Data sections

An observation log record bridges a sampling log (a field collection event) and a provision (a laboratory protocol). For the Agrolab wetlab data, each entry records which sampling log’s samples were analysed, under which protocol, and how they were handled in the lab. Individual observations are later linked to these log records.

Prerequisites

Notebook cell

In load_ai4sh_wetlab_data.ipynb, the Manage Agrolab observation log cell runs:

process_file = 'import_data/wetlab/agrolab/manage_process/manage_observation_log.json'

structured_process_D, scheme_params_D = Initiate_process(notebook_path, scheme_file, process_file)

if structured_process_D is not None:
    Run_process(structured_process_D, scheme_params_D)

Manage process file

Path: ./ai4sh/import_data/wetlab/agrolab/manage_process/manage_observation_log.json

{
  "process": [
    {
      "root_process_id": "import_tabular_data",
      "process": "manage_observation_log",
      "delete": false,
      "overwrite": false,
      "parameters": {
        "sampling_log_id__sampling_log_name": "ai4sh_dk_foulum_2024",
        "provision_id__provision_name": "ai4sh-agrolab",
        "contact_name": "thomas gumbricht",
        "contact_email": "thomas.gumbricht@natgeo.su.se",
        "name": "auto",
        "preparation_id__preparation_name": "ds2",
        "preservation_id__preservation_name": "ds2",
        "storage_id__storage_name": "amb",
        "transportation_id__transportation_name": "none",
        "laboratory": true
      }
    }
  ]
}

The example file contains 12 entries — one per field site sampling log.

Parameters

Parameter Description
sampling_log_id__sampling_log_name FK lookup: parent sampling log by name
provision_id__provision_name FK lookup: Agrolab provision record (defines the indicators measured)
contact_name Name of the responsible person
contact_email Email of the responsible person
name Log name — "auto" generates <sampling_log_name>@<provision_name>
preparation_id__preparation_name FK lookup: sample preparation method used (e.g. ds2 = dried and sieved to 2 mm)
preservation_id__preservation_name FK lookup: preservation method
storage_id__storage_name FK lookup: storage condition (e.g. amb = ambient)
transportation_id__transportation_name FK lookup: transportation method
laboratory Boolean — true for laboratory-based analyses

Auto-naming

When name is set to "auto", the framework generates the observation log name as <sampling_log_name>@<provision_name>. For example, the entry above produces the name ai4sh_dk_foulum_2024@ai4sh-agrolab. This name is then used as the FK reference in the observation manage file via observation_log_id__observation_log_name.

Next step

Proceed to Manage Agrolab observation.

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