cidgoh / DataHarmonizer

A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions from the National Microbiome Data Collaborative (NMDC), the LinkML development team, and others.
MIT License
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display linkml names but export linkml titles for NMDC #266

Closed turbomam closed 2 years ago

turbomam commented 2 years ago

see https://github.com/microbiomedata/DataHarmonizer/tree/master/docs/template/soil_emsl_jgi_mg

esp https://github.com/microbiomedata/DataHarmonizer/blob/master/docs/template/soil_emsl_jgi_mg/data.js

specifically

  {
    "fieldName": "Metadata- MIxS Required",
    "children": [
      {
        "fieldName": "broad-scale environmental context",
        "capitalize": "",
        "ontology_id": "MIXS:0000012",
        "datatype": "select",
        "source": "",
        "dataStatus": null,
        "xs:minInclusive": "",
        "xs:maxInclusive": "",
        "requirement": "required",
        "description": "Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO\u2019s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS",
        "guidance": "Pattern hint: {termLabel} {[termID]}",
        "examples": "oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean",
        "exportField": {
          "soil_emsl_jgi_mg": [
            {
              "field": "env_broad_scale"
            }
          ]
      }
}
turbomam commented 2 years ago

NMDC doesn't use the export mechanism anymore, so I will close this issue.

I've had DH configurations that displayed and exported labels in the way I requested above, but I always had a hard time recreating that on fresh setups. So maybe it just needs better documentation?