways or at different levels of granularity
that aren't fully understood. Later on we should separate homology from
analogy, but I think there should always be some kind of uber ontology
that allows searching for analogy. So while parts of uberon may get a
formal homology treatise, there are parts that will remain useful purely
as analogous groupings. In fact, I see this as a process of gradual
reclassification in terms of homology as we learn.

If nothing else uberon can help people consider where we want to go from
here.

== Use Cases ==

Currently used in OBD. See http://www.berkeleybop.org/obd

See for example:
[http://obd.berkeleybop.org/OBDUI/obdPhenotypeAll2008/html/node/UBERON:FMA_54398-MA_0001906-XAO_0003084-ZFA_0001273 lower jaw] annotations

A query for "lower jaw" in Uberon returns mouse genes, zebrafish genes and human genes that are somehow implicated in phenotypes of the lower jaw. This query also uses [http://wiki.geneontology.org/index.php/XP:mammalian_phenotype_xp MP-XP]

* [http://obd.berkeleybop.org/OBDUI/obdPhenotypeAll2008/html/node/UBERON%3AFMA_12513-MIAA_0000283-XAO_0000181 eyeball] annotations

Uberon may also be used to make GO xps, also for facilitating analysis in OBD. See [http://wiki.geneontology.org/index.php/XP:biological_process_xp_anatomy#Generic_vs_specific_anatomy_ontologies biological_process_xp_anatomy]

== Methods ==

We subdivide ontologies into those that are species-centric (scAOs) and generic (gAOs). An example of an scAO is the Foundational Model of Anatomy (FMA), which is human-centric. Some scAOs may be applicable further up the taxonomic hierarchy above the species level - for example, the adult mouse anatomy (MA) CHECK WITH MGI EXACTLY HOW FAR UP IT IS APPLICABLE AND VALID FOR. The Gene Ontology cellular component ontology is an example of a gAO at the subcellular level, applicable to prokaryotyes and eukaryotes. The OBO Cell Ontology (CL) is a gAO that represents different kinds of cells across a variety of phyla. Of course, gAOs may contain classes that are only applicable for certain taxonomic subsets. Some ontologies are 'inbetween' - for example the TAO is an anatomy ontology applicable for teleost (bony fish) which is more general than the zebrafish anatomy ontology (ZFA) yet more specific than a true gAO.

We tend to find that scAOs sit at the gross anatomical level (presumably at least in part due to the higher cross-species diversity at this level). Some scAOs also delved into cellular and subcellular territory (eg ZFA and FBbt). CARO is a very general gAO that defines a set of high level classes to be used across AOs. MIAA is a gAO that defines a minimal set of anatomy terms to be used in microarray annotation.

Our approach is homology-neutral. We seek to group classes from multiple anatomical ontologies regardless of whether the relation between the anatomical entities (AEs) is one of homology or analogy (e.g. convergent evolution). This approach is driven by pragmaticism rather than biology - we hope that future efforts will extend this with a more phylogenetically valid approach as outlined in [REF:CARO], and described at the multi-species anatomy ontology meeting [REF].

We first sought to collate all sources of putative homology and analogy between the AEs in different species-centric anatomy ontologies (scAOs). Sometimes these came from the ontology themselves, in the form of xref tags in the underlying obo file. The xref tag has no fixed semantics, but is by convention used to link scAOs to gAOs - see for example OBO Mappings. For the mouse-human mappings we relied on [REF:Bodenreider et al]. In other cases we had to create our own mappings by running the Obol S3 algorithm (simple synonym and stemming) which performs basic text-based matching.

We then sought to eliminate as many non-isomorphic (1-1) pairwise mappings as possible. This was done on an ad-hoc basis by a non-expert by occasional consultation with experts. This aspect could use further curation.

We collected grouping classes based on mappings. We used an extremely promiscuous grouping algorithm, finding the maximally self-connected sets. This undoubtedly results in some meaningless classes. Each grouping class was given an ID and placed in ontology called UBERON. This ontology includes is_a links incoming from the external AOs, and the superset of all synonyms and definitions from the external AOs.

Finally we added links to the ontology based on links in the external AOs. Again, we were extremely liberal in what we accepted: if an external AO contained a link (X,R,Y) (asserted or logically entailed) we also created a link (X',R,Y'), where X<->X' and Y<->Y' are mappings. This ultra-liberal policy undoubtedly creates invalid links. The goal is to create the maximal set for now, and curate this in future. 3 cyclic links were generated, these were manually removed.

UBERON:Main Page

2009-01-12T22:37:19Z

Cjm: /* Status and Availability */

Uberon is a multi-species anatomy ontology created to facilitate comparison of phenotypes across multiple species and to use in definition GO biological process terms.

The first iteration of Uberon was generated semi-automatically from the union of existing species-centric anatomy ontologies. As such, it contained many errors and biological falsehoods. The guiding principles deliberately err on the side of generating false positives in query results.

In addition, there has been a fairly light amount of curation of Uberon. New versions of species-centric AOs are periodically aligned against Uberon and incorporated.

== Status and Availability ==

* [http://www.obofoundry.org/cgi-bin/detail.cgi?id=uberon OBO Foundry Page]
* [http://www.obofoundry.org/obo/UBERON Browse term list]

This is an alpha release, Uberon still contains many mistakes

== Continued Development ==

We hope that there will eventually be resources for a biologically sound multi-species anatomy ontology - when this arrives Uberon will have served its purpose and can disappear into the night.

In the intermediate time, Uberon can serve as a strawman ontology, and a useful source of empirical results illustrating the need for a properly curated multi-species anatomy ontology with highly specific classes.

== Relationship to other ontologies ==

Uberon contains xref tags pointing to other ontology terms. These can be interpreted as reverse is_a links.

=== MIAA ===

MIAA is undoubtedly better than Uberon in that it is manually curated. However, Uberon has more specific and granular classes than MIAA (Uberon has 2000, MIAA 400). Uberon also attempts to employ is_a, part_of and developmental relations in the same manner as species specific ontologies (sometimes wrongly) - it attempts (not entirely successfully) to be an ontology. MIAA is more of a terminology.

Uberon subsumes MIAA (MIAA was one of the inputs), and includes xrefs to MIAA IDs.

=== CARO ===

CARO represents very general upper level types. Uberon extends CARO

=== species-centric anatomy ontologies ===

Uberon links to these via xrefs. In addition, there is a separate mapping file that provides is_a links between ssAO IDs and Uberon IDs. This is to facilitate subsumption based reasoning (eg queries for uberon:lower_jaw should return ma:lower_jaw)

== Homology ==

Uberon was constructed around analogy rather than homology, purely as a matter of expediency. In fact Uberon may even contain classes that represent groupings that are not even analagous (these are errors and should be remobed).

uberon has utility despite not having formal phylogenetic representation. Here is why:

What uberon does do that is really important is that it allows biologists
to search for analogy too. A lot of things that are considered analogous
are really homologous, just in ways or at different levels of granularity
that aren't fully understood. Later on we should separate homology from
analogy, but I think there should always be some kind of uber ontology
that allows searching for analogy. So while parts of uberon may get a
formal homology treatise, there are parts that will remain useful purely
as analogous groupings. In fact, I see this as a process of gradual
reclassification in terms of homology as we learn.

If nothing else uberon can help people consider where we want to go from
here.

== Use Cases ==

Currently used in OBD. See http://www.berkeleybop.org/obd

See for example:
[http://obd.berkeleybop.org/OBDUI/obdPhenotypeAll2008/html/node/UBERON:FMA_54398-MA_0001906-XAO_0003084-ZFA_0001273 lower jaw] annotations

A query for "lower jaw" in Uberon returns mouse genes, zebrafish genes and human genes that are somehow implicated in phenotypes of the lower jaw. This query also uses [http://wiki.geneontology.org/index.php/XP:mammalian_phenotype_xp MP-XP]

* [http://obd.berkeleybop.org/OBDUI/obdPhenotypeAll2008/html/node/UBERON%3AFMA_12513-MIAA_0000283-XAO_0000181 eyeball] annotations

Uberon may also be used to make GO xps, also for facilitating analysis in OBD. See [http://wiki.geneontology.org/index.php/XP:biological_process_xp_anatomy#Generic_vs_specific_anatomy_ontologies biological_process_xp_anatomy]

== Methods ==

We subdivide ontologies into those that are species-centric (scAOs) and generic (gAOs). An example of an scAO is the Foundational Model of Anatomy (FMA), which is human-centric. Some scAOs may be applicable further up the taxonomic hierarchy above the species level - for example, the adult mouse anatomy (MA) CHECK WITH MGI EXACTLY HOW FAR UP IT IS APPLICABLE AND VALID FOR. The Gene Ontology cellular component ontology is an example of a gAO at the subcellular level, applicable to prokaryotyes and eukaryotes. The OBO Cell Ontology (CL) is a gAO that represents different kinds of cells across a variety of phyla. Of course, gAOs may contain classes that are only applicable for certain taxonomic subsets. Some ontologies are 'inbetween' - for example the TAO is an anatomy ontology applicable for teleost (bony fish) which is more general than the zebrafish anatomy ontology (ZFA) yet more specific than a true gAO.

We tend to find that scAOs sit at the gross anatomical level (presumably at least in part due to the higher cross-species diversity at this level). Some scAOs also delved into cellular and subcellular territory (eg ZFA and FBbt). CARO is a very general gAO that defines a set of high level classes to be used across AOs. MIAA is a gAO that defines a minimal set of anatomy terms to be used in microarray annotation.

Our approach is homology-neutral. We seek to group classes from multiple anatomical ontologies regardless of whether the relation between the anatomical entities (AEs) is one of homology or analogy (e.g. convergent evolution). This approach is driven by pragmaticism rather than biology - we hope that future efforts will extend this with a more phylogenetically valid approach as outlined in [REF:CARO], and described at the multi-species anatomy ontology meeting [REF].

We first sought to collate all sources of putative homology and analogy between the AEs in different species-centric anatomy ontologies (scAOs). Sometimes these came from the ontology themselves, in the form of xref tags in the underlying obo file. The xref tag has no fixed semantics, but is by convention used to link scAOs to gAOs - see for example OBO Mappings. For the mouse-human mappings we relied on [REF:Bodenreider et al]. In other cases we had to create our own mappings by running the Obol S3 algorithm (simple synonym and stemming) which performs basic text-based matching.

We then sought to eliminate as many non-isomorphic (1-1) pairwise mappings as possible. This was done on an ad-hoc basis by a non-expert by occasional consultation with experts. This aspect could use further curation.

We collected grouping classes based on mappings. We used an extremely promiscuous grouping algorithm, finding the maximally self-connected sets. This undoubtedly results in some meaningless classes. Each grouping class was given an ID and placed in ontology called UBERON. This ontology includes is_a links incoming from the external AOs, and the superset of all synonyms and definitions from the external AOs.

Finally we added links to the ontology based on links in the external AOs. Again, we were extremely liberal in what we accepted: if an external AO contained a link (X,R,Y) (asserted or logically entailed) we also created a link (X',R,Y'), where X<->X' and Y<->Y' are mappings. This ultra-liberal policy undoubtedly creates invalid links. The goal is to create the maximal set for now, and curate this in future. 3 cyclic links were generated, these were manually removed.

Special:Badtitle/NS200:Revised 2008

2008-12-18T23:55:58Z

Cjm: /* Absent and friends */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absence and counting ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

Previously PATO was an ''is_a'' hierarchy. We have introduced additional relations to better represent complex qualities. Most of these can be ignored for annotation purposes, but are useful for analyzing phenotypes

=== Sub-qualities and has_part ===

We allow for some complex qualities to be composed from other qualities using ''has_part''. For example:

* bang sensitive ''has_part"" paralyzed
* degenerate ''has_part'' hypertrophic
* swollen ''has_part'' increased size AND ''has_part'' protruding

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

Previously there was no way to tell the 'direction' of PATO quality types such as increased size and decreased weight. We have introduced 2 relations to help.

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
</pre>

Examples:

* increased speed ''increased_in_magnitude_relative_to'' normal

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
</pre>

Examples:

* spherical ''has_cross_section'' round

The goal is not to have a perfect system for geometric reasoning - we just need some coherent way to group together annotations from different perspectives

== Images ==

We are now trying to include images for many quality types. These are tagged using xref:s from the Image IDspace.

<pre>
[Term]
id: PATO:0001866
name: prolate
def: "A spheroid in which the polar diameter is longer than the equatorial diameter." [Wikipedia:Wikipedia "http://en.wikipedia.org/wiki/Prolate"]
subset: cell_quality
subset: value_slim
synonym: "prolate spheroid" RELATED []
xref: Image:http\://upload.wikimedia.org/wikipedia/commons/8/88/ProlateSpheroid.png
is_a: PATO:0001865 ! spheroid
</pre>

These should be visible with some configuration in the OE image plugin

SO:Composite Terms

2008-12-14T01:17:20Z

Cjm: Replacing page with 'Redirected to: [http://wiki.geneontology.org/index.php/SO:Composite_Terms Composite_Terms] on GO wiki'

Redirected to: [http://wiki.geneontology.org/index.php/SO:Composite_Terms Composite_Terms] on GO wiki

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:32:12Z

Cjm: /* has_cross_section */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

Previously PATO was an ''is_a'' hierarchy. We have introduced additional relations to better represent complex qualities. Most of these can be ignored for annotation purposes, but are useful for analyzing phenotypes

=== Sub-qualities and has_part ===

We allow for some complex qualities to be composed from other qualities using ''has_part''. For example:

* bang sensitive ''has_part"" paralyzed
* degenerate ''has_part'' hypertrophic
* swollen ''has_part'' increased size AND ''has_part'' protruding

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

Previously there was no way to tell the 'direction' of PATO quality types such as increased size and decreased weight. We have introduced 2 relations to help.

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
</pre>

Examples:

* increased speed ''increased_in_magnitude_relative_to'' normal

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
</pre>

Examples:

* spherical ''has_cross_section'' round

The goal is not to have a perfect system for geometric reasoning - we just need some coherent way to group together annotations from different perspectives

== Images ==

We are now trying to include images for many quality types. These are tagged using xref:s from the Image IDspace.

<pre>
[Term]
id: PATO:0001866
name: prolate
def: "A spheroid in which the polar diameter is longer than the equatorial diameter." [Wikipedia:Wikipedia "http://en.wikipedia.org/wiki/Prolate"]
subset: cell_quality
subset: value_slim
synonym: "prolate spheroid" RELATED []
xref: Image:http\://upload.wikimedia.org/wikipedia/commons/8/88/ProlateSpheroid.png
is_a: PATO:0001865 ! spheroid
</pre>

These should be visible with some configuration in the OE image plugin

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:29:22Z

Cjm: /* has_cross_section */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

Previously PATO was an ''is_a'' hierarchy. We have introduced additional relations to better represent complex qualities. Most of these can be ignored for annotation purposes, but are useful for analyzing phenotypes

=== Sub-qualities and has_part ===

We allow for some complex qualities to be composed from other qualities using ''has_part''. For example:

* bang sensitive ''has_part"" paralyzed
* degenerate ''has_part'' hypertrophic
* swollen ''has_part'' increased size AND ''has_part'' protruding

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

Previously there was no way to tell the 'direction' of PATO quality types such as increased size and decreased weight. We have introduced 2 relations to help.

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
</pre>

Examples:

* increased speed ''increased_in_magnitude_relative_to'' normal

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
</pre>

Examples:

* spherical ''has_cross_section'' round

The goal is not to have a perfect system for geometric reasoning - we just need some coherent way to group together annotations from different perspectives

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:27:05Z

Cjm: /* Magnitudinal Relations */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

Previously PATO was an ''is_a'' hierarchy. We have introduced additional relations to better represent complex qualities. Most of these can be ignored for annotation purposes, but are useful for analyzing phenotypes

=== Sub-qualities and has_part ===

We allow for some complex qualities to be composed from other qualities using ''has_part''. For example:

* bang sensitive ''has_part"" paralyzed
* degenerate ''has_part'' hypertrophic
* swollen ''has_part'' increased size AND ''has_part'' protruding

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

Previously there was no way to tell the 'direction' of PATO quality types such as increased size and decreased weight. We have introduced 2 relations to help.

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
</pre>

Examples:

* increased speed ''increased_in_magnitude_relative_to'' normal

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:25:22Z

Cjm: /* Magnitudinal Relations */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

Previously PATO was an ''is_a'' hierarchy. We have introduced additional relations to better represent complex qualities. Most of these can be ignored for annotation purposes, but are useful for analyzing phenotypes

=== Sub-qualities and has_part ===

We allow for some complex qualities to be composed from other qualities using ''has_part''. For example:

* bang sensitive ''has_part"" paralyzed
* degenerate ''has_part'' hypertrophic
* swollen ''has_part'' increased size AND ''has_part'' protruding

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:24:49Z

Cjm: /* New Relations */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

Previously PATO was an ''is_a'' hierarchy. We have introduced additional relations to better represent complex qualities. Most of these can be ignored for annotation purposes, but are useful for analyzing phenotypes

=== Sub-qualities and has_part ===

We allow for some complex qualities to be composed from other qualities using ''has_part''. For example:

* bang sensitive ''has_part"" paralyzed
* degenerate ''has_part'' hypertrophic
* swollen ''has_part'' increased size AND ''has_part'' protruding

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:23:51Z

Cjm: /* Sub-qualities and has_part */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

=== Sub-qualities and has_part ===

We allow for some complex qualities to be composed from other qualities using ''has_part''. For example:

* bang sensitive ''has_part"" paralyzed
* degenerate ''has_part'' hypertrophic
* swollen ''has_part'' increased size AND ''has_part'' protruding

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:21:42Z

Cjm: /* Absent and friends */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the ''reciprocal_of'' relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

(note a few terms have been renamed in a more intuitive way since this graph was created)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

=== Sub-qualities and has_part ===

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:20:19Z

Cjm: /* Absent and friends */

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has number of c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has number of [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! count in organism [WAS: count]
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the reciprocal_of relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

=== Sub-qualities and has_part ===

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:16:26Z

Cjm:

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This page is a summary of the changes

Note that all changes were made in accordance with OBO lifecycle principles. No ID was destroyed, all obsolete IDs have a replaced_by tag

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has or lacks parts of type *** c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! presence or absence in organism ***
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the reciprocal_of relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

=== Sub-qualities and has_part ===

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:15:06Z

Cjm:

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This is a summary of the changes

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has or lacks parts of type *** c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! presence or absence in organism ***
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the reciprocal_of relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

=== Sub-qualities and has_part ===

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Revised 2008

2008-12-11T01:14:38Z

Cjm:

At the end of 2008 we made a number of changes to PATO. At first these went into a fork of the ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

These have now been moved in to the main ontology:

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality.obo quality.obo]

This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

The old hierarchy was:

is_a PATO:0000051 ! morphology
is_a PATO:0000060 ! pattern
is_a PATO:0000132 ! spatial pattern
is_a PATO:0000140 ! placement
is_a PATO:0001032 ! position

In the new hierarchy, placement and position have been merged, and placement is now a sibling of morphology and a parent of pattern. The thinking is that pattern implies a repetition of placement. Pattern and spatial pattern have been merged, as these are qualities of continuants (vs. temporal patterns which are dealt with elsewhere in pato).

is_a PATO:0000051 ! morphology
is_a PATO:0000140 ! placement (synonym position)
is_a PATO:0000132 ! spatial pattern (synonym pattern)

Additionally, some of the children of placement that were having to do with repetition of some kind, are now children of spatial pattern. Examples are aggregated, decussate, etc.

Also, anteriorly, posteriorly, dorsally and ventrally rotated were obsoleted and added as replaced by terms to the mislocalized terms, 'mislocalized anteriorly' etc. as these definitions were almost identical and did not refer to rotation about an axis, the previous parent of the rotated terms.

Angle and orientation were merged and renamed 'angular placement.' Since these qualities refer to the relationship between two entities, they were made children of 'relational spatial quality'.

Polarity was moved to be a child of placement, and cellular polarity was obsoleted and given a consider relationship to 'polarity', to avoid multiple inheritance. The existing polarity terms can refer to either organismal level or cellular level (or other).

=== Functionality terms ===

There were some redundant and/or confusing functionality terms as well. We've merged non-functional and functional failure, and decreased functionality and partial functionality. The new arrangement is parallel to how we've constructed extra/fewer/absent parts. We've obsoleted 'enhanced', since its definition, "increased, intensified" and its previous location under 'behavioral quality' suggested either increased or additional functionality, which are now represented distinctly. 'impaired' , also a child of 'behavioral quality' has been obsoleted too. Its definition was "diminished, damaged, or weakened." This is similar but not identical to disfunctional and a consider term has been added.

The old hierarchy was:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional
is_a PATO:0001640 ! functional failure
is_a PATO:0001642 ! partial functionality
is_a PATO:0001510 ! functional
is_a PATO:0001624 ! decreased functionality
is_a PATO:0001625 ! increased functionality
is_a PATO:0001511 ! non-functional

The new hierarchy is:

is_a PATO:0001509 ! functionality
is_a PATO:0001641 ! disfunctional *** synonym related:impaired
is_a PATO:00011624 ! decreased functionality *** synonym exact:partial functionality
is_a PATO:0001511 ! non-functional *** synonym exact:functional failure
is_a PATO:0001510 ! functional
is_a PATO:0001625 ! increased functionality
is_a PATO:0001559 ! having extra function

=== Plasty terms ===

There had been multiple ways to say the same thing with regard to under or over development of a structure. There was also multiple ways to say that something did not develop. The old hierarchy was:

is_a PATO:0000141 ! structure
is_a PATO:0000644 ! hyperplastic
is_a PATO:0000640 ! dysplastic
is_a PATO:0000942 ! underdeveloped
is_a PATO:0000943 ! overdeveloped
is_a PATO:0000645 ! hypoplastic
is_a PATO:0001483 ! aplastic
is_a PATO:0000117 ! size
is_a PATO:0000586 ! increased size
is_a PATO:0000584 ! hypertrophic
is_a PATO:0000587 ! decreased size
is_a PATO:0000585 ! hypotrophic

is_a PATO:0000070 ! presence
is_a PATO:0000462 ! absent

is_a PATO:0001555 ! extra or missing physical and functional parts
is_a PATO:0001557 ! lacking physical part

In the new hierarchy, we've merged 'underdeveloped' and 'hypoplastic' into 'decreased size', 'overdeveloped' and 'hyperplastic' into increased size, and 'aplastic' into 'absent'. Dysplastic remains as a separate child of structure, as it refers to more than just size.

Also, keep in mind that a number of related terms regarding growth can be found as process qualities, namely:

is_a PATO:0001433 ! growth quality of occurrent
is_a PATO:0002019 ! aplastic growth
is_a PATO:0001490 ! heterochronic growth
is_a PATO:0001749 ! paedomorphic growthDEF:.. growth of an organism, structure, or group of organisms has an decreased outcome.
is_a PATO:0001752 ! peramorphic growth DEF:..growth of an organism, structure, or group of organisms has an increased outcome.

These terms can be used in conjunction with GO anatomical processes to describe the growth of an anatomical structure.

=== Cellular Potency ===

These terms were redefined to be more consistent with common usage and to make disjoint classes.

=== Color Improvements ===

'Color' and its children have been revised to more accurately take into account hue, saturation and intensity parts. 'Color' is now a sibling of 'chromatic property', rather than a child. Colors have been redefined and rearranged to be consistent with general methods of color classification.

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has or lacks parts of type *** c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! presence or absence in organism ***
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the reciprocal_of relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

=== Sub-qualities and has_part ===

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>

Special:Badtitle/NS200:Pre vs Post Coordinating

2008-11-03T03:08:46Z

Cjm: /* Downloading */

==Background==

See also

http://wiki.geneontology.org/index.php/Category:Cross_Products

There is also a [http://docs.google.com/Doc?docid=d2xd966_86qs99ndp&hl=en draft of a paper in progress] - email cjm to view

==Reconciling pre and post coordinated phenotype descriptions==

PRELIMINARY DOCUMENT! IN PROGRESS!

There are two paradigms for representing phenotypes and phenotype-like
entities (1) use ontologies of ''pre-coordinated'' phenotypes, such as MP
or plant_trait (PT) or (2) ''post-coordinate'' the phenotype description
using terms from an ontology of qualities (eg PATO) and terms from
ontologies of quality-bearers (eg GO, AOs, CL, ...); this is the
EQ-annotation methodology

Both approaches have their advantages, and they are in fact entirely
compatible, provided you follow the SOP laid out here. It is even
possible to mix and match these approaches.

This methodology is applicable not just to "phenotypes" or "traits",
however we choose to define these terms, but to any kind of
[[Glossary#Dependent_Entity|Dependent Entity]], such as diseases, syndromes, disorders
and even roles.

The methodology hinges on the provision of
[[Glossary#Aristotelian_Definition|Aristotelian Definition]]s of pre-coordinated phenotype
terms in a computable format.

Below we provide some examples, taken from MP and PT

==Defining Specific Phenotypes==

Here are some examples of (somewhat trivial) aristotelian
(genus-differentia) definitions of mammalian phenotypes:

If we take the MP term "big ears" (MP:0000017), this can be defined as
the genus "large"/"largeness" (PATO:0000586) inhering in an "ear"
(MA:0000236).

In OBO-1.2 syntax this can be represented as:

[Term]
id: MP:0000017
name: big ears
namespace: MPheno.ontology
def: "outer ears of a greater than normal size" []
is_a: MP:0002177 ! abnormal outer ear morphology
intersection_of: PATO:0000586 ! large size
intersection_of: inheres_in MA:0000236 ! ear

Of course, an ontology editor will not manipulate the syntax
directly. This will be visible in oboedit in the "cross products" box

Note that our definition here is different from the text definition,
which has the genus as "ear" and the differentia has "having a greater
than normal size". We could write this in OBO syntax as:

[Term]
id: MP:0000017
name: big ears
namespace: MPheno.ontology
def: "outer ears of a greater than normal size" []
is_a: MP:0002177 ! abnormal outer ear morphology
intersection_of: MA:0000236 ! ear
intersection_of: has_quality PATO:0000586 ! large size

The first form is prefered, despite the fact the english phrasing is
more contorted. The reason is that a phenotype ontology should define
phenotypes, and not the entities in which phenotypes occur. The genus
term is the primary is_a parent, and it makes sense for the phenotype
ontology to be arranged on the quality axis, and not the anatomical
axis.

If we go the second route, consider the problems that will be
encountered defining terms like "sensitivity to chlorine"

Another way to record the same information is pheno-syntax. This is a convenient shorthand for combinatorial descriptions of phenotypes

E= MA:0000236 Q= PATO:0000586

==Results: plant_trait==

So far we've analyzed the plant_trait ontology. We refer to this
ontology as PT ontology here.

Our focus is on phenotypes that are applicable to human health and
disease; however, the PT ontology is easier to use to illustrate
patterns that can also be applied to MP (Mammalian Phenotype)

[http://www.fruitfly.org/~cjm/obol Obol] was used to generate prospective definitions for all PT terms -
these were examined and fixed manually by a non-domain expert
(CJM).

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#plant_trait_xp

====OBO-Edit====

If you are using OBO-Edit, then you can paste the following URL directly into the obo-edit load box:

* http://purl.org/obo/obo-all/plant_trait_xp/plant_trait_xp.imports.obo

(you may want to use the 'advanced' option and allow dangling references)

The above .obo file contains just import statements - to pull in the relevant obo files, as well as the main xp file (this means you will need an internet connection, even if you download the file for use later)

====OWL Editors====

* http://purl.org/obo/obo-all/plant_trait_xp/plant_trait_xp.imports.owl

Not yet fully tested. You may need to allocate additional heap, as this imports a lot of ontologies.

===Summary===

Summary of Results as follows:

===Standard EQ Terms===

The standard PT term is a pre-coordinated EQ term; this can easily be
defined as:

A <Q> *which* inheres_in an <E>

ie a quality carried by a bearer entity

This can easily be represented as a logical definition; below is an
example in oboformat

[Term]
id: TO:0000227
name: root length
namespace: plant_trait_ontology
def: "Average maximum length of the root of a plant in a study." []
synonym: "MRD" []
synonym: "MRL" []
synonym: "RTLG" []
synonym: "maximum root depth" []
synonym: "maximum root length" []
is_a: TO:0000043 ! root anatomy and morphology trait
intersection_of: PATO:0000122 ! length
intersection_of: inheres_in PO:0009005 ! root

Providing these definitions in oboformat has the following advantages:

- PATO definitions of qualities can be shared and reused

- The oboedit reasoner can keep PT in sync with PO and PATO, and
perform automatic DAG placement of terms

- PATO terms can be used to query PT-annotated phenotypes

- PO terms can be used to query PT-annotated phenotypes (eg "halogen
sensitivity" can be used as a query, even though this term is not in PT)

===Sensitivity Terms===

This is the other major class of terms. There are lots of sensitivity
terms. These are represented using the definition pattern:

sensitivity which is *towards* <chemical>

For example (again, in obo format):

[Term]
id: TO:0000029
name: chlorine sensitivity
namespace: plant_trait_ontology
def: "Sensitivity to the chlorine content in the growth medium. Chloride helps regulate the correct pH (acid/alkaline) balance. This is a major electrolyte in the living cell besides sodium and potassium. It is available to the cell mainly in the form of NaCl and KCl salts." []
synonym: "CHLORSN" []
is_a: TO:0000080 ! micronutrient sensitivity
intersection_of: PATO:0000085 ! sensitivity
intersection_of: towards CHEBI:23116 ! chlorine

Providing these definitions in oboformat has the following advantages:

- CHEBI definitions of qualities can be shared and reused

- The oboedit reasoner can keep PT in sync with CHEBI, and
perform automatic DAG placement of terms when/if CHEBI changes

- CHEBI terms can be used to query PT-annotated phenotypes

==== Nutrients ====

See this tracker item:

* http://sourceforge.net/tracker/index.php?func=detail&aid=1718383&group_id=76834&atid=835557

====Environment ontology====

There is also a plant-centric environment ontology (EO). This could be generalised for other uses.

Some of the ''sensitivity'' terms referred to environments or parts of the environment that are not at the chemical/molecular level. EO was used to define some of these, for example:

[Term]
id: TO:0000188
name: drought sensitivity
namespace: plant_trait_ontology
def: "Drought sensitivity is highly interactive with crop phenology, plant growth prior to stress, and timing, duration, and intensity of drought stress. For many soils, it takes at least 2 rainless weeks to cause marked differences in drought sensitivity during the vegetative stage and at least 7 rainless days during the reproductive stage to cause severe drought injury. Leaf rolling precedes leaf drying during drought. Repeated ratings are recommended through progress of the drought." []
synonym: "DRS" []
synonym: "DRSN" []
synonym: "drought susceptibility" []
is_a: TO:0000394 ! drought related trait
intersection_of: PATO:0000085 ! sensitivity
intersection_of: towards EO:0007404 ! drought environment

these will need closer examination. Some of the EO terms could themselves be decomposed, eg soil alkilinity

===Ratios, proportions and compositions===

Many PT terms include ratios:

[Term]
id: TO:0000278
name: root to shoot ratio
namespace: plant_trait_ontology
synonym: "RTSHRO" []
synonym: "r/s" []
synonym: "root/shoot ratio" []
is_a: TO:0000043 ! root anatomy and morphology trait

Course of action: we will add a term "proportionality" to PATO
http://sourceforge.net/tracker/index.php?func=detail&aid=1606404&group_id=76834&atid=595654

intersection_of: PATO:<<new-term-proportionality>>
intersection_of: towards PO:0009005 ! root
intersection_of: relative_to PO:0009006 ! shoot

Some of the PT ratios can be expressed using the relational quality '''PATO:composition''', which can take an additional 2 arguments:

[Term]
id: TO:0000372
name: amylose to amylopectin ratio
namespace: plant_trait_ontology
def: "Ratio of amount of amylose to amylopectin content." []
synonym: "AMYAMYPCTRO" []
is_a: TO:0000097 ! amylopectin content
is_a: TO:0000196 ! amylose content
intersection_of: PATO:0000025 !composition
intersection_of: towards CHEBI:28102 ! amylose
intersection_of: relative_to CHEBI:28057 ! amylopectin

Note the is_a links to amylopectin content and amylose content. Is this correct? In actual fact we have a reversal of magnitude here, as the magnitude of this parent increases, the magnitude of the child will decrease

===Synonyms===

PT uses lots of synonyms, but does not assign a scope
(exact/broad/narrow). This makes it harder to glean the exact meaning
of a term from the synonym.

===Relative===

PT uses terms like '''relative growth rate'''. It is not clear how this is different from '''growth rate'''. This seems to be a difference in how the term is ''used''.

===Disease resistance phenotypes===

PT has many disease resistance terms; eg:

[Term]
id: TO:0000323
name: stem rot disease resistance
namespace: plant_trait_ontology
def: "Causal agent: Magnaporthe salvinii (Nakataea sigmoidea, Sclerotium oryzae), and Helminthosporium sigmoideum var. irregulare. Symptoms: dark lesions develop on the stems near the water line. Small, dark bodies (sclerotia) develop, weaken the stem and cause lodging." []
synonym: "CULMROTRS" []
synonym: "SR" []
is_a: TO:0000439 ! fungal disease resistance

These would be easy to define if we had an orthogonal ontology of
plant diseases and infectious agents. The definition pattern would be:

A <TO:resistance> which *towards* <InfectiousAgent>

This will be easier to do for mammalian phenotypes since these
orthogonal ontologies are being developed. It is recommended the POC
develops such a separate ontology for plants.

===Assay-specific terms===

Example: root dry weight

It is unclear how to proceed with these. No action was taken for these.

===Conjunctive terms===

Example: lemma and palea related traits

Example: lemma and palea pubescence

I think these should be defined as:

a pubescence which inheres_in the lemma and inheres_in the palea

ie the necessary and sufficient conditions are that both the lemma and palea are pubsescent

can the same quality instances inhere in 2 entities?

===Inconsistency of Term name syntax===

Compare: "shrunken endosperm" with "leaf length"

In one case the adjectival noun (naming the quality) precedes the noun
(naming the bearer entity); in other cases it succeeds it.

It is recommended all prefered terms follow the same lexical pattern
(unless community usage or plain english trumps this).

===Missing anatomy terms===

Example: canopy temperature

"canopy" should be the name of a type in the plant_anatomy ontology

===Use of "other"===

Example: other miscellaneous trait
Example: other nutrient sensitivity

OBO Foundry principles dictate avoidance of "other"

===Use of word "quality"===

PATO and PT's use of the word quality is not univocal. PATO uses the term to mean "property" whereas TO uses it to mean a more nebulous subjective(?) quality. Perhaps within the plant trait community the meaning of this term is more fixed, if so, it should be defined somewhere. Does it simply mean healthiness? If so, it would be good to use the same PATO term, at least as a synonym

[Term]
id: TO:0000587
name: endosperm quality
alt_id: TO:0000150
related_synonym: "End" []
related_synonym: "endosperm quality (sensu Poaceae)" []
is_a: TO:0000162 ! seed quality

===Redundancy===

There is some redundancy with GO Molecular Function activity terms

For example:

[Term]
id: TO:0000284
name: ADP glucose pyrophosphorylase activity
namespace: plant_trait_ontology
def: "Catalysis of the reaction: ATP + alpha-D-glucose 1-phosphate = diphosphate + ADP-glucose." []

A phenotype ontology should be orthogonal to an ontology of molecular
function. It is not clear how the above term would be used in
phenotype annotation.

There is a case for including malfunctions, loss of function and gain
of function in a phenotype ontology, but this should be made explicit

===Complex Phenotypes===

It's too hard to even attempt to automatically generate definitions
for these; logical definitions should be provided manually. For example:

[Term]
id: TO:0000169
name: chinsurah boro CMS
namespace: plant_trait_ontology
def: "Abortion of microspore development at trinucleate stage" []

This could be defined in terms of "microspore development"
(GO:0009555), "trinucleate stage" (term required in plant
developmental stage ontology)

===Other difficult cases===

Example: photoperiod sensitivity

===Errors and inconsistencies detected===

The following were detected as a direct result of this approach

in PO, panicle is a synonym for inflorescence; in TO, panicle color is_a inflorescence color

[Term]
id: TO:0000201
name: panicle color
namespace: plant_trait_ontology
def: "Variation in color of the panicle inflorescence." []
synonym: "PNCL" []
is_a: TO:0000581 ! inflorescence color

similarly, panicle/inflorescence length, weight, shape

==Results: Mammalian Phenotype (MP)==

The MP ontology proved more difficult to analyze automatically -
changes to Obol and/or manual editing of logical definitions may be
required.

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#mammalian_phenotype_xp

====OBO-Edit====

If you are using OBO-Edit, then you can paste the following URL directly into the obo-edit load box:

* http://purl.org/obo/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.obo

(you may want to use the 'advanced' option and allow dangling references)

The above .obo file contains just import statements - to pull in the relevant obo files, as well as the main xp file (this means you will need an internet connection, even if you download the file for use later)

====OWL Editors====

* http://purl.org/obo/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.owl

Not yet fully tested. You may need to allocate additional heap, as this imports a lot of ontologies.

===Visualising Results===

As well as oboedit and owl editors, the cross-products can be viewed in the experimental [http://www.berkeleybop.org/obol Obol] branch of Amigo. For example, to see what terms are defined using the PATO term ''hypoplastic'', see:

* [http://www.berkeleybop.org/amigo/obol?goto=detail_page&data_class=term&id=PATO%3a0000645 PATO:0000645]

Here we can see the following terms defined:

# nasal bone hypoplasia
# maxilla hypoplasia
# mandible hypoplasia
# liver hypoplasia
# adrenal gland hypoplasia
# bulbourethral gland hypoplasia
# spleen hypoplasia
# forebrain hypoplasia
# telencephalon hypoplasia
# cerebellum hypoplasia
# pulmonary hypoplasia
# skin hypoplasia

Following the like to [http://www.berkeleybop.org/amigo/obol?goto=detail_page&data_class=term&id=MP%3a0001178 pulmonary hyoplasia] shows you the term in the original MP context (a DAG) and also a "decomposed view" showing separate trees for the genus and differentium:

[[Image:amigo-pulmonary-hypoplasia.jpg]]

This page is just meant for illustration - for display to a biologist end-user this would be compacted; the upper levels of PATO would not be shown.

===Term Syntax===

The syntax of the term names in MP differs from PT; a common ''lexical'' pattern
in MP is:

* VALUE - ENTITY - ATTRIBUTE

===Example: increased brown fat cell amount===

One example of an MP term following the above pattern is:

* "<increased> <brown fat cell> <amount>"

Which has the text definition: "increased amount of thermogenic tissue
in the body that is composed of cells containing multiple small fat
droplets"

As a first attempt at a logical definition:

* genus: PATO:0000420 ("increased number")
* differentia: ''inheres_in'' MA:0000057 ("brown fat")

Represented in obo format as:

intersection_of: PATO:0000420 ! increased number
intersection_of: inheres_in MA:0000057 ! brown fat tissue

However, this is not quite right, as it is not an "increased number"
of "brown fat" tissue, it is a larger "portion size".

At the time of writing this PATO term is not defined so we're not sure
if this is applicable.

(TODO)

There are many advantages to explicitly defining MP terms using PATO
and MA in this fashion. Reasoners can be used to keep the ontologies
in sync (either the oboedit reasoner or one of any number of owl
reasoners). PATO definitions and MP definitions can be shared and
reused.

===Complex phenotypes in mammals===

Many phenotypes such as "ovary hypoplasia" or "degenerate molars" are a single quality inhering in a single entity (or collection of entities - eg the collection of all molars in an individual organism).

For others such as "holoprosencephaly" or "osteoporosis", it may be an interconnected collection of qualities inhering in the same or different parts. We can still define these as conjunctions of EQs, but this is where we start crossing the grey line between the dependent continuants known as 'phenotypes' into the dependent continuants known as 'disorders'...

It is also important to distinguish between the definition, which captures the necessary and sufficient conditions, from the gloss/additional notes; eg MP defines holoprosencephaly as:

presence of a single forebrain hemisphere or lobe; often accompanied by a deficit in median facial development

Thus the logical definition should only refer to the part before the semicolon. (genus: PATO:having_a_single_part, differentia: towards MA:forebrain_hemisphere). The part after the semicolon ("often accompanied by...") is useful, but is statistical and are neither necessary nor sufficient so should be captured by other means.

===Issue: species-specificity===

Whilst the MP represents mammalian phenotypes, we do not have a common
mammalian anatomical ontology. It will take some time before CARO
reaches the level of granularity required.

We recommend that since the focus of MP is biased towards the mouse
and mouse models of human disease [CHECK THIS STMT], we treat it is a
mouse phenotype ontology, with a view to migrating the definitions
towards some kind of FMA/MA synthesis when such an ontology becomes
available.

===Absence-oriented terms===

The absence case is different from normal EQ phenotypes - the absence
does not inhere in the entity that is absent, since this entity does
not exist!

We treat these the same as "sensitivity to..." terms. The absence
inheres in the organism as a whole (or the anatomical entity which is
missing the part)

[Term]
id: MP:0000766
name: absent tongue squamous epithelium
namespace: MPheno.ontology
def: "missing the scaly epithelial layer of the tongue" []
synonym: "absence of tongue squamous epithelium" []
synonym: "loss of tongue squamous epithelium" []
is_a: MP:0000765 ! abnormal tongue squamous epithelium morphology

Could be defined as:

An <lacking_of_a_part> which inheres_in <organism> and towards <tongue squamous epithelium>

The "inheres_in <organism>" part of the definition can be omitted

in obo format:

intersection_of: PATO:lacks_part
intersection_of: towards MA:tongue_squamous_epithelium

See [[PATO:Absent]] for more discussion on this

==="Other" categories===

MP contains some terms such as "other metabolic defect" - the use of "other" is to be avoided

===Root term===

The root of the MP is the term "phenotype ontology". There are relations such as "cellular phenotype" is_a "phenotype ontology". The root term should be changed to "phenotype".

===Inconsistencies detected===

A number of inconsistencies were detected.

Example of inconsistency between MP and OBO-Cell:

[[Image:oboedit-amacrine.jpg]]

Here the oboedit reasoner has found an unstated implied link (blue squiggly arrow) between 'abnormal amacrine cell morphology' and 'abnormal interneuron morphology'. In the split pane display we see the reason for this inference: OBO-Cell states that 'amacrine cell' ''is_a'' 'interneuron'.

The logical definitions will also be used for comparing phenotypes across organisms once OBD is populated.

==Results: Worm Phenotype (WP)==

Defining xps for the WP is still in preliminary stages

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#worm_phenotype_xp

==Results: Human Phenotype (HP)==

Defining xps for the HP is still in preliminary stages

Example:

<pre>
[Term]
id: HP:0000110 ! renal dysplasia
intersection_of: PATO:0000640 ! dysplastic
intersection_of: inheres_in FMA:7203 ! kidney
</pre>

A few tracker items have been submitted [https://sourceforge.net/tracker2/?atid=1112722&group_id=76834 to the HP tracker] based on running the oboedit reasoner over HP-XP

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#human_phenotype_xp

Quick URLs:

* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp.xp.html HTML Table] (large)
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp.obo obo] - xps in obo format
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp.obo.html obo.html] - xps in obo format (syntax highlights)
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp-imports.obo imports.obo] give this URL to oboedit
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp-imports.owl imports.owl] give this URL to Protege

==Conclusions==

Providing formal computable definitions of pre-coordinated phenotype
terms in terms of basic qualities (PATO) and bearer entities (eg AOs)
will make both styles of phenotype annotation commensurable, promote
sharing of core ontologies and reusable ontology "building blocks"

More work is required to curate these logical definitions in phenotype
ontologies. This preliminary analysis suggests some of this can be
automated.

Special:Badtitle/NS200:Pre vs Post Coordinating

2008-11-03T02:22:52Z

Cjm: /* Results: Human Phenotype (HP) */

==Background==

See also

http://wiki.geneontology.org/index.php/Category:Cross_Products

There is also a [http://docs.google.com/Doc?docid=d2xd966_86qs99ndp&hl=en draft of a paper in progress] - email cjm to view

==Reconciling pre and post coordinated phenotype descriptions==

PRELIMINARY DOCUMENT! IN PROGRESS!

There are two paradigms for representing phenotypes and phenotype-like
entities (1) use ontologies of ''pre-coordinated'' phenotypes, such as MP
or plant_trait (PT) or (2) ''post-coordinate'' the phenotype description
using terms from an ontology of qualities (eg PATO) and terms from
ontologies of quality-bearers (eg GO, AOs, CL, ...); this is the
EQ-annotation methodology

Both approaches have their advantages, and they are in fact entirely
compatible, provided you follow the SOP laid out here. It is even
possible to mix and match these approaches.

This methodology is applicable not just to "phenotypes" or "traits",
however we choose to define these terms, but to any kind of
[[Glossary#Dependent_Entity|Dependent Entity]], such as diseases, syndromes, disorders
and even roles.

The methodology hinges on the provision of
[[Glossary#Aristotelian_Definition|Aristotelian Definition]]s of pre-coordinated phenotype
terms in a computable format.

Below we provide some examples, taken from MP and PT

==Defining Specific Phenotypes==

Here are some examples of (somewhat trivial) aristotelian
(genus-differentia) definitions of mammalian phenotypes:

If we take the MP term "big ears" (MP:0000017), this can be defined as
the genus "large"/"largeness" (PATO:0000586) inhering in an "ear"
(MA:0000236).

In OBO-1.2 syntax this can be represented as:

[Term]
id: MP:0000017
name: big ears
namespace: MPheno.ontology
def: "outer ears of a greater than normal size" []
is_a: MP:0002177 ! abnormal outer ear morphology
intersection_of: PATO:0000586 ! large size
intersection_of: inheres_in MA:0000236 ! ear

Of course, an ontology editor will not manipulate the syntax
directly. This will be visible in oboedit in the "cross products" box

Note that our definition here is different from the text definition,
which has the genus as "ear" and the differentia has "having a greater
than normal size". We could write this in OBO syntax as:

[Term]
id: MP:0000017
name: big ears
namespace: MPheno.ontology
def: "outer ears of a greater than normal size" []
is_a: MP:0002177 ! abnormal outer ear morphology
intersection_of: MA:0000236 ! ear
intersection_of: has_quality PATO:0000586 ! large size

The first form is prefered, despite the fact the english phrasing is
more contorted. The reason is that a phenotype ontology should define
phenotypes, and not the entities in which phenotypes occur. The genus
term is the primary is_a parent, and it makes sense for the phenotype
ontology to be arranged on the quality axis, and not the anatomical
axis.

If we go the second route, consider the problems that will be
encountered defining terms like "sensitivity to chlorine"

Another way to record the same information is pheno-syntax. This is a convenient shorthand for combinatorial descriptions of phenotypes

E= MA:0000236 Q= PATO:0000586

==Results: plant_trait==

So far we've analyzed the plant_trait ontology. We refer to this
ontology as PT ontology here.

Our focus is on phenotypes that are applicable to human health and
disease; however, the PT ontology is easier to use to illustrate
patterns that can also be applied to MP (Mammalian Phenotype)

[http://www.fruitfly.org/~cjm/obol Obol] was used to generate prospective definitions for all PT terms -
these were examined and fixed manually by a non-domain expert
(CJM).

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#plant_trait_xp

====OBO-Edit====

If you are using OBO-Edit, then you can paste the following URL directly into the obo-edit load box:

* http://purl.org/obo/obo-all/plant_trait_xp/plant_trait_xp.imports.obo

(you may want to use the 'advanced' option and allow dangling references)

The above .obo file contains just import statements - to pull in the relevant obo files, as well as the main xp file (this means you will need an internet connection, even if you download the file for use later)

====OWL Editors====

* http://purl.org/obo/obo-all/plant_trait_xp/plant_trait_xp.imports.owl

Not yet fully tested. You may need to allocate additional heap, as this imports a lot of ontologies.

===Summary===

Summary of Results as follows:

===Standard EQ Terms===

The standard PT term is a pre-coordinated EQ term; this can easily be
defined as:

A <Q> *which* inheres_in an <E>

ie a quality carried by a bearer entity

This can easily be represented as a logical definition; below is an
example in oboformat

[Term]
id: TO:0000227
name: root length
namespace: plant_trait_ontology
def: "Average maximum length of the root of a plant in a study." []
synonym: "MRD" []
synonym: "MRL" []
synonym: "RTLG" []
synonym: "maximum root depth" []
synonym: "maximum root length" []
is_a: TO:0000043 ! root anatomy and morphology trait
intersection_of: PATO:0000122 ! length
intersection_of: inheres_in PO:0009005 ! root

Providing these definitions in oboformat has the following advantages:

- PATO definitions of qualities can be shared and reused

- The oboedit reasoner can keep PT in sync with PO and PATO, and
perform automatic DAG placement of terms

- PATO terms can be used to query PT-annotated phenotypes

- PO terms can be used to query PT-annotated phenotypes (eg "halogen
sensitivity" can be used as a query, even though this term is not in PT)

===Sensitivity Terms===

This is the other major class of terms. There are lots of sensitivity
terms. These are represented using the definition pattern:

sensitivity which is *towards* <chemical>

For example (again, in obo format):

[Term]
id: TO:0000029
name: chlorine sensitivity
namespace: plant_trait_ontology
def: "Sensitivity to the chlorine content in the growth medium. Chloride helps regulate the correct pH (acid/alkaline) balance. This is a major electrolyte in the living cell besides sodium and potassium. It is available to the cell mainly in the form of NaCl and KCl salts." []
synonym: "CHLORSN" []
is_a: TO:0000080 ! micronutrient sensitivity
intersection_of: PATO:0000085 ! sensitivity
intersection_of: towards CHEBI:23116 ! chlorine

Providing these definitions in oboformat has the following advantages:

- CHEBI definitions of qualities can be shared and reused

- The oboedit reasoner can keep PT in sync with CHEBI, and
perform automatic DAG placement of terms when/if CHEBI changes

- CHEBI terms can be used to query PT-annotated phenotypes

==== Nutrients ====

See this tracker item:

* http://sourceforge.net/tracker/index.php?func=detail&aid=1718383&group_id=76834&atid=835557

====Environment ontology====

There is also a plant-centric environment ontology (EO). This could be generalised for other uses.

Some of the ''sensitivity'' terms referred to environments or parts of the environment that are not at the chemical/molecular level. EO was used to define some of these, for example:

[Term]
id: TO:0000188
name: drought sensitivity
namespace: plant_trait_ontology
def: "Drought sensitivity is highly interactive with crop phenology, plant growth prior to stress, and timing, duration, and intensity of drought stress. For many soils, it takes at least 2 rainless weeks to cause marked differences in drought sensitivity during the vegetative stage and at least 7 rainless days during the reproductive stage to cause severe drought injury. Leaf rolling precedes leaf drying during drought. Repeated ratings are recommended through progress of the drought." []
synonym: "DRS" []
synonym: "DRSN" []
synonym: "drought susceptibility" []
is_a: TO:0000394 ! drought related trait
intersection_of: PATO:0000085 ! sensitivity
intersection_of: towards EO:0007404 ! drought environment

these will need closer examination. Some of the EO terms could themselves be decomposed, eg soil alkilinity

===Ratios, proportions and compositions===

Many PT terms include ratios:

[Term]
id: TO:0000278
name: root to shoot ratio
namespace: plant_trait_ontology
synonym: "RTSHRO" []
synonym: "r/s" []
synonym: "root/shoot ratio" []
is_a: TO:0000043 ! root anatomy and morphology trait

Course of action: we will add a term "proportionality" to PATO
http://sourceforge.net/tracker/index.php?func=detail&aid=1606404&group_id=76834&atid=595654

intersection_of: PATO:<<new-term-proportionality>>
intersection_of: towards PO:0009005 ! root
intersection_of: relative_to PO:0009006 ! shoot

Some of the PT ratios can be expressed using the relational quality '''PATO:composition''', which can take an additional 2 arguments:

[Term]
id: TO:0000372
name: amylose to amylopectin ratio
namespace: plant_trait_ontology
def: "Ratio of amount of amylose to amylopectin content." []
synonym: "AMYAMYPCTRO" []
is_a: TO:0000097 ! amylopectin content
is_a: TO:0000196 ! amylose content
intersection_of: PATO:0000025 !composition
intersection_of: towards CHEBI:28102 ! amylose
intersection_of: relative_to CHEBI:28057 ! amylopectin

Note the is_a links to amylopectin content and amylose content. Is this correct? In actual fact we have a reversal of magnitude here, as the magnitude of this parent increases, the magnitude of the child will decrease

===Synonyms===

PT uses lots of synonyms, but does not assign a scope
(exact/broad/narrow). This makes it harder to glean the exact meaning
of a term from the synonym.

===Relative===

PT uses terms like '''relative growth rate'''. It is not clear how this is different from '''growth rate'''. This seems to be a difference in how the term is ''used''.

===Disease resistance phenotypes===

PT has many disease resistance terms; eg:

[Term]
id: TO:0000323
name: stem rot disease resistance
namespace: plant_trait_ontology
def: "Causal agent: Magnaporthe salvinii (Nakataea sigmoidea, Sclerotium oryzae), and Helminthosporium sigmoideum var. irregulare. Symptoms: dark lesions develop on the stems near the water line. Small, dark bodies (sclerotia) develop, weaken the stem and cause lodging." []
synonym: "CULMROTRS" []
synonym: "SR" []
is_a: TO:0000439 ! fungal disease resistance

These would be easy to define if we had an orthogonal ontology of
plant diseases and infectious agents. The definition pattern would be:

A <TO:resistance> which *towards* <InfectiousAgent>

This will be easier to do for mammalian phenotypes since these
orthogonal ontologies are being developed. It is recommended the POC
develops such a separate ontology for plants.

===Assay-specific terms===

Example: root dry weight

It is unclear how to proceed with these. No action was taken for these.

===Conjunctive terms===

Example: lemma and palea related traits

Example: lemma and palea pubescence

I think these should be defined as:

a pubescence which inheres_in the lemma and inheres_in the palea

ie the necessary and sufficient conditions are that both the lemma and palea are pubsescent

can the same quality instances inhere in 2 entities?

===Inconsistency of Term name syntax===

Compare: "shrunken endosperm" with "leaf length"

In one case the adjectival noun (naming the quality) precedes the noun
(naming the bearer entity); in other cases it succeeds it.

It is recommended all prefered terms follow the same lexical pattern
(unless community usage or plain english trumps this).

===Missing anatomy terms===

Example: canopy temperature

"canopy" should be the name of a type in the plant_anatomy ontology

===Use of "other"===

Example: other miscellaneous trait
Example: other nutrient sensitivity

OBO Foundry principles dictate avoidance of "other"

===Use of word "quality"===

PATO and PT's use of the word quality is not univocal. PATO uses the term to mean "property" whereas TO uses it to mean a more nebulous subjective(?) quality. Perhaps within the plant trait community the meaning of this term is more fixed, if so, it should be defined somewhere. Does it simply mean healthiness? If so, it would be good to use the same PATO term, at least as a synonym

[Term]
id: TO:0000587
name: endosperm quality
alt_id: TO:0000150
related_synonym: "End" []
related_synonym: "endosperm quality (sensu Poaceae)" []
is_a: TO:0000162 ! seed quality

===Redundancy===

There is some redundancy with GO Molecular Function activity terms

For example:

[Term]
id: TO:0000284
name: ADP glucose pyrophosphorylase activity
namespace: plant_trait_ontology
def: "Catalysis of the reaction: ATP + alpha-D-glucose 1-phosphate = diphosphate + ADP-glucose." []

A phenotype ontology should be orthogonal to an ontology of molecular
function. It is not clear how the above term would be used in
phenotype annotation.

There is a case for including malfunctions, loss of function and gain
of function in a phenotype ontology, but this should be made explicit

===Complex Phenotypes===

It's too hard to even attempt to automatically generate definitions
for these; logical definitions should be provided manually. For example:

[Term]
id: TO:0000169
name: chinsurah boro CMS
namespace: plant_trait_ontology
def: "Abortion of microspore development at trinucleate stage" []

This could be defined in terms of "microspore development"
(GO:0009555), "trinucleate stage" (term required in plant
developmental stage ontology)

===Other difficult cases===

Example: photoperiod sensitivity

===Errors and inconsistencies detected===

The following were detected as a direct result of this approach

in PO, panicle is a synonym for inflorescence; in TO, panicle color is_a inflorescence color

[Term]
id: TO:0000201
name: panicle color
namespace: plant_trait_ontology
def: "Variation in color of the panicle inflorescence." []
synonym: "PNCL" []
is_a: TO:0000581 ! inflorescence color

similarly, panicle/inflorescence length, weight, shape

==Results: Mammalian Phenotype (MP)==

The MP ontology proved more difficult to analyze automatically -
changes to Obol and/or manual editing of logical definitions may be
required.

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#mammalian_phenotype_xp

====OBO-Edit====

If you are using OBO-Edit, then you can paste the following URL directly into the obo-edit load box:

* http://purl.org/obo/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.obo

(you may want to use the 'advanced' option and allow dangling references)

The above .obo file contains just import statements - to pull in the relevant obo files, as well as the main xp file (this means you will need an internet connection, even if you download the file for use later)

====OWL Editors====

* http://purl.org/obo/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.owl

Not yet fully tested. You may need to allocate additional heap, as this imports a lot of ontologies.

===Visualising Results===

As well as oboedit and owl editors, the cross-products can be viewed in the experimental [http://www.berkeleybop.org/obol Obol] branch of Amigo. For example, to see what terms are defined using the PATO term ''hypoplastic'', see:

* [http://www.berkeleybop.org/amigo/obol?goto=detail_page&data_class=term&id=PATO%3a0000645 PATO:0000645]

Here we can see the following terms defined:

# nasal bone hypoplasia
# maxilla hypoplasia
# mandible hypoplasia
# liver hypoplasia
# adrenal gland hypoplasia
# bulbourethral gland hypoplasia
# spleen hypoplasia
# forebrain hypoplasia
# telencephalon hypoplasia
# cerebellum hypoplasia
# pulmonary hypoplasia
# skin hypoplasia

Following the like to [http://www.berkeleybop.org/amigo/obol?goto=detail_page&data_class=term&id=MP%3a0001178 pulmonary hyoplasia] shows you the term in the original MP context (a DAG) and also a "decomposed view" showing separate trees for the genus and differentium:

[[Image:amigo-pulmonary-hypoplasia.jpg]]

This page is just meant for illustration - for display to a biologist end-user this would be compacted; the upper levels of PATO would not be shown.

===Term Syntax===

The syntax of the term names in MP differs from PT; a common ''lexical'' pattern
in MP is:

* VALUE - ENTITY - ATTRIBUTE

===Example: increased brown fat cell amount===

One example of an MP term following the above pattern is:

* "<increased> <brown fat cell> <amount>"

Which has the text definition: "increased amount of thermogenic tissue
in the body that is composed of cells containing multiple small fat
droplets"

As a first attempt at a logical definition:

* genus: PATO:0000420 ("increased number")
* differentia: ''inheres_in'' MA:0000057 ("brown fat")

Represented in obo format as:

intersection_of: PATO:0000420 ! increased number
intersection_of: inheres_in MA:0000057 ! brown fat tissue

However, this is not quite right, as it is not an "increased number"
of "brown fat" tissue, it is a larger "portion size".

At the time of writing this PATO term is not defined so we're not sure
if this is applicable.

(TODO)

There are many advantages to explicitly defining MP terms using PATO
and MA in this fashion. Reasoners can be used to keep the ontologies
in sync (either the oboedit reasoner or one of any number of owl
reasoners). PATO definitions and MP definitions can be shared and
reused.

===Complex phenotypes in mammals===

Many phenotypes such as "ovary hypoplasia" or "degenerate molars" are a single quality inhering in a single entity (or collection of entities - eg the collection of all molars in an individual organism).

For others such as "holoprosencephaly" or "osteoporosis", it may be an interconnected collection of qualities inhering in the same or different parts. We can still define these as conjunctions of EQs, but this is where we start crossing the grey line between the dependent continuants known as 'phenotypes' into the dependent continuants known as 'disorders'...

It is also important to distinguish between the definition, which captures the necessary and sufficient conditions, from the gloss/additional notes; eg MP defines holoprosencephaly as:

presence of a single forebrain hemisphere or lobe; often accompanied by a deficit in median facial development

Thus the logical definition should only refer to the part before the semicolon. (genus: PATO:having_a_single_part, differentia: towards MA:forebrain_hemisphere). The part after the semicolon ("often accompanied by...") is useful, but is statistical and are neither necessary nor sufficient so should be captured by other means.

===Issue: species-specificity===

Whilst the MP represents mammalian phenotypes, we do not have a common
mammalian anatomical ontology. It will take some time before CARO
reaches the level of granularity required.

We recommend that since the focus of MP is biased towards the mouse
and mouse models of human disease [CHECK THIS STMT], we treat it is a
mouse phenotype ontology, with a view to migrating the definitions
towards some kind of FMA/MA synthesis when such an ontology becomes
available.

===Absence-oriented terms===

The absence case is different from normal EQ phenotypes - the absence
does not inhere in the entity that is absent, since this entity does
not exist!

We treat these the same as "sensitivity to..." terms. The absence
inheres in the organism as a whole (or the anatomical entity which is
missing the part)

[Term]
id: MP:0000766
name: absent tongue squamous epithelium
namespace: MPheno.ontology
def: "missing the scaly epithelial layer of the tongue" []
synonym: "absence of tongue squamous epithelium" []
synonym: "loss of tongue squamous epithelium" []
is_a: MP:0000765 ! abnormal tongue squamous epithelium morphology

Could be defined as:

An <lacking_of_a_part> which inheres_in <organism> and towards <tongue squamous epithelium>

The "inheres_in <organism>" part of the definition can be omitted

in obo format:

intersection_of: PATO:lacks_part
intersection_of: towards MA:tongue_squamous_epithelium

See [[PATO:Absent]] for more discussion on this

==="Other" categories===

MP contains some terms such as "other metabolic defect" - the use of "other" is to be avoided

===Root term===

The root of the MP is the term "phenotype ontology". There are relations such as "cellular phenotype" is_a "phenotype ontology". The root term should be changed to "phenotype".

===Inconsistencies detected===

A number of inconsistencies were detected.

Example of inconsistency between MP and OBO-Cell:

[[Image:oboedit-amacrine.jpg]]

Here the oboedit reasoner has found an unstated implied link (blue squiggly arrow) between 'abnormal amacrine cell morphology' and 'abnormal interneuron morphology'. In the split pane display we see the reason for this inference: OBO-Cell states that 'amacrine cell' ''is_a'' 'interneuron'.

The logical definitions will also be used for comparing phenotypes across organisms once OBD is populated.

==Results: Worm Phenotype (WP)==

Defining xps for the WP is still in preliminary stages

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#worm_phenotype_xp

==Results: Human Phenotype (HP)==

Defining xps for the HP is still in preliminary stages

Example:

<pre>
[Term]
id: HP:0000110 ! renal dysplasia
intersection_of: PATO:0000640 ! dysplastic
intersection_of: inheres_in FMA:7203 ! kidney
</pre>

A few tracker items have been submitted [https://sourceforge.net/tracker2/?atid=1112722&group_id=76834 to the HP tracker] based on running the oboedit reasoner over HP-XP

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#human_phenotype_xp

Quick URLs:

* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp.xp.html HTML Table] (large)
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp.obo obo] - xps in obo format
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp.obo obo] - xps in obo format (syntax highlights)
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp-imports.obo imports.obo] give this URL to oboedit
* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp-imports.owl imports.owl] give this URL to Protege

==Conclusions==

Providing formal computable definitions of pre-coordinated phenotype
terms in terms of basic qualities (PATO) and bearer entities (eg AOs)
will make both styles of phenotype annotation commensurable, promote
sharing of core ontologies and reusable ontology "building blocks"

More work is required to curate these logical definitions in phenotype
ontologies. This preliminary analysis suggests some of this can be
automated.

FMAInOwl

2008-10-13T03:14:33Z

Cjm: /* Obo Translation */

We have created a transformation for the FMA into OWL that pursues the following two goals:

1. representing only the information that is explicitly present in the frames representation of the FMA or that can be directly inferred from the semantics of Protege frames;

2. representing al l the information that is present in the frames representation of the FMA, thus producing an OWL representation for the complete FMA.

The '''description''' of the transformation is available as an SMI Technical report [http://smi.stanford.edu/smi-web/research/details.jsp?PubId=1234 SMI-2007-1234]

The '''OWL representation''' of the FMA is available at [http://bioontology.org/projects/ontologies/fma http://bioontology.org/projects/ontologies/fma]

If you want to access the OWL file directly, point your OWL tool (e.g. the Protege OWL ontology editor) to

[http://bioontology.org/projects/ontologies/fma/fmaOwlFullComponent_2_0.owl http://bioontology.org/projects/ontologies/fma/fmaOwlFullComponent_2_0.owl]

Note that it will use owl:imports to import another OWL ontology in the same directory ([http://bioontology.org/projects/ontologies/fma/fmaOwlDlComponent_2_0.owl http://bioontology.org/projects/ontologies/fma/fmaOwlDlComponent_2_0.owl]).

The '''conversion script''' is also available: download the [[Media:fmaToOWL_v2.zip|FMA-TO-OWL Converter]]

The conversion script takes the following arguments:

- the path to the Protege project with the frames version of the FMA

- the namespace to use for the OWL DL component

- the namespace to use for the OWL Full component

Note: the following files (available in the Protege installation directory must also be on the classpath): icu4j_3_4.jar:iri.jar:xercesImpl.jar:protege.jar:commons-logging.jar:jena.jar:driver.jar:protege-owl.jar

== Obo Translation ==

There is an ''alpha'' version of the translation of the FMA2 to obo

* [http://obo.svn.sourceforge.net/viewvc/obo/fma-conversion/trunk/fma2_obo.obo?view=log fma2_obo.obo] on OBO sourceforge

This is based on a translation of the OWL above by cjm. It is independent of yet dependent on the OWL translation above.

The translation captures a subset of the relations used in the FMA (specifically spatial relations) and of the metadata (synonyms). The goal is to conform to OBO and RO guidelines.

UPDATE: 2008/10/12

* Pre-release available on [http://www.obofoundry.org/cgi-bin/detail.cgi?id=fma_lite FMA Page at OBO]
* [http://www.berkeleybop.org/ontologies/obo-all/fma_lite_prerelease/fma_lite_prerelease.owl fma_lite_prerelease.owl]

Please contact the obo-admin list concerning the obo translation

OBD:Similarity Statistics

2008-10-09T20:00:25Z

Cjm: /* Inter-species comparisons */

OBD has various capabilities for computing the similarity between entities based on ontology annotations.

OBD is flexible with respect to what kind of annotations and ontologies are used. For example:

* Based on phenotypes annotations, what mouse genes (or genotypes) are similar to the human gene EPB41?
* Based on GO annotations, what is the correlation between similarity between functional annotations and sequence similarity?
* Based on annotations of microbes to environmental habitats, what organisms have similar profiles to a particular microbe?

Here we will use annotations of genes, alleles and genotypes to phenotypes for illustrative purposes, but the methods are generic.

== Use of reasoner ==

All similarity statistics are run using the pre-reasoned database. If a gene affects the hippocampus it also affects the brain. If a mutation affects the permeability of a mitochondrial membrane, it also affects the permeability of a membrane. This ensure that annotations are different levels of granularity and specificity are compared, commonalities are found.

== Inter-species comparisons ==

In cases where we want to compare anatomical terms across species we reason using [[UBERON:Main_Page|Uberon]]

== Statistics ==

See the javadoc for [http://www.berkeleybop.org/obd/docs/org/obd/model/stats/SimilarityPair.html SimilarityPair]

[[Category:OBD]]

OBD:Similarity Statistics

2008-10-09T19:28:55Z

Cjm:

OBD has various capabilities for computing the similarity between entities based on ontology annotations.

OBD is flexible with respect to what kind of annotations and ontologies are used. For example:

* Based on phenotypes annotations, what mouse genes (or genotypes) are similar to the human gene EPB41?
* Based on GO annotations, what is the correlation between similarity between functional annotations and sequence similarity?
* Based on annotations of microbes to environmental habitats, what organisms have similar profiles to a particular microbe?

Here we will use annotations of genes, alleles and genotypes to phenotypes for illustrative purposes, but the methods are generic.

== Use of reasoner ==

All similarity statistics are run using the pre-reasoned database. If a gene affects the hippocampus it also affects the brain. If a mutation affects the permeability of a mitochondrial membrane, it also affects the permeability of a membrane. This ensure that annotations are different levels of granularity and specificity are compared, commonalities are found.

== Inter-species comparisons ==

In cases where we want to compare anatomical terms across species we reason using [[Uberon:Main_Page|Uberon]]

== Statistics ==

See the javadoc for [http://www.berkeleybop.org/obd/docs/org/obd/model/stats/SimilarityPair.html SimilarityPair]

[[Category:OBD]]

Special:Badtitle/NS200:Pre vs Post Coordinating

2008-10-05T23:08:09Z

Cjm: /* Results: Worm Phenotype (WP) */

==Background==

See also

http://wiki.geneontology.org/index.php/Category:Cross_Products

There is also a [http://docs.google.com/Doc?docid=d2xd966_86qs99ndp&hl=en draft of a paper in progress] - email cjm to view

==Reconciling pre and post coordinated phenotype descriptions==

PRELIMINARY DOCUMENT! IN PROGRESS!

There are two paradigms for representing phenotypes and phenotype-like
entities (1) use ontologies of ''pre-coordinated'' phenotypes, such as MP
or plant_trait (PT) or (2) ''post-coordinate'' the phenotype description
using terms from an ontology of qualities (eg PATO) and terms from
ontologies of quality-bearers (eg GO, AOs, CL, ...); this is the
EQ-annotation methodology

Both approaches have their advantages, and they are in fact entirely
compatible, provided you follow the SOP laid out here. It is even
possible to mix and match these approaches.

This methodology is applicable not just to "phenotypes" or "traits",
however we choose to define these terms, but to any kind of
[[Glossary#Dependent_Entity|Dependent Entity]], such as diseases, syndromes, disorders
and even roles.

The methodology hinges on the provision of
[[Glossary#Aristotelian_Definition|Aristotelian Definition]]s of pre-coordinated phenotype
terms in a computable format.

Below we provide some examples, taken from MP and PT

==Defining Specific Phenotypes==

Here are some examples of (somewhat trivial) aristotelian
(genus-differentia) definitions of mammalian phenotypes:

If we take the MP term "big ears" (MP:0000017), this can be defined as
the genus "large"/"largeness" (PATO:0000586) inhering in an "ear"
(MA:0000236).

In OBO-1.2 syntax this can be represented as:

[Term]
id: MP:0000017
name: big ears
namespace: MPheno.ontology
def: "outer ears of a greater than normal size" []
is_a: MP:0002177 ! abnormal outer ear morphology
intersection_of: PATO:0000586 ! large size
intersection_of: inheres_in MA:0000236 ! ear

Of course, an ontology editor will not manipulate the syntax
directly. This will be visible in oboedit in the "cross products" box

Note that our definition here is different from the text definition,
which has the genus as "ear" and the differentia has "having a greater
than normal size". We could write this in OBO syntax as:

[Term]
id: MP:0000017
name: big ears
namespace: MPheno.ontology
def: "outer ears of a greater than normal size" []
is_a: MP:0002177 ! abnormal outer ear morphology
intersection_of: MA:0000236 ! ear
intersection_of: has_quality PATO:0000586 ! large size

The first form is prefered, despite the fact the english phrasing is
more contorted. The reason is that a phenotype ontology should define
phenotypes, and not the entities in which phenotypes occur. The genus
term is the primary is_a parent, and it makes sense for the phenotype
ontology to be arranged on the quality axis, and not the anatomical
axis.

If we go the second route, consider the problems that will be
encountered defining terms like "sensitivity to chlorine"

Another way to record the same information is pheno-syntax. This is a convenient shorthand for combinatorial descriptions of phenotypes

E= MA:0000236 Q= PATO:0000586

==Results: plant_trait==

So far we've analyzed the plant_trait ontology. We refer to this
ontology as PT ontology here.

Our focus is on phenotypes that are applicable to human health and
disease; however, the PT ontology is easier to use to illustrate
patterns that can also be applied to MP (Mammalian Phenotype)

[http://www.fruitfly.org/~cjm/obol Obol] was used to generate prospective definitions for all PT terms -
these were examined and fixed manually by a non-domain expert
(CJM).

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#plant_trait_xp

====OBO-Edit====

If you are using OBO-Edit, then you can paste the following URL directly into the obo-edit load box:

* http://purl.org/obo/obo-all/plant_trait_xp/plant_trait_xp.imports.obo

(you may want to use the 'advanced' option and allow dangling references)

The above .obo file contains just import statements - to pull in the relevant obo files, as well as the main xp file (this means you will need an internet connection, even if you download the file for use later)

====OWL Editors====

* http://purl.org/obo/obo-all/plant_trait_xp/plant_trait_xp.imports.owl

Not yet fully tested. You may need to allocate additional heap, as this imports a lot of ontologies.

===Summary===

Summary of Results as follows:

===Standard EQ Terms===

The standard PT term is a pre-coordinated EQ term; this can easily be
defined as:

A <Q> *which* inheres_in an <E>

ie a quality carried by a bearer entity

This can easily be represented as a logical definition; below is an
example in oboformat

[Term]
id: TO:0000227
name: root length
namespace: plant_trait_ontology
def: "Average maximum length of the root of a plant in a study." []
synonym: "MRD" []
synonym: "MRL" []
synonym: "RTLG" []
synonym: "maximum root depth" []
synonym: "maximum root length" []
is_a: TO:0000043 ! root anatomy and morphology trait
intersection_of: PATO:0000122 ! length
intersection_of: inheres_in PO:0009005 ! root

Providing these definitions in oboformat has the following advantages:

- PATO definitions of qualities can be shared and reused

- The oboedit reasoner can keep PT in sync with PO and PATO, and
perform automatic DAG placement of terms

- PATO terms can be used to query PT-annotated phenotypes

- PO terms can be used to query PT-annotated phenotypes (eg "halogen
sensitivity" can be used as a query, even though this term is not in PT)

===Sensitivity Terms===

This is the other major class of terms. There are lots of sensitivity
terms. These are represented using the definition pattern:

sensitivity which is *towards* <chemical>

For example (again, in obo format):

[Term]
id: TO:0000029
name: chlorine sensitivity
namespace: plant_trait_ontology
def: "Sensitivity to the chlorine content in the growth medium. Chloride helps regulate the correct pH (acid/alkaline) balance. This is a major electrolyte in the living cell besides sodium and potassium. It is available to the cell mainly in the form of NaCl and KCl salts." []
synonym: "CHLORSN" []
is_a: TO:0000080 ! micronutrient sensitivity
intersection_of: PATO:0000085 ! sensitivity
intersection_of: towards CHEBI:23116 ! chlorine

Providing these definitions in oboformat has the following advantages:

- CHEBI definitions of qualities can be shared and reused

- The oboedit reasoner can keep PT in sync with CHEBI, and
perform automatic DAG placement of terms when/if CHEBI changes

- CHEBI terms can be used to query PT-annotated phenotypes

==== Nutrients ====

See this tracker item:

* http://sourceforge.net/tracker/index.php?func=detail&aid=1718383&group_id=76834&atid=835557

====Environment ontology====

There is also a plant-centric environment ontology (EO). This could be generalised for other uses.

Some of the ''sensitivity'' terms referred to environments or parts of the environment that are not at the chemical/molecular level. EO was used to define some of these, for example:

[Term]
id: TO:0000188
name: drought sensitivity
namespace: plant_trait_ontology
def: "Drought sensitivity is highly interactive with crop phenology, plant growth prior to stress, and timing, duration, and intensity of drought stress. For many soils, it takes at least 2 rainless weeks to cause marked differences in drought sensitivity during the vegetative stage and at least 7 rainless days during the reproductive stage to cause severe drought injury. Leaf rolling precedes leaf drying during drought. Repeated ratings are recommended through progress of the drought." []
synonym: "DRS" []
synonym: "DRSN" []
synonym: "drought susceptibility" []
is_a: TO:0000394 ! drought related trait
intersection_of: PATO:0000085 ! sensitivity
intersection_of: towards EO:0007404 ! drought environment

these will need closer examination. Some of the EO terms could themselves be decomposed, eg soil alkilinity

===Ratios, proportions and compositions===

Many PT terms include ratios:

[Term]
id: TO:0000278
name: root to shoot ratio
namespace: plant_trait_ontology
synonym: "RTSHRO" []
synonym: "r/s" []
synonym: "root/shoot ratio" []
is_a: TO:0000043 ! root anatomy and morphology trait

Course of action: we will add a term "proportionality" to PATO
http://sourceforge.net/tracker/index.php?func=detail&aid=1606404&group_id=76834&atid=595654

intersection_of: PATO:<<new-term-proportionality>>
intersection_of: towards PO:0009005 ! root
intersection_of: relative_to PO:0009006 ! shoot

Some of the PT ratios can be expressed using the relational quality '''PATO:composition''', which can take an additional 2 arguments:

[Term]
id: TO:0000372
name: amylose to amylopectin ratio
namespace: plant_trait_ontology
def: "Ratio of amount of amylose to amylopectin content." []
synonym: "AMYAMYPCTRO" []
is_a: TO:0000097 ! amylopectin content
is_a: TO:0000196 ! amylose content
intersection_of: PATO:0000025 !composition
intersection_of: towards CHEBI:28102 ! amylose
intersection_of: relative_to CHEBI:28057 ! amylopectin

Note the is_a links to amylopectin content and amylose content. Is this correct? In actual fact we have a reversal of magnitude here, as the magnitude of this parent increases, the magnitude of the child will decrease

===Synonyms===

PT uses lots of synonyms, but does not assign a scope
(exact/broad/narrow). This makes it harder to glean the exact meaning
of a term from the synonym.

===Relative===

PT uses terms like '''relative growth rate'''. It is not clear how this is different from '''growth rate'''. This seems to be a difference in how the term is ''used''.

===Disease resistance phenotypes===

PT has many disease resistance terms; eg:

[Term]
id: TO:0000323
name: stem rot disease resistance
namespace: plant_trait_ontology
def: "Causal agent: Magnaporthe salvinii (Nakataea sigmoidea, Sclerotium oryzae), and Helminthosporium sigmoideum var. irregulare. Symptoms: dark lesions develop on the stems near the water line. Small, dark bodies (sclerotia) develop, weaken the stem and cause lodging." []
synonym: "CULMROTRS" []
synonym: "SR" []
is_a: TO:0000439 ! fungal disease resistance

These would be easy to define if we had an orthogonal ontology of
plant diseases and infectious agents. The definition pattern would be:

A <TO:resistance> which *towards* <InfectiousAgent>

This will be easier to do for mammalian phenotypes since these
orthogonal ontologies are being developed. It is recommended the POC
develops such a separate ontology for plants.

===Assay-specific terms===

Example: root dry weight

It is unclear how to proceed with these. No action was taken for these.

===Conjunctive terms===

Example: lemma and palea related traits

Example: lemma and palea pubescence

I think these should be defined as:

a pubescence which inheres_in the lemma and inheres_in the palea

ie the necessary and sufficient conditions are that both the lemma and palea are pubsescent

can the same quality instances inhere in 2 entities?

===Inconsistency of Term name syntax===

Compare: "shrunken endosperm" with "leaf length"

In one case the adjectival noun (naming the quality) precedes the noun
(naming the bearer entity); in other cases it succeeds it.

It is recommended all prefered terms follow the same lexical pattern
(unless community usage or plain english trumps this).

===Missing anatomy terms===

Example: canopy temperature

"canopy" should be the name of a type in the plant_anatomy ontology

===Use of "other"===

Example: other miscellaneous trait
Example: other nutrient sensitivity

OBO Foundry principles dictate avoidance of "other"

===Use of word "quality"===

PATO and PT's use of the word quality is not univocal. PATO uses the term to mean "property" whereas TO uses it to mean a more nebulous subjective(?) quality. Perhaps within the plant trait community the meaning of this term is more fixed, if so, it should be defined somewhere. Does it simply mean healthiness? If so, it would be good to use the same PATO term, at least as a synonym

[Term]
id: TO:0000587
name: endosperm quality
alt_id: TO:0000150
related_synonym: "End" []
related_synonym: "endosperm quality (sensu Poaceae)" []
is_a: TO:0000162 ! seed quality

===Redundancy===

There is some redundancy with GO Molecular Function activity terms

For example:

[Term]
id: TO:0000284
name: ADP glucose pyrophosphorylase activity
namespace: plant_trait_ontology
def: "Catalysis of the reaction: ATP + alpha-D-glucose 1-phosphate = diphosphate + ADP-glucose." []

A phenotype ontology should be orthogonal to an ontology of molecular
function. It is not clear how the above term would be used in
phenotype annotation.

There is a case for including malfunctions, loss of function and gain
of function in a phenotype ontology, but this should be made explicit

===Complex Phenotypes===

It's too hard to even attempt to automatically generate definitions
for these; logical definitions should be provided manually. For example:

[Term]
id: TO:0000169
name: chinsurah boro CMS
namespace: plant_trait_ontology
def: "Abortion of microspore development at trinucleate stage" []

This could be defined in terms of "microspore development"
(GO:0009555), "trinucleate stage" (term required in plant
developmental stage ontology)

===Other difficult cases===

Example: photoperiod sensitivity

===Errors and inconsistencies detected===

The following were detected as a direct result of this approach

in PO, panicle is a synonym for inflorescence; in TO, panicle color is_a inflorescence color

[Term]
id: TO:0000201
name: panicle color
namespace: plant_trait_ontology
def: "Variation in color of the panicle inflorescence." []
synonym: "PNCL" []
is_a: TO:0000581 ! inflorescence color

similarly, panicle/inflorescence length, weight, shape

==Results: Mammalian Phenotype (MP)==

The MP ontology proved more difficult to analyze automatically -
changes to Obol and/or manual editing of logical definitions may be
required.

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#mammalian_phenotype_xp

====OBO-Edit====

If you are using OBO-Edit, then you can paste the following URL directly into the obo-edit load box:

* http://purl.org/obo/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.obo

(you may want to use the 'advanced' option and allow dangling references)

The above .obo file contains just import statements - to pull in the relevant obo files, as well as the main xp file (this means you will need an internet connection, even if you download the file for use later)

====OWL Editors====

* http://purl.org/obo/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.imports.owl

Not yet fully tested. You may need to allocate additional heap, as this imports a lot of ontologies.

===Visualising Results===

As well as oboedit and owl editors, the cross-products can be viewed in the experimental [http://www.berkeleybop.org/obol Obol] branch of Amigo. For example, to see what terms are defined using the PATO term ''hypoplastic'', see:

* [http://www.berkeleybop.org/amigo/obol?goto=detail_page&data_class=term&id=PATO%3a0000645 PATO:0000645]

Here we can see the following terms defined:

# nasal bone hypoplasia
# maxilla hypoplasia
# mandible hypoplasia
# liver hypoplasia
# adrenal gland hypoplasia
# bulbourethral gland hypoplasia
# spleen hypoplasia
# forebrain hypoplasia
# telencephalon hypoplasia
# cerebellum hypoplasia
# pulmonary hypoplasia
# skin hypoplasia

Following the like to [http://www.berkeleybop.org/amigo/obol?goto=detail_page&data_class=term&id=MP%3a0001178 pulmonary hyoplasia] shows you the term in the original MP context (a DAG) and also a "decomposed view" showing separate trees for the genus and differentium:

[[Image:amigo-pulmonary-hypoplasia.jpg]]

This page is just meant for illustration - for display to a biologist end-user this would be compacted; the upper levels of PATO would not be shown.

===Term Syntax===

The syntax of the term names in MP differs from PT; a common ''lexical'' pattern
in MP is:

* VALUE - ENTITY - ATTRIBUTE

===Example: increased brown fat cell amount===

One example of an MP term following the above pattern is:

* "<increased> <brown fat cell> <amount>"

Which has the text definition: "increased amount of thermogenic tissue
in the body that is composed of cells containing multiple small fat
droplets"

As a first attempt at a logical definition:

* genus: PATO:0000420 ("increased number")
* differentia: ''inheres_in'' MA:0000057 ("brown fat")

Represented in obo format as:

intersection_of: PATO:0000420 ! increased number
intersection_of: inheres_in MA:0000057 ! brown fat tissue

However, this is not quite right, as it is not an "increased number"
of "brown fat" tissue, it is a larger "portion size".

At the time of writing this PATO term is not defined so we're not sure
if this is applicable.

(TODO)

There are many advantages to explicitly defining MP terms using PATO
and MA in this fashion. Reasoners can be used to keep the ontologies
in sync (either the oboedit reasoner or one of any number of owl
reasoners). PATO definitions and MP definitions can be shared and
reused.

===Complex phenotypes in mammals===

Many phenotypes such as "ovary hypoplasia" or "degenerate molars" are a single quality inhering in a single entity (or collection of entities - eg the collection of all molars in an individual organism).

For others such as "holoprosencephaly" or "osteoporosis", it may be an interconnected collection of qualities inhering in the same or different parts. We can still define these as conjunctions of EQs, but this is where we start crossing the grey line between the dependent continuants known as 'phenotypes' into the dependent continuants known as 'disorders'...

It is also important to distinguish between the definition, which captures the necessary and sufficient conditions, from the gloss/additional notes; eg MP defines holoprosencephaly as:

presence of a single forebrain hemisphere or lobe; often accompanied by a deficit in median facial development

Thus the logical definition should only refer to the part before the semicolon. (genus: PATO:having_a_single_part, differentia: towards MA:forebrain_hemisphere). The part after the semicolon ("often accompanied by...") is useful, but is statistical and are neither necessary nor sufficient so should be captured by other means.

===Issue: species-specificity===

Whilst the MP represents mammalian phenotypes, we do not have a common
mammalian anatomical ontology. It will take some time before CARO
reaches the level of granularity required.

We recommend that since the focus of MP is biased towards the mouse
and mouse models of human disease [CHECK THIS STMT], we treat it is a
mouse phenotype ontology, with a view to migrating the definitions
towards some kind of FMA/MA synthesis when such an ontology becomes
available.

===Absence-oriented terms===

The absence case is different from normal EQ phenotypes - the absence
does not inhere in the entity that is absent, since this entity does
not exist!

We treat these the same as "sensitivity to..." terms. The absence
inheres in the organism as a whole (or the anatomical entity which is
missing the part)

[Term]
id: MP:0000766
name: absent tongue squamous epithelium
namespace: MPheno.ontology
def: "missing the scaly epithelial layer of the tongue" []
synonym: "absence of tongue squamous epithelium" []
synonym: "loss of tongue squamous epithelium" []
is_a: MP:0000765 ! abnormal tongue squamous epithelium morphology

Could be defined as:

An <lacking_of_a_part> which inheres_in <organism> and towards <tongue squamous epithelium>

The "inheres_in <organism>" part of the definition can be omitted

in obo format:

intersection_of: PATO:lacks_part
intersection_of: towards MA:tongue_squamous_epithelium

See [[PATO:Absent]] for more discussion on this

==="Other" categories===

MP contains some terms such as "other metabolic defect" - the use of "other" is to be avoided

===Root term===

The root of the MP is the term "phenotype ontology". There are relations such as "cellular phenotype" is_a "phenotype ontology". The root term should be changed to "phenotype".

===Inconsistencies detected===

A number of inconsistencies were detected.

Example of inconsistency between MP and OBO-Cell:

[[Image:oboedit-amacrine.jpg]]

Here the oboedit reasoner has found an unstated implied link (blue squiggly arrow) between 'abnormal amacrine cell morphology' and 'abnormal interneuron morphology'. In the split pane display we see the reason for this inference: OBO-Cell states that 'amacrine cell' ''is_a'' 'interneuron'.

The logical definitions will also be used for comparing phenotypes across organisms once OBD is populated.

==Results: Worm Phenotype (WP)==

Defining xps for the WP is still in preliminary stages

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#worm_phenotype_xp

==Results: Human Phenotype (HP)==

Defining xps for the HP is still in preliminary stages

A few tracker items have been submitted based on running the oboedit reasoner over HP-XP

===Downloading===

Logical definitions file available at:

* http://www.berkeleybop.org/ontologies/#human_phenotype_xp

* [http://www.berkeleybop.org/ontologies/obo-all/human_phenotype_xp/human_phenotype_xp.xp.html HTML Table] (large)
* [http://www.berkeleybop.org/ontologies/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp.obo obo] - just the xps
* [http://www.berkeleybop.org/ontologies/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp-imports.obo imports.obo] give this URL to oboedit
* [http://www.berkeleybop.org/ontologies/obo-all/mammalian_phenotype_xp/mammalian_phenotype_xp-imports.owl imports.owl] give this URL to Protege

==Conclusions==

Providing formal computable definitions of pre-coordinated phenotype
terms in terms of basic qualities (PATO) and bearer entities (eg AOs)
will make both styles of phenotype annotation commensurable, promote
sharing of core ontologies and reusable ontology "building blocks"

More work is required to curate these logical definitions in phenotype
ontologies. This preliminary analysis suggests some of this can be
automated.

Special:Badtitle/NS200:Revised 2008

2008-10-03T01:04:31Z

Cjm: /* Absent and friends */

* [http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/quality-revised.obo quality-revised.obo]

This contains a number of fixes to improve PATO. Some can be rolled into the main PATO immediately, others require a more cautious approach.

== Friendlier Terminology ==

current:

is_a PATO:0001236 ! quality of occurrent ***
is_a PATO:0001239 ! monadic quality of occurrent ***
is_a PATO:0001240 ! relational quality of occurrent ***
is_a PATO:0001241 ! quality of continuant ***
is_a PATO:0001237 ! monadic quality of continuant ***
is_a PATO:0001238 ! relational quality of continuant ***

This terrified biologists and it was unneccessary to expose everyone to BFO terminology

revised:

is_a PATO:0001236 ! process quality ***
is_a PATO:0001239 ! normal quality of a process ***
is_a PATO:0001240 ! relational quality of a process ***
is_a PATO:0001241 ! physical object quality ***
is_a PATO:0001237 ! normal quality of a physical entity ***
is_a PATO:0001238 ! relational quality of a physical entity ***

The old terminology is supported as synonyms:

is_a PATO:0001236 ! process quality *** [SYNONYM: "quality of occurrent" (exact)] [SYNONYM: "quality of a process" (exact)] [SYNONYM: "quality of process" (exact)]
is_a PATO:0001239 ! normal quality of a process *** [SYNONYM: "monadic quality of process" (exact)] [SYNONYM: "normal quality of process" (exact)] [SYNONYM: "monadic quality of occurrent" (exact)] [SYNONYM: "monadic quality of a occurrent" (exact)]
is_a PATO:0001433 ! growth quality of occurrent *** [SYNONYM: "growth timing quality" (related)]
is_a PATO:0001240 ! relational quality of a process *** [SYNONYM: "relational quality of a process" (exact)] [SYNONYM: "relational quality of occurrent" (exact)] [SYNONYM: "relational quality of a occurrent" (exact)]
is_a PATO:0001241 ! physical object quality *** [SYNONYM: "quality of an object" (exact)] [SYNONYM: "quality of continuant" (exact)] [SYNONYM: "quality of a continuant" (exact)]
is_a PATO:0001237 ! normal quality of a physical entity *** [SYNONYM: "monadic quality of an object" (narrow)] [SYNONYM: "single bearer quality of a physical entity" (exact)] [SYNONYM: "singly inhering of a physical entity" (exact)] [SYNONYM: "monadic quality of a continuant" (exact)] [SYNONYM: "monadic quality of continuant" (exact)] [SYNONYM: "monadic quality of a physical entity" (exact)]
is_a PATO:0001238 ! relational quality of a physical entity *** [SYNONYM: "relational quality of an object " (exact)] [SYNONYM: "multiply inhering quality of a physical entity " (exact)] [SYNONYM: "multiple bearer quality of a physical entity " (exact)] [SYNONYM: "relational quality of continuant" (exact)] [SYNONYM: "relational quality of a continuant" (exact)]

Definitions also improved (see file)

== Ontology Content Changes ==

Melissa and Chris made various merges, new terms and graph rearrangements

=== Single is_a hierarchy ===

Everything now has a single [[is_a]] parent

=== Shape Hierarchy Improvements ===

Current PATO has a flat list of shape terms, many of which have similarities in reality

In the proposed revised PATO we introduce higher level grouping terms, such as "convex 3D shape" and "concave 3D shape". We also introduce the cross-section relation (above) to relate 3d shapes to 2d shapes. t is important to differentiate these; yet at the same time we must be able to correlate phenotypes described in terms of 3d shapes with those described in terms of cross-section.

A lot more work is probably needed here

Sample of new hierarchy:

is_a PATO:0002007 ! convex 3-D shape
is_a PATO:0001357 ! pulvinate
is_a PATO:0001865 ! spheroid
is_a PATO:0000409 ! oblate
is_a PATO:0001866 ! prolate
is_a PATO:0001891 ! ovate
is_a PATO:0001872 ! cuboid
is_a PATO:0001873 ! cylindrical
is_a PATO:0001874 ! discoid
is_a PATO:0002008 ! concave 3-D shape
is_a PATO:0000948 ! heart shaped
is_a PATO:0001409 ! spindle-shaped
is_a PATO:0001871 ! reniform
is_a PATO:0001876 ! dumbbell-shaped
is_a PATO:0001879 ! U-shaped
is_a PATO:0001882 ! limaciform
is_a PATO:0001883 ! clavate
is_a PATO:0001890 ! tripartite
is_a PATO:0001200 ! T-shaped
is_a PATO:0001201 ! Y-shaped
is_a PATO:0002009 ! branchiness
is_a PATO:0000402 ! branched
is_a PATO:0001784 ! bifurcated
is_a PATO:0001967 ! actinodromous
is_a PATO:0001968 ! parallelodromous
is_a PATO:0001969 ! craspedodromous
is_a PATO:0001970 ! brochidodromous
is_a PATO:0001971 ! cladodromous
is_a PATO:0001972 ! reticulodromous
is_a PATO:0000414 ! unbranched

previously many of these terms went directly under "shape"

=== Position / Placement ===

This was tidied up

=== Plasty terms ===

Melissa fixed these

== Absent and friends ==

See for summary of issues [[PATO:Absent]]

Current PATO has this:

/ PATO:0000001 ! quality
is_a PATO:0000068 ! qualitative
is_a PATO:0000070 ! presence ***
is_a PATO:0000462 ! absent ***
is_a PATO:0000463 ! conspicuous
is_a PATO:0000464 ! inconspicuous
is_a PATO:0000467 ! present
is_a PATO:0001241 ! quality of continuant
is_a PATO:0001238 ! relational quality of continuant
is_a PATO:0001555 ! extra or missing physical and functional parts ***
is_a PATO:0001556 ! lacking function
is_a PATO:0001557 ! lacking physical part
is_a PATO:0001559 ! having extra function
is_a PATO:0001560 ! having extra physical parts
is_a PATO:0001568 ! having decreased function
is_a PATO:0001569 ! having decreased physical parts
is_a PATO:0001905 ! having physical part

Issues:

* no way of correlating 'absent' annotations with 'lacking physical part' annotations
* confusing

The revision attempts to fix this.

The core is_a hierarchy looks as follows. Here "c" is the cardinality of the has_part relation between bearer (E) towards the additional entity type (E2)

/ PATO:0000001 ! quality
is_a PATO:0001241 ! physical object quality
is_a PATO:0001238 ! relational quality of a physical entity c
is_a PATO:0001555 ! has or lacks parts of type *** c <= n
is_a PATO:0001905 ! has normal numbers of parts of type c = n
is_a PATO:0001999 ! lacks parts or has fewer parts of type c < n
is_a PATO:0002000 ! lacks all parts of type c = 0
is_a PATO:0001557 ! lacks all physical parts of type c = 0 (physical parts only)
is_a PATO:0002001 ! has fewer parts of type 0 < c < n
is_a PATO:0002002 ! has extra parts of type c > n

The same, with definitions:

is_a PATO:0001238 ! relational quality of a physical entity [DEF: "A physical entity quality which exists in relation towards some other entity. Contrast with: normal (monadic) quality of a physical entity"]
is_a PATO:0001555 ! has or lacks parts of type *** [DEF: "The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts."]
is_a PATO:0001905 ! has normal numbers of parts of type [DEF: "The bearer of this quality has_part = n, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]
is_a PATO:0001999 ! lacks parts or has fewer parts of type [DEF: "The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type."]
is_a PATO:0002000 ! lacks all parts of type [DEF: "A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e."]
is_a PATO:0001557 ! lacks all physical parts of type [DEF: "A relational quality of continuant inhering in a bearer by virtue of its lacking a physical part as specified by the additional entity."]
is_a PATO:0002001 ! has fewer parts of type [DEF: "The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly."]
is_a PATO:0002002 ! has extra parts of type [DEF: "The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part."]

Ideally we would get rid of "absent" but curators like it and we risk alienating them. Thus we provide two ways of saying the same thing using a parallel hierarchy:

is_a PATO:0000070 ! presence or absence in organism ***
is_a PATO:0000467 ! present in normal numbers in organism
is_a PATO:0000470 ! present in greater numbers in organism
is_a PATO:0001473 ! duplicated
is_a PATO:0001996 ! absent from or present in fewer numbers in organism
is_a PATO:0000462 ! absent from organism
is_a PATO:0001997 ! present in fewer numbers in organism

These are linked via the reciprocal_of relation. This is best seen in OE:

[[Media:pato-absent.png]] (click for graph)

Note that "absent from organism" is not a real quality as it cannot inhere in anything. However, we can convert legacy annotations using the reciprocal mapping.

== New Relations ==

=== Sub-qualities and has_part ===

<pre>
[Typedef]
id: has_part
name: has_part
def: "Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2." [PATOC:CJM]
comment: We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'
created_by: cjm
creation_date: 2008-08-12T03:01:56Z
</pre>

=== Magnitudinal Relations ===

We introduce the ''magnitude'' function, which maps qualities to a unit-invariant scale. Scalar qualities are those such as temperature, weight etc that can be arranged in a total ordering.

We do not use this function directly in PATO. However, the function is used to define two new relations:

<pre>
[Typedef]
id: increased_in_magnitude_relative_to
name: increased_in_magnitude_relative_to
def: "q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:14Z

[Typedef]
id: decreased_in_magnitude_relative_to
name: decreased_in_magnitude_relative_to
def: "q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale." [PATOC:CJM]
comment: This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'
created_by: cjm
creation_date: 2008-08-12T05:20:34Z
</pre>

=== has_cross_section ===

Current PATO has 2d and 3d shapes mixed together. pato-revised takes more care to separate these. However, we still need a way of connecting 3d shapes to their 2d counterparts. We do this by means of the notion of taking a slice of the 3d object and examining its cross-section:

<pre>
[Typedef]
id: has_cross_section
name: has_cross_section
def: "s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2." [PATOC:CJM]
comment: Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round
created_by: cjm
creation_date: 2008-08-11T11:37:34Z
</pre>