Biological Metadata

Biological metadata are informative of the biological object and its growth conditions.

Definitions

Here is a list of biological metadata and their definition:

• species: the species of the biological object analysed, eg: "Arabidopsis thaliana";
• seed stock: an identifier of the seed stock used, eg: "Col-0", "186.AV.L1", ...;
• plant id: an identifier for the plant, eg: "GT1";
• growth environment: , eg: "Lyon - Indoor";
• growth conditions: growth condition used, eg: "LD", "SD", "LD+SD";
• treatment: specific treatment applied, if any, eg: "Auxin 1mM";
• DAG: Days After Germination or age of the plant in days, eg: 40;
• sample: part of the plant used, if any, eg: "main stem";
• experiment id: an identifier for the experiment, eg: "dry plant";
• dataset id: the Omero dataset identifier for the biological dataset, eg: 12;

Configuration

Todo

How is it defined in a TOML configuration file ?

Database location

Located in metadata/metadata.json and found under the object top level section, it contains biologically relevant information such as the studied species, its age and growth conditions. This information is not restricted in its format but should contain a minimal set of entries.

Todo

Defines the minimal set of entries! Use the MIAPPE standard?

JSON example

Example of a metadata/metadata.json file for biological metadata:

    "object": {
        "age": "62d",
        "culture": "LD",
        "environment": "Lyon indoor",
        "experiment_id": "living plant",
        "object": "plant",
        "plant_id": "Col0_26_10_2018_B",
        "sample": "main stem",
        "species": "Arabidopsis thaliana",
        "stock": "186AV.L1",
        "treatment": "none"
    }