Plant Trait Ontology Design Patterns

Note: Copied from: https://github.com/Planteome/ibp-crossproducts/wiki/Current-Status-of-Formal-Definitions-in-TO on 7-7-2016 and updated.

This page lists the design patterns currently used and under development in the TO. The goal is to unify the existing patterns, to validate them, in order to use them as templates for TermGenie.

“Simple” Morphological traits

 [‘physical object quality’ (PATO:0001241)] and inheres_in [PO|GO]

• Current EA: 'physical object quality' and ('inheres in' some 'plant anatomical entity')

** Currently does not encompass GO cellular components, how can these be included? ** Can we declare them to be 'plant anatomical entities (which they really are)??

e.g. chloroplast, cell wall etc

• eg: id: TO:0000017 name: plant morphology trait def: "A plant trait (TO:0000387) which is a morphological quality of a plant anatomical entity (PO:0025131) or a constituent cellular component (GO:0005575) contained therein."

• Note that here a decision was made to use PATO:0001241 ! physical object quality to encompass plant morphological traits, rather than the PATO morphology (PATO:0000051) which only covers size, shape or structure (not color). Note: PATO morphology does include "number_of"

has_number_of

 Was : ‘amount’ (PATO:0000070) and inheres_in [PO](already changed by Laurel)
 Now : ‘has number of’ (PATO:0001555) and inheres_in [PO]

• 'inheres_in' the thing you're counting, 'occurs_in' whatever larger entity

• eg: number of anthers in a stamen 'has number of' and ('occurs in' some stamen) and ('inheres in' some anther)

• See the discussion here: Feb_18th,_2016_Ontology_Working_Group_Meeting

absent- number of entities is zero: (about 12 instances)

• in PATO

Frequency (sensu a number per surface area)

 ‘amount’ (PATO:0000070) and inheres_in [PO] and part_of [PO]
 ‘has number of’ (PATO:0001555) and inheres_in [PO]

Angle

 ’orientation’ (PATO:0000133) and  inheres_in [PO]

Quality traits

  ‘quality trait’ (TO:0000597) and inheres_in [PO]

Composition, content, concentration

Content

 ‘amount’ (PATO:0000070) and inheres_in [CHEBI]
 ‘amount’ (PATO:0000070) and inheres_in [CHEBI] and occurs_in [PO]
 ‘composition’ (PATO:0000025)  and inheres_in [CHEBI]

Concentration

 ‘concentration of’ (PATO:0000033) and inheres_in [CHEBI]

Composition

 ‘composition’ (PATO:0000025)  and inheres_in [CHEBI]

Biotic and Abiotic stress

note that the diseases come from EO

Sensitivity and response

 ‘sensitivity toward’ (PATO:0000085) and inheres_in [CHEBI|EO]  and occurs_in ‘whole plant’ (PO:0000003)
 ‘sensitivity toward’ (PATO:0000085) and inheres_in [GO] (ex:TO:0000095)
 ‘sensitivity toward’ (PATO:0000085) and inheres_in [EO] (ex:TO:0000177)

Resistance

  ‘resistance to’ (PATO:0001046) and inheres_in [EO]  and occurs_in ‘whole plant’ (PO:0000003)

Stress trait

  [TO] and and inheres_in [GO] (ex:TO:0000237)

Tolerance

  ‘tolerant to’ (PATO:0000515) and inheres_in [EO] 

Ratio

 ‘proportionality to’ (PATO:0001470) and inheres_in [PO|GO|TO|CHEBI] relative_to [PO|GO|TO|CHEBI]
 ‘proportionality to’ (PATO:0001470) and has_dividend_entity [CHEBI] and has_divisor_entity [CHEBI] and has_ratio_quality ‘amount’ (PATO:0000070)
 ‘proportionality to’ (PATO:0001470) and inheres_in [PATO] and occurs_in [PO] and relative_to [PATO]
  (same as number 1: ‘proportionality to’ (PATO:0001470) and inheres_in [CHEBI] relative_to [TO])

Process related

Activity (process quality)

  ‘process quality’ (PATO:0001236) and inheres_in [GO process|GO molecular function]

Time

  ‘time’ (PATO:0000165) and inheres_in [TO|GO process]

Rate

  ‘rate’ (PATO:0000161) and inheres_in [GO process]

Growth and development traits

 Was: ‘quality’ (PATO:0000001) and inheres_in [GO process] (already changed by Laurel)
 Now: ‘process quality’ (PATO:0001236) and inheres_in [GO process]

cycle trait

 ‘process quality’ (PATO:0001236) and inheres_in [GO process|