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def: Shape quality inhering in a bearer expanding outward, or having parts expanding outward, from a center point.
is_a: shape

• Wasila and Alex

To verify source and make candidate releases

A spheroid shape quality inhering in a bearer by virtue of the bearer's being nearly, but not perfectly, spherical.

is_a: spheroid PATO:0001865

Please add "posteriorly directed" as an exact synonym for 'posterior orientation' PATO:0002497

def: A positional quality inhering in a bearer by virtue of some aspect of that bearer beginning from a position on another entity.

is_a: position
Please add to relational slim

Thanks,
Wasila and Alex

1. Update editors doc to document release process
2. Include derived pato.owl in repo
3. Use git tags to make a permanent URL for each release
4. Register /obo/pato/releases/ on OCLC

I think it's confusing having the googlecode sticking around. It looks like you also check the obo back into the severely deprecated sourceforge CVS George - I think we should just stop this.

I propose the following:

1. We go through everything on the googlecode tracker and make items in github
2. Shut down the googlecode project; or alternately moving the files into an Attic directly, and ceasing to make derived commits here.
3. cvs rm the entry in sf CVS

In principle we could keep googlecode and cvs going as readonly mirrors, but this just confuses things

I also propose we punt on #4 til this is done, one step at a time

See https://code.google.com/p/pato/source/diff?spec=svn89&r=89&format=side&path=/trunk/quality_edit.obo

IDs were accidentally rewritten. No option except obsolete the range and do again.

Here is the end of the diff:

 [Term]
 id: PATO:0002528
-name: borderline intensity
-def: "An intensity which is borderline in it its effect or force as compared to baseline or normal." []
-subset: hpo_slim
-is_a: PATO:0000049 ! intensity
-created_by: haendel
-creation_date: 2014-05-26T06:42:21Z
+name: bipartite
+def: "A multipartite quality inhering in a bearer by virtue of the bearer being divided into two parts." [PATOC:WD]
+subset: value_slim
+is_a: PATO:0002510 ! multipartite
+created_by: wasila.dahdul
+creation_date: 2014-08-12T11:12:13Z

 [Term]
 id: PATO:0002529
-name: profound intensity
-def: "An intensity which is characterized by being very severe." [PATO:MAH]
-subset: hpo_slim
-is_a: PATO:0000049 ! intensity
-created_by: haendel
-creation_date: 2014-05-26T06:44:11Z
+name: plowshare shaped
+def: "A shape quality inhering in a bearer by virtue of the bearer's being shaped like a plowshare." [PATOC:WD<new dbxref>]
+subset: value_slim
+synonym: "plow-share shaped" EXACT []
+xref: Image:http\://2.bp.blogspot.com/_TbkIC-eqFNM/S66IJ3omNWI/AAAAAAAAFSk/pzThLJPvYZw/s1600/ard-detail.gif
+is_a: PATO:0000052 ! shape
+created_by: wasila.dahdul
+creation_date: 2014-08-12T11:23:12Z

 [Term]
 id: PATO:0002530
-name: episodic
-def: "An occurrence quality inhering in a bearer by virtue of the bearer's having a course that occurs occasionally." [PATO:MAH]
-subset: hpo_slim
-is_a: PATO:0000057 ! occurrence
-created_by: haendel
-creation_date: 2014-05-26T06:50:16Z
+name: peg-like
+def: "A shape quality inhering in a bearer by virtue of the bearer's having a short and stout cylindrical shape." [PATOC:WD]
+subset: value_slim
+is_a: PATO:0000052 ! shape
+created_by: wasila.dahdul
+creation_date: 2014-08-12T11:30:08Z

 [Term]
 id: PATO:0002531
-name: refractory
-def: "An occurrence of a process during which time there is an inability to change the course, extent, or repetition of the process." [PATO:MAH]
-subset: hpo_slim
-is_a: PATO:0000057 ! occurrence
-created_by: haendel
-creation_date: 2014-05-26T13:09:29Z
+name: boomerang shaped
+def: "A shape quality inhering in a bearer by virtue of the bearer's having a shape like a boomerang, with two arms connected at an angle." [PATOC:WD]
+subset: value_slim
+is_a: PATO:0000052 ! shape
+created_by: wasila.dahdul
+creation_date: 2014-08-12T11:32:16Z

 [Term]
 id: PATO:0002532
-name: secondary
-def: "A quality in which the effect or outcome is not primary or the focus of the observation." [PATO:MAH]
-subset: hpo_slim
-is_a: PATO:0000068 ! qualitative
-created_by: haendel
-creation_date: 2014-05-26T13:17:45Z
+name: subovoid
+def: "A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a shape not quite ovoid. approximately ovoid." [merriam-webster:http\://www.merriam-webster.com/dictionary/subovoid]
+subset: value_slim
+is_a: PATO:0001865 ! spheroid
+created_by: wasila.dahdul
+creation_date: 2014-08-12T11:51:38Z

+[Term]
+id: PATO:0002533
+name: concavo-convex
+def: "A shape quality that obtains by virtue of the bearer being concave on one side and convex on the other." [merriam-webster:http\://www.merriam-webster.com/dictionary/concavo-convex]
+subset: value_slim
+synonym: "concavoconvex" EXACT []
+is_a: PATO:0002005 ! concavity
+created_by: wasila.dahdul
+creation_date: 2014-08-12T11:56:13Z
+
+[Term]
+id: PATO:0002534
+name: ring shaped
+def: "A shape quality inhering in a bearer by virtue of the bearer's having a shape like a ring (a circular shape enclosing a space)." [PATOC:WD]
+subset: value_slim
+is_a: PATO:0000052 ! shape
+created_by: wasila.dahdul
+creation_date: 2014-08-12T12:01:56Z
+
+[Term]
+id: PATO:0002535
+name: spur shaped
+def: "A shape quality inhering in a bearer by virtue of the bearer's possessing a small, spike-like shape." [PATOC:WD]
+subset: value_slim
+is_a: PATO:0000052 ! shape
+created_by: wasila.dahdul
+creation_date: 2014-08-12T12:07:44Z

pato suffers the problem that i was over-eager to align it with bfo back in the day. Sorry.

As @gkoutos has pointed out increased temperature is not a quality. Many people use PATO values (and attributes - e.g. abnormal temperature) to bin some kind of change, transition or difference in quality. This is not universally true for all uses - many groups use PATO as if it were a quality.

Given this, the only way to make pato consistent with these different usages whilst aligning to a strict UO is to formally define the classes as unions, similar to the disjunctive strategy for snomed laid about by Stefan Schulz here: http://www.jbiomedsem.com/content/2/S2/S6

E.g. roughly:

• pato:temperature = (formal) temperature OR change in temperature
• pato:increased temperature = change, direction: increased, thing changed: temperature

This would of course be largely hidden from the majority of pato users, who would continue to use pato as a convenient subclass hierarchy.

To formalize the above further, we need to fill in the gap we have created for a more formal quality ontology. There are various practical options; e.g. seed this from existing PATO classes (a case of an ontology giving birth to a more primitive one). I think this would be a good chance to modularize. Basic qualities that are applicable across anything physical could go in one ontology (and work with WashU folks on their Q ontology?). Morphology in another. PATO would then be auto-classified according to these more basic ontologies.

We would also have to think about the second clause of the disjunction - what is a change. I would argue for occurrent here, but will write justification separately.

Again, the majority of bio users wouldn't care. Those of a more formal bent would presumably rejoice, and start gradually migrating from the disjunctive classes to the axiomatic. We would automatically build pato using a disjunction-aware reasoner, e.g. hermit. There may some additional churn - e.g. NTRs may have to go in first via the axiomatic ontology and then autopopulate a triad in PATO, but this should be doable.

Note that if changes in qualities are not qualities then inheres_in becomes invalid. I think there will be no shedding of tears if we stop using this in the bio community.

For aligning with quantitative data, PATO inc/dec maps to two columns in a data table. E.g. a term increased sea surface temperature is a bin/grouping for two values, a before and after (with the explicit times recorded outside pato, pato is just for the bins).

This doesn't address QoPs. Either way, PATO could shield itself via the disjunctive strategy.

Some of the specific details can be worked out later. For now this is a rough outline of the strategy to garner thoughts and reactions.

labiolingually compressed
def: A quality inhering in a bearer by virtue of the bearer's being compressed from the side facing the lips to the side facing the tongue.
is_a flattened

mesiodistally compressed
def: A quality inhering in a bearer by virtue of the bearer's being compressed from the side facing the midline of the jaw to the side opposite the midline.
is_a flattened

Required for every ontology

id: PATO:0002124
name: laminar
def: "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." [PATOC:GVG]
is_a: PATO:0000141  ! structure

s/processing/possessing/?

Add syn: "layered"?

It would be good to have a list of examples of structures that have this quality and those that don't.

presumably basal lamina?

All epithelia? Or only those that are adjacent to some other layer?

Definition: A shape quality inhering on a bearer by virtue of a bearer's having sides of different lengths, different curvatures, or unequal angles.
is_a: shape

def: Cuspidate quality inhering in a bearer by virtue of the bearer's possessing a single cusp.
is_a: cuspidate

After some discussion, we have decided the 'absence', 'presence' and 'number' terms are not so bad.

We might like to restore some of George's original labels

• count -> amount (better for "abnormal level" terms)
• FOO in organism -> increased/decreased amount

Sometimes simple is best!

Please indicate +1/-1 here

Please add "unicuspid" as a related synonym for 'conical' PATO:0002021

def: A variability quality inhering in the bearer by virtue of the bearer having a variable number or count of an entity.

is_a: variability
towards: count

• Wasila and alex

Hi,

we should continue to discuss how to express that atretic, stenosis, and closure do have more in common that just "morphology". The current idea was that all of them can only refer to some tunnel- or passage-like structure.

Sebastian

Please add 'faint' as a synonym of inconspicuous PATO:0000464

Please add as a related synonym for 'decreased size' PATO:0000587

is_a: branched

def: having many fine filaments or branches that give a feathery appearance: for example, resembling a feather. (def from http://www.oxforddictionaries.com/us/definition/american_english/plumose)

FYPO has a great many processual phenotypes, including some in which the occurrence of a process is decreased, and others where a process that normally occurs isn't observed at all.

Decreased occurrence is straightforward, using PATO:0002052 ! decreased occurrence, e.g.

decreased shmoo formation
equivalent to
'decreased occurrence'
and (inheres_in some 'mating projection assembly')

For mutants in which a process doesn't (detectably), we have logically defined "abolished process" terms using PATO:0001558 ! lacking processual parts, e.g.

abolished shmoo formation
equivalent to
'lacking processual parts'
and (towards some 'mating projection assembly')

It's not explicit in the logical def, but the lack-of-process is assumed to inhere in the cell.

Various PomBase curators and users would like to see ontology structures in which "abolished process" is a descendant rather than a sibling of "decreased [occurrence of] process", a la

decreased shmoo formation
-- [is_a] abolished shmoo formation

Their rationale is that if a normal process isn't occuring at all, it's occurring less than in wild type.

First, is our approach to "abolished process" terms sensible, especially the current logical definitions? Or should we change -- or even abandon -- it?

Second, is there a good way to accommodate a 'decreased x' is_a 'abolished x' arrangement within FYPO? To date, we haven't asserted these links, and they don't get inferred from the PATO structure ('decreased occurrence' and 'lackiing processual parts' are in fairly different branches of PATO). But we could put something in FYPO that would lead a reasoner to infer decreased is_a abolished for process phenotypes, e.g.:

decreased biological process
-- [is_a] abolished biological process

Assuming we retain 'abolished process' terms, is there any reason not to do this for FYPO?

I'm also enquiring on the phenotype-ontologies-editors mailing list.

Thanks,
Midori

New term: differentiated from
Def: A morphology quality inhering in a bearer by virtue of the bearer's being morphologically distinguishable from another entity

Please add to relational slim

exact synonym: distinct from

Note this is different from 'differentiated' PATO:0002099 which is a cellular quality.

curved lingually
is_a curved
def: A curvature quality inhering in a bearer by virtue of the bearer's being curved towards the tongue.

def: Having the shape of a pear; tapering near the top and bulging toward the base or bottom. From thefreedictionary.com

• Wasila and Alex

New term: 'surrounded by'
synonym: enclosed by
def: A positional quality inhering in a bearer by virtue of the bearer's being enclosed on all sides by another entity.
(example: coracoid foramen surrounded by coracoid and scapula"
is_a: position
reciprocal_of : 'surrounding' PATO:0001772

• add to relational slim

For existing term 'surrounding' PATO:0001772, please add synonym 'enclosing' and add reciprical_of: 'surrounded by' (new term above).

Please add 'exits through' (related synonym) to 'protruding out of' PATO:0001646

Please add "clumped" as a synonym for 'aggregated' PATO:0001629

Add a README-editors file documenting

• ID ranges - see #22
• release process - currently we just copy pato_edit.obo to pato.obo, commit and push
• design patterns etc

New terms:
'complete structure'
is_a: structure
def: A structural quality inhering in a bearer by virtue of the bearer being fully formed compared to entities lacking parts
inverse_of: incomplete structure

'incomplete structure'
is_a: structure
def: A structural quality inhering in a bearer by virtue of the bearer's lacking parts or having a reduced form compared to fully formed entities
inverse_of: complete structure

Note from project creation docs:

If you intend to have multiple people editing, then the cnido-idranges.owl file will be essential. You can edit this directly in Protege (but it may actually be easier to edit the file in a text editor). Assign each editor an ID range here (just follow the existing file as an example). Note that currently Protege does not read this file, so this just serves as formal documentation.

In future, id-ranges may be superseded by urigen servers, but for now they provide a useful way of avoiding collisions

Please add "composed of" as a synonym of "composition" PATO:0000025

Editors should have write access

In principle anyone can fork and then the people with github permissions can accept pull requests,but tthis may be too complex, especially post #4

Either CC-0 or CC-BY

We could use existing obophenotype org

orgs are free. We could also set up an org that is just 'pato'. This has certain advantages for setting up a website using github

Def: Shaped like a ring
Syn: annular

Also: create import modules

These are terms that describe the shape of mammalian teeth:

• hypsodont
  Definition: Hypsodont dentition is characterized by high-crowned teeth and enamel which extends far past the gum line, which provides extra material for wear and tear.
  is_a: shape
  include axiom: hypsodont inheres_in some ('tooth crown' and bearer_of 'decreased
  height')
• brachydont
  synonym: brachyodont
  is_a: shape
  include axiom: brachydont inheres_in some ('tooth crown' and bearer_of 'increased
  height')

Definition: Brachyodont is a type of dentition characterized by low-crowned teeth. Human teeth are brachydont.

definitions from: Damuth and Janis, 2011 Biological Reviews 86:733-758
doi: 10.1111/j.1469-185X.2011.00176.x

def: A quality inhering in a bearer by virtue of the bearer's resembling the form of a paddle.
is_a: shape

• Wasila and Alex

A shape that is almost an ellipse.
Is_a: shape

• Wasila and Alex

I'm using the Oort GUI to do FYPO releases, and it fails to parse PATO when I point it to the PURL http://purl.obolibrary.org/obo/pato.owl . Oddly, if I download the file from the PURL, and point Oort to the resulting local copy, it parses without a hitch.

(I first noticed this last week, but thought it might be transient or a problem with my network connection at home. Now I'm also seeing it in the office, so here you go.)

This is what I get when I try the PURL:

2015-03-24 13:10:29 ERROR Internal error:
Problem parsing http://purl.obolibrary.org/obo/pato.owl
Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation.
The following parsers were tried:

1. RDFXMLParser
2. OWLXMLParser
3. OWLFunctionalSyntaxOWLParser
4. TurtleOntologyParser
5. OWLOBOParser
6. KRSS2OWLParser
7. ManchesterOWLSyntaxOntologyParser

Detailed logs:

Parser: RDFXMLParser
org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.

Parser: OWLXMLParser
org.xml.sax.SAXParseException: White spaces are required between publicId and systemId.

Parser: OWLFunctionalSyntaxOWLParser
Encountered " "< "" at line 1, column 1.
Was expecting:
"Ontology" ...
(Line 0)

Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:

Parser: OWLOBOParser
org.coode.owlapi.obo.parser.TokenMgrError: Lexical error at line 1, column 51. Encountered: "\n" (10), after : ""

Parser: KRSS2OWLParser
de.uulm.ecs.ai.owlapi.krssparser.ParseException: Encountered " ">" " "" at line 1, column 1.
Was expecting:

Parser: ManchesterOWLSyntaxOntologyParser
Encountered '' at line 1 column 1. Expected either 'Ontology:' or 'Prefix:' (Line 1)

def: A 3-D shape that is half of a sphere.
is_a: 3-D shape

• Wasila and Alex

Depends on #3

'tapered size'
synonym: gradient of size

def: A size quality inhering in an entity or set of entities in which size increases or decreases along the extent of the entity or set. For example, some species have teeth that are progressively smaller towards the posterior length of the jaw

'continuous with'
is_a: position

definition: A positional quality inhering in a bearer by virtue of the bearer possessing an uninterrupted or unbroken connection or spatial distribution relative to the position of another entity.

add to relational slim

New term request: 'single'
def: A quality inhering in a bearer by virtue of the bearer's being present as one entity.

is_a: 'present' PATO:0000467
Comment: Need to discuss this as possibly equivalent to PATO:0000070 'count' = 1.

Alex and Wasila (Phenoscape)

def: A diameter that remains constant throughout the extent of an entity.
is_a: diameter