View source for Sept 15th, 2015- Ontology Working Group Meeting

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''

Connection details:  Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261
 
* In attendance: LC, MAL, AM, PJ, BS, CM

* Link to recording- Video: [[File:Ontology WG 9-15-15.mp4|thumb|Ontology WG 9-15-15 video]]
* Link to recording- Audio: [[File:Ontology WG 9-15-15 audio.m4a|thumb|Ontology WG 9-15-15 audio]] 

=Agenda=
== 1. Upcoming Plant Ontology Release #21 ==
- Many changes and updates to the PO which will accompany the PSDS paper submission
* Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
* PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN- 
* Timeline- within the next 2 weeks
* For more information: [http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]

* New association data developed from the [http://wiki.plantontology.org/index.php/Plant_Pheontype_Pilot_Project_2015] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

==2. Planteome.org Update:==
* Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release. 
* This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
* We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.


* New association data developed from MaizeGDB (Mary Schaeffer)
* Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to  explore root development"
** [https://dl.sciencesocieties.org/publications/tpg/first-look The Plant Genome doi:10.3835/plantgenome2015.04.0025]
** Accepted paper, posted 08/07/2015. 
** Update of the Nimblegen Microarray data - more tissues, not so much background noise

== 3.  Plant Trait Ontology: == 
Questions from Barry about how to define the traits:

===Anatomy and Morphology traits===
'''> Are there any traits which are not anatomy and morphology traits?'''

''There are 8 different branches in the TO, anatomy and morphology trait is just one.''

[[File:TO-top level.png|TO-top level.png.jpg]]

''* Note that there is a still a class "other miscellaneous traits" which we are planning to get rid of soon. ''

'''> Is there a definition of 'anatomy trait' and of  'morphology trait'?'''
* LC: My understanding of the meaning of anatomy and morphology in botany are as follows: the anatomy is the internal structure and the morphology is the external structure.  This is consistent with the definitions of plant anatomy and morphology in common use: 

* '''From Evert, RF and Eichhorn, SE (2006). Esau's Plant Anatomy: Meristems, Cells, And Tissues Of The Plant Body: Their Structure, Function, And Development''', 3rd Edition. Wiley-Liss. ISBN:0471738433: "Anatomy is the study of the internal structure of organism, morphology is the study of their external structure.  

* Morphology (biology): Morphology is a branch of biology dealing with the study of the form and structure of organisms and their specific structural features.[http://www.oxforddictionaries.com].  This includes aspects of the outward appearance (shape, structure, colour, pattern,size), i.e., external morphology (eidonomy) as well as the form and structure of the internal parts like bones and organs, i.e., internal morphology or anatomy. 


* morphology (PATO:0000051): A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.

'''> Are they logically disjoint? '''
* Based on some definitions, they are logically disjoint, but others define morphology to encompass both internal and external features.

'''> The term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?'''
* ''The class is designed to be inclusive- covering physical traits that are either internal (anatomy) or external (morphology), so 'anatomy trait or morphology trait' would perhaps be more correct. Even better would be to call them plant''

====Test classification of some of the subclasses of PSA+M traits  as either anatomy or morphology traits:====

===== Examples of morphological (external) trait classes =====
* awn length, width, thickness, color, presence (?)
* leaf margin serrated
* seedling hypocotyl size
* axillary bud shape
* plant cell shape, size, length
* embryo shape, shootless embryo
* flower or floret color, type, diameter, length, number, shape, etc
* chasmogamous flower, cleistogamus flower
* ear (infructescence) circumference, aspect, color, length, weight, position shape, diameter, circumference
* inflorescence (incl. panicle, spikelet, tassel) size, width, branching, color, density, depth, diameter, exsertion, number, presence, shape, texture, type, waxiness, weight, etc
* axillary bud number, shape, size, prominence
* leaf attitude, color, weight, cover, volume, flexibility, height, number, pubescence, adherence, shape, size, rolling, phyllotaxy, area, nitrogen content, pigment content, gloss, drying, stomatal frequency, temperature, necrosis, 
* leaf lamina area, color, length, splitting, width, pubescence, joint bending, etc

===== Examples of anatomy (internal) trait classes: =====
* leaf vein color, size
* leaf midvein thickness

''Thus I feel that we could change the name of this class to "plant morphological trait", which would encompass both the internal and external structure, appearance and form. '''

* Current term name def'n: '''anatomy and morphology trait (TO:0000017): A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''
** Comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

* ''This definition will need to be revised if we keep this name for the class. It could be rewritten with a definition of what the  

* Proposed revised name and def'n: plant morphological trait (TO:0000017): A plant trait (TO:0000387) which is "associated with"  physical traits that are either internal (anatomy) or external (morphology) of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.'''

cell wall (GO:0005618); chloroplast (GO:0009507)

== Objection to using: 'associated with' ==
> BS: (a) it is vague (b) it will block reasoning 
''I agree that it is vague and would prefer a more precise statement, although textual definition will not block reasoning.''

Example anatomy and morphology trait classes: 
* stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
* stem size (TO:0000954): A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).

stem size (TO:0000954): A stem morphological trait (TO:0000361) which is the size (PATO:0000117) of a stem (PO:0009047).

was: A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047). 


> Suggestions: 
* "stem number =def. a trait of a plant which is the number of stems of the plant"    and so on for the other cases
''the trait is not the number of stems on the plant, but it describes the number of stems.  This is not in the genus-differentia format ''

''stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which '''is''' the number of stems (PO:0009047) in the shoot system of a plant.''

* Examples from other from [http://obofoundry.github.io/ OBO_Foundry_Ontologies] that concern traits: 

e.g. Vertebrate Trait Ontology: [http://www.berkeleybop.org/ontologies/vt.owl] -- “related to”
* body size trait (VT:0100005): Any measurable or observable characteristic '''related to''' the overall physical magnitude of an organism.
* body temperature trait (VT:0005535): Any measurable or observable characteristic '''related to''' the level of heat maintained by a living being.

e.g. Animal Trait Ontology:
[http://147.99.159.184:8080/webprotege/#ATOL] -- “related to”

How are traits defined using formal relations? 

* name: has_quality  (id: RO:0000086)
* def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" 
* property_value: IAO:0000112 "this apple has quality this red color" xsd:string
* property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the 
* bearer does not exist." xsd:string
* property_value: IAO:0000118 "has_quality" xsd:string

Possible solution using relations from RO:

ear shape (TO:0000964):  An infructescence anatomy or morphology trait (TO:0000920) 
an ear infructescence (PO:0025597) has_quality shape.

e.g.

inheres_in
 
Example from BATTO:  http://www.ontobee.org/browser/index.php?o=oba
    
[Term]
id: TO:0000431 ! ear length
intersection_of: BATTO:0000001 ! biological attribute
intersection_of: affects_quality PATO:0000122 ! length
intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

== 4.  Update from Bioversity: == 
* Progress on mapping the CO vocabularies and creating cross products
On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions
 
Plant Trait definition (what I understand of what is a trait): A plant trait is a quality of Process or a quality of a plant Entity.

Plant Trait definition (Manchester syntax): supposed to be the translation of the above definition (what do you think?)
   Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))
Intersection of a quality and either a Process or a Plant Entity. 

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color. Does this sound good?

Note: I didn't find the URIs of the BFO properties

=== Examples ===
'''Seed Color'''
   color and ('inheres in' some seed)
Intersection of Color (specifically dependent continuant) and a specifically dependent continuant (indeed, the domain of inheres_in is specifically dependent continuant) that exists only if seed exists.

'''Aluminium Tolerance'''
   'tolerant to' and ('inheres in' some ('aluminum nutrient regimen' and 'whole plant'))
Intersection of Tolerant to and a specifically dependent continuant that depends on both the presence of a plant and an aluminum nutrient regimen

'''Amylose content (of the tuberous root)'''
   composition and ('inheres in' some (amylose and ('continuant part of' some 'tuberous root')))
Intersection of Composition and a specifically dependent continuant that exists only if ( the intersection of amylose and a continuant (which is a part of a tuberous root)  )exists.

'''Flowering Time'''
   time and ('s depends on' some (flowering and ('has participant' some 'flowering stage')))
Intersection of Time and a specifically dependent continuant that exists only if the intersection of (the Process Flowering and A Process that exists only the Flowering stage exists) exists

=== From OBA: ===

Plant trait:
   'biological attribute' and ('occurs in' some 'whole plant') and ('has quality' some quality)
Intersection of a biological attribute and a process (domain of occurs in a process) and an independent continuant (I assume that the domain of has quality is an independent continuant)

seed color
   'biological attribute' and ('has quality' some color) and ('attribute of' some 'seed coat')
Intersection of an Biological Attribute and an independent continuant (I assume that the domain of has quality is an independent continuant, so something that have a color) and something that have an attribute (attribute of is not described, and I am not able to guess the domain of the property)

== 5. Proposed: Ontology Development Meeting in Corvallis early November- == 
Please see the notes here: [[Planteome_Curator_workshop_Fall_2015]]

== 6. Updates on the ICBO meeting ==

==Next meeting: [[Sept_22nd,_2015-_Ontology_Working_Group_Meeting]] ==