Crop Ontology Pages: Difference between revisions

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=List of Crops and IDs=
=List of Crops and IDs=
According to the project timeline, the crops that will be linked to the reference ontologies are:
According to the project timeline, the crops that will be linked to the reference ontologies are:
{| border="1" class="sortable"
|-
! Crops
! Prefixes
|-
| Maize
| CO_322
|-
| Rice
| 320
|-
| Wheat
| 321 (traits) and 121 (anatomy)
|-
| Cassava
| 334
|-
| Cowpea
| 340
|-
| Chickpea
| 338
|-
| Potato
| 330
|-
| Sorghum
| 324
|-
| Soybean
| 336
|-
| Barley
| 323
|-
| Common Bean
| 335
|-
| Groundnut
| 337
|-
| Pearl Millet
| 327
|-
| Pigeon Pea
| 341
|-
| Musa
| 325 (traits) and 125 (anatomy)
|-
| Sweet Potato
| 331
|-
| Yam
| 333
|-
| Other crops ?????
|
|}
Note: The trait ontologies start with 3XX whereas the anatomy ontologies start with 1XX.
==Trait Template==
==Structure of the Trait Template V4==
Currently, the Trait Template V4 is uploaded onto the CO website.
The Trait Template is used to gather information on traits along with their methods and scales of measurement.
An (unique) ID is created by the system for each trait, method and scale (several IDs are created when the scale is categorical).
** But for now, if two methods or scales are the same (e.g. seed length and leaf length are measured in centimeters), different IDs are created, which is far from being ideal or even ontologically correct.
===Trait Template V4 columns: ===
* IBFieldbook
* Name of submitting scientist
* Institution
* Language of submission (only in ISO 2 letter codes)
* Date of submission
* Crop
For each trait, some meta-information is added (5 first columns)
* Name of Trait
* Abbreviated name
* Synonyms (separate by commas)
* Trait ID for modification, Blank for New
* Description of Trait
* How is this trait routinely used?
* Trait Class
* Method ID for modification, Blank for new
* Name of Method
* Describe how measured (method)
* Growth Stage
* Bibliographic Reference
* Comments
* Scale ID for modification, Blank for new
*Type of Measure (Continuous, Discrete or Categorical)
*For Continuous: units of measurement
*For Continuous: reporting units (if different from measurement)
*For Continuous: minimum
*For Continuous: maximum
*For Discrete: Name of scale or units of measurement
*For Categorical: Name of rating scale
*For Categorical: Class 1 - value = meaning
*For Categorical: Class 2 - value = meaning
*For Categorical: Class 3 - value = meaning
*For Categorical: Class 4 - value = meaning
*For Categorical: Class 5 - value = meaning
==Structure of the Trait Template V5 (Léo is still working on it with Julian Pietragalla from CIMMYT) ==
Note the structure can  still evolve. Template V5 is still a draft
{| {{table}}
{| {{table}}
| align="center" style="background:#f0f0f0;"|'''Column'''
| align="center" style="background:#f0f0f0;"|'''CROPS'''
| align="center" style="background:#f0f0f0;"|'''Description'''
| align="center" style="background:#f0f0f0;"|'''Crop Ids'''
|-
| align="center" style="background:#f0f0f0;"|'''Prefixes'''
| Curation||Comments for curation
| align="center" style="background:#f0f0f0;"|'''Map to prefixes recommended by Chris'''
|-
| Scientist||Name of scientist submitting variable
|-
| Institution||Name of institution submitting variable
|-
| Language||2 letter ISO code for language in which variable data is submitted
|-
| Date||Date the variable was submitted
|-
| Crop||Crop name
|-
| Trait ID||Term ID for trait as generated by the system. Use an existing ID to modify data for that trait. If left blank the system will automatically generate a new ID.
|-
| Trait||Trait name (property)
|-
| Entity||A trait must follow the convention "Trait" = "Entity" + "Attribute", eg for "grain colour", attribute = "grain"
|-
| Attribute||eg for "grain colour", entity = "colour"
|-
| Trait synonyms||Acronym/abbreviated name.
|-
| Trait abbreviation||Recommended trait name abbreviation
|-
| Trait abbreviation synonyms||Other trait name abbreviations
|-
| Trait description||Textual description of trait.
|-
| Trait class||General class to which trait belongs.
|-
| Trait status||recommended, standard, obsolete,
|-
| Trait Xref||Cross reference of the trait e.g., Xref to TO
|-
| Method ID|| Term ID for method as generated by the system. Use an existing ID to modify data for that method. If left blank the system will automatically generate a new ID.
|-
| Method|| (Short) method name.
|-
| Method description|| Textual description of method.
|-
|-
| Formula|| For computational methods, express the formula using variable names
| Maize||322||CO_322||IBPCO:322xxxx
|-
|-
| Method class|| Measurement, Counting, Rating, Estimation, Scoring, Computation
| Rice||320||CO_320||IBPCO:320xxxx
|-
|-
| Method reference|| Biobliographical reference describing method.
| Wheat||321||CO_321||IBPCO:321xxxx
|-
|-
| Scale id||Term ID for scale as generated by the system. Use an existing ID to modify data for that scale. If left blank the system will automatically generate a new ID.
| Cassava||334||CO_334||IBPCO:334xxxx
|-
|-
| Scale name||[Guidelines to be defined for naming the scale]
| Cowpea||340||CO_340||IBPCO:340xxxx
|-
|-
| Scale class||Numerical, Nominal, Ordinal, Text, Code, Time, Duration
| Chickpea||338||CO_338||IBPCO:338xxxx
|-
|-
| Decimal places||For numerical, number of decimal places of report
| Potato||330||CO_330||IBPCO:330xxxx
|-
|-
| Lower limit||Minimum value (used for validation) for numerical and date
| Sorghum||324||CO_324||IBPCO:324xxxx
|-
|-
| Upper limit||Maximum value (used for validation).
| Soybean||336||CO_336||IBPCO:336xxxx
|-
|-
| Scale Xref||Cross reference to the scale, eg to a unit repository like "improved UO"
| Barley||323||CO_323||IBPCO:323xxxx
|-
|-
| Categorie i||Class value and meaning of the category "i" with "i" a positive integer
| Common Bean||335||CO_335||IBPCO:335xxxx
|-
|-
| Variable name||Name of the variable, it follows a naming convention described in guidelines
| Groundnut||337||CO_337||IBPCO:337xxxx
|-
|-
| Variable synonyms||Other names given to this variable
| Pearl millet||327||CO_327||IBPCO:327xxxx
|-
|-
| Context of use||Indication of how trait is routinely used. If several context of use, separate with ","
| Pigeon Pea||341||CO_341||IBPCO:341xxxx
|-
|-
| Growth stage|| Growthstage at which measurement is made. Follow standards. If variable used in time series, leave blank
| Musa||325 (traits) and 125 (anatomy)||CO_325 and CO_125||IBPCO:325xxxx and IBPCO:125xxxx
|-
|-
| Variable status||Obsolete, Legacy, Standard // institution1, institution2, Recommended, Experimental, Revision
| Sweet Potato||331||CO_331||IBPCO:331xxxx
|-
|-
| CV Term ID||ID generated by BMS
| Yam||333||CO_333||IBPCO:333xxxx
|-
|-
| Variable Xref||
| Other crops ???||||||
|}
|}


Revision as of 08:25, 22 June 2015

Introduction to The Crop Ontology

The Crop Ontology website consists of 5 sections:

  1. Phenotypes and Traits Ontology
  2. Plant Anatomy & Development Ontology
  3. General Germplasm Ontology
  4. Location and Environmental Ontology
  5. Structural and Functional Genomic Ontology

There are 3 ways of creating “ontologies” on the Crop Ontology website

  1. Upload a Trait Dictionary (TD) in Excel. (Note, the TD is only used to store and load information about traits, thus it cannot be used for uploading ontologies that would belong to the other categories)
  2. Upload an OBO file. They can be used to create ontologies in any of the 5 sections
  3. Ontologies can be built from scratch using the website dedicated interface. Are there any examples of these?

Storage and Downloading

  • Once the files are uploaded or some terms are submitted using the web interface, the data are stored in a noSQL database (Google App Engine Datastore).
  • The ontologies can be downloaded in various formats: CSV, OBO, SKOS and JSON. The structures of the different formats are described in the following sections.
  • Note that because there is no exact mapping between the different formats some compromises has been made. Not all the information is available in the different formats.

List of Crops and IDs

According to the project timeline, the crops that will be linked to the reference ontologies are:

CROPS Crop Ids Prefixes Map to prefixes recommended by Chris
Maize 322 CO_322 IBPCO:322xxxx
Rice 320 CO_320 IBPCO:320xxxx
Wheat 321 CO_321 IBPCO:321xxxx
Cassava 334 CO_334 IBPCO:334xxxx
Cowpea 340 CO_340 IBPCO:340xxxx
Chickpea 338 CO_338 IBPCO:338xxxx
Potato 330 CO_330 IBPCO:330xxxx
Sorghum 324 CO_324 IBPCO:324xxxx
Soybean 336 CO_336 IBPCO:336xxxx
Barley 323 CO_323 IBPCO:323xxxx
Common Bean 335 CO_335 IBPCO:335xxxx
Groundnut 337 CO_337 IBPCO:337xxxx
Pearl millet 327 CO_327 IBPCO:327xxxx
Pigeon Pea 341 CO_341 IBPCO:341xxxx
Musa 325 (traits) and 125 (anatomy) CO_325 and CO_125 IBPCO:325xxxx and IBPCO:125xxxx
Sweet Potato 331 CO_331 IBPCO:331xxxx
Yam 333 CO_333 IBPCO:333xxxx
Other crops ???

OBO files

OBO file structure

OBO files are created using the obo2owl library (which should sound familiar ;-)).

The main issue with the Trait Template is that because different IDs can be created for the same “thing” (e.g. the term “cm” will get different IDs if different traits are measured in cm), different obo terms can have the same name (but different IDs).

That is a problem when our users tried to import the OBO files in a Chado database.

  • Consequently, I created a little script that created OBO files where all the names are unique in a given namespace. The script has not be inserted in the website yet but it will be soon. Example of an OBO files on Github. (MAL)
TD column OBO element
Crop Used for setting up the namespace
Name of Trait name
Trait ID for modification, Blank for New Term + id
Description of Trait definition
Trait Class Term +id + name + is-a
Language of submission (only in ISO 2 letter codes) We have only English OBO files.
Name of submitting scientist created_by
Institution Not used
Date of submission creation_date
Abbreviated name synonym [EXACT]
Synonyms (separate by commas) synonym [EXACT]
How is this trait routinely used Not used
Name of method name
Method ID for modification, Blank for New Term + id + method_of
Describe how measured (method definition
Bibliographic Reference xref
Growth Stage Not used
Comments Not used
Scale ID for modification, Blank for New Term + id + scale_of
Type of Measure (Continuous, Discrete or Categorical Not used
For Continuous: units of measurement name
For Discrete: Name of scale or units of measurement name
For Categorical: Name of rating scale name
For Categorical: Class 1 - value = meaning Term + name + is-a
For Categorical: Class 2 - value = meaning Term + name + is-a
For Categorical: Class 3 - value = meaning Term + name + is-a
For Categorical: Class 4 - value = meaning Term + name + is-a


SKOS files

SKOS file structure

TD column SKOS
Crop Used for setting up the namespace
Name of Trait skos:prefLabel
Trait ID for modification, Blank for New Local Name (URI) + rdf: type skos:concept
Description of Trait skos:definition
Trait Class rdf:type Skos:Concept + skos:broader
Language of submission (only in ISO 2 letter codes) xml:lang of the literals. SKOS files are multilingual (if we have the info)
Name of submitting scientist foaf:Person (not set so far but will be soon)
Institution foaf:Organization (not set so far but will be soon)
Date of submission dc:date (not set so far but will be soon)
Abbreviated name skos:altLabel
Synonyms (separate by commas) skos:altLabel
How is this trait routinely used Not used
Name of method skos:prefLabel
Method ID for modification, Blank for New Local Name (URI) + rdf: type skos:concept
Describe how measured (method skos:definition
Bibliographic Reference Not set (dc: bibliographicCitation?)
Growth Stage skos:related (not set so far)
Comments skos:editorialNote
Scale ID for modification, Blank for New Local Name (URI) + rdf: type skos:concept
Type of Measure (Continuous, Discrete or Categorical Not used
For Continuous: units of measurement skos:prefLabel
For Discrete: Name of scale or units of measurement skos:prefLabel
For Categorical: Name of rating scale skos:prefLabel
For Categorical: Class 1 - value = meaning Local Name (URI) + rdf: type skos:concept
For Categorical: Class 2 - value = meaning Local Name (URI) + rdf: type skos:concept
For Categorical: Class 3 - value = meaning Local Name (URI) + rdf: type skos:concept
For Categorical: Class 4 - value = meaning Local Name (URI) + rdf: type skos:concept
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