Crop Ontology Pages
From Planteome.org
Contents
Introduction to The Crop Ontology
The Crop Ontology website consists of 5 sections:
- Phenotypes and Traits Ontology
- crop specific trait ontologies. contains also the methods and the scales of measurement
- crop list: Maize, Rice, Wheat, Cassava, Cowpea, Chickpea, Potato, Sorghum, Soybean, Barley, Common Bean, Groundnut, Pearl millet, Pigeon Pea, Musa, Sweet Potato, Yam, Oat, Vitis
- Plant Anatomy & Development Ontology
- Banana anatomy
- Plant Ontology (PO)
- Wheat Plant Anatomy and Development Ontology: Defines growth stages of wheat
- General Germplasm Ontology
- FAO/IPGRI Multi-Crop Passport Descriptor ontology : Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, 2004
- GCP Germplasm ontology: General germplasm descriptors
- ICIS germplasm methods ontology: adaptation of the ICIS germplasm methods table
- Location and Environmental Ontology
- Country and Location ontology: Official ISO 3166-1 alpha-2, alpha-3 and numeric country codes
- Crop Research ontology: Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation
- Structural and Functional Genomic Ontology
- Bioversity molecular markers ontology: Adapted from Descriptors for Genetic Markers Technologies (2004)
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 ??? |
Trait Dictionary V5
Mapping TD to OBO
| TDv5 Elements | Description | Stored in CO website | OBO element |
| Curation | Comments for curation | NO | NO |
| 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. | Yes | Ontology ID (trait namespace) |
| Trait | Trait name (property) | Yes | name (trait namespace) |
| Entity | A trait must follow the convention "Trait" = "Entity" + "Attribute", eg for "grain colour", attribute = "grain" | Yes | Crossproduct to PO |
| Attribute | eg for "grain colour", entity = "colour" | Yes | Crossproduct to PATO |
| Trait synonyms | Acronym/abbreviated name. | Yes | synonym (trait namespace) |
| Trait abbreviation | Trait name abbreviation. If several abbrevations, separate with comas. The recommended abbreviation must be the first in the list. | Yes | synonym (trait namespace) |
| Trait description | Textual description of trait. | Yes | def (trait namespace) |
| Trait class | General class to which trait belongs. Concensus trait classes are morphological, phenological, agronomical, physiological, abiotic stress, biotic stress, biochemical, quality traits and fertility traits | Yes | is_a |
| Trait status | Status of the trait. Trait can be tagged as recommended, standard for , deprecated, legacy | Yes | is_obsolete |
| Trait Xref | Cross reference of the trait e.g., Xref to TO | Yes | xref |
| 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. | Yes | id |
| Method | (Short) method name. | Yes | name (method namespace) |
| Method description | Textual description of method. | Yes | def (method namespace) |
| Formula | For computational methods, express the formula using variable names | Yes | NO |
| Method class | Measurement, Counting, Estimation, Computation | Yes | NO |
| Method reference | Biobliographical reference describing method. | Yes | Xref |
| 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. | Yes | id |
| Scale name | [Guidelines to be defined for naming the scale] | Yes | name (scale namespace) |
| Scale class | Numerical, Nominal, Ordinal, Text, Code, Time, Duration | Yes | NO |
| Decimal places | For numerical, number of decimal places of report | Yes | NO |
| Lower limit | Minimum value (used for validation) for numerical and date | Yes | NO |
| Upper limit | Maximum value (used for validation). | Yes | NO |
| Scale Xref | Cross reference to the scale, eg to a unit repository like "improved UO" | Yes | Xref |
| Category n | If the scale is categorical, class value and meaning of the n-th category. It possible to create as many category columns as necessary, as long as they are called "Category " | Yes | Yes |
| Variable 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. | Yes | Ontology ID (variable namespace) |
| Variable name (abbreviated) | Name of the variable following the convetion __. Variable name must be unique. | Yes | synonym (variable namespace) |
| Variable synonyms | Other names given to this variable | Yes | synonym (variable namespace) |
| Context of use | Indication of how trait is routinely used. If several context of use, separate with "," | Yes | NO |
| Growth stage | Growthstage at which measurement is made. Follow standards. If variable used in time series, leave blank | Yes | NO |
| Variable status | Obsolete, Legacy, Standard for , Recommended, Experimental, Revision | Yes | is_obsolete |
| CV Term ID | ID generated by BMS | Yes | NO |
| Variable Xref | Yes | Xref | |
| Scientist | Name of scientist submitting variable. | Yes | NO |
| Institution | Name of institution submitting variable | Yes | NO |
| Language | 2 letter ISO code for language in which variable data is submitted. | Yes | NO |
| Date | Date the variable was submitted. | Yes | NO |
| Crop | Crop name. | Yes | Yes |
| Full variable name | customized name. For new variables -> concatenation of by in | ||
| variable definition | T: /n M: /n S: |
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 |
