Crop Ontology Pages
Introduction to The Crop Ontology
The Crop Ontology website consists of 5 sections:
- Phenotypes and Traits Ontology
- Plant Anatomy & Development Ontology
- General Germplasm Ontology
- Location and Environmental Ontology
- Structural and Functional Genomic Ontology
There are 3 ways of creating “ontologies” on the Crop Ontology website
- 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)
- Upload an OBO file. They can be used to create ontologies in any of the 5 sections
- 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 |