Crop Ontology Pages

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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