Crop Ontology Pages

Introduction to The Crop Ontology

The Crop Ontology website consists of 5 sections:

1. Phenotypes and Traits Ontology
   1. crop specific trait ontologies. contains also the methods and the scales of measurement
   2. 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
2. Plant Anatomy & Development Ontology
   1. Banana anatomy
   2. Plant Ontology (PO)
   3. Wheat Plant Anatomy and Development Ontology: Defines growth stages of wheat
3. General Germplasm Ontology
   1. FAO/IPGRI Multi-Crop Passport Descriptor ontology : Adapted from FAO/Bioversity Multi-Crop Passport Descriptors, 2004
   2. GCP Germplasm ontology: General germplasm descriptors
   3. ICIS germplasm methods ontology: adaptation of the ICIS germplasm methods table
4. Location and Environmental Ontology
   1. Country and Location ontology: Official ISO 3166-1 alpha-2, alpha-3 and numeric country codes
   2. Crop Research ontology: Describes experimental design, environmental conditions and methods associated with the crop study/experiment/trail and their evaluation
5. Structural and Functional Genomic Ontology
   1. Bioversity molecular markers ontology: Adapted from Descriptors for Genetic Markers Technologies (2004)

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