README.md 3.22 KB
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Copyright (c) 2015, INRA  
All rights reserved.  
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Each ontology have its own license and owner(s).

This repostiory stores the phenotyping ontologies developped by INRA and its Partner.

# Repository file

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The `ontology-repository.json` file list all the ontologies available with the BreedingAPI/CropOntology JSON format. You can specify metadata on every observation variable ontologies like specified in the [Breeding API specifications](https://github.com/plantbreeding/API/blob/master/Specification/ObservationVariables/README.md). The `ontologyName` and the `ontologyDbId` fields in the repository must perfeclty match the same fields on the variables of that ontology in the JSON file.
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## Updating ontologies

When updating an ontology, please update the ontology version in the repository file. [Semantic versioning](http://semver.org/) is recommended.

# Structure

```
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├── Beet
├── Brassica
├── Maize
├── Melon
├── Miscanthus
├── ProteinCrop
├── Rice
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├── Tree
├── Vitis
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├── Walnut
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├── Wheat
├── Environment
├── Others
├── ontology-repository.json
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├── README.md
└── Tools
    ├── archived-DB_Export.tar.gz
    ├── MANAGE_ONTOLOGY
    └── manage_ontology.properties

```

One folder per species group.
> Note: other species groups are likely to be added in the future (example: Solenaceae).
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Each folder contains at least the ontology in the CropOntology TDV5 format (excel) and JSON format. It can also contains the ontology in other formats (CSV, Adonis), protocol files, a readme file, a licence file, archives or working directories...
```
├── Tree
│   ├── Adonis_WoodyPlantOntology.zip
│   ├── archive
│   ├── CO_357-Woody Plant Ontology.json
│   ├── T4F_D21_submitted.pdf
│   ├── WoodyPlantOntology.xls
│   └── work
└── Vitis
    ├── archive
    ├── CO_356-Vitis inra ontology.json
    ├── LICENSE
    ├── Liste_des_descripteus_OIV_pour_les_varietes_et_especes_de_vitis__2e_edition_5langues_04_2008.pdf
    ├── README_ontology-vitis.md
    ├── Vitis-inra-ontology.csv
    └── Vitis-inra-ontology.xls
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```

The `Others` folder contains automatically generated ontologies from the GnpIS database. The ontologies in this folder will be moved to a dedicated folder once they are curated in the CropOntology TVD5 format.

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The `ontology-repository.json` file list all the ontologies available.

The `Tools` folder contains scripts to manage ontologies, in particular the talend `MANAGE_ONTOLOGY` who allows you to check then transform a CropOntology TDV5 format in JSON and Adonis format. 

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## Naming recommendations

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For each species group there can be several ontologies. For instance, Wheat will have INRA Phenotyping Ontology and Small Grain Cereal Network Ontology.
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In this case, each ontology has a group of file with the same name pattern :
- `SpeciesGroup-<ProjectOrComunity>-ontology.xls`
- `SpeciesGroup-<ProjectOrComunity>-ontology.json`
- `SpeciesGroup-<ProjectOrComunity>-ontology.adonis.xml`
- `SpeciesGroup-<ProjectOrComunity>-ontology.owl`

Example :
- `Wheat-inra-ontology.xls`
- `Wheat-small-grain-network-ontology.xls`