Sept 22nd, 2015- Ontology Working Group Meeting

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Agenda

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

  • In attendance: LC, AM, EA, MAL, PJ, CM,

1. Ontology Development Meeting in Corvallis early November-

Discussion of scheduling and what would be covered.


Please see the notes here: Planteome_Curator_workshop_Fall_2015

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).

> 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.

e.g. Vertebrate Trait Ontology: [1] -- “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: [2] -- “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)



Next meeting: Sept 29th

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