Knowledge-Graph-Hub / kg-microbe

https://knowledge-graph-hub.github.io/kg-microbe/index.html
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ingest BacDive "sample type" data #192

Open realmarcin opened 3 months ago

realmarcin commented 3 months ago

This is somewhat complex in that there is a wide variety of terms with different specificities. Some look like titles of a study and will fail NER. Our first pass here is NER against ENVO and the bacdive CAT environment hierarchy.

    "Isolation, sampling and environmental information": {
        "isolation": {
            "@ref": 21959,
            "sample type": "mangrove soil",

These are the most frequent terms:

3040 soil 2724 soil with plant residues 1390 Soil 1261 Human blood 562 Human 519 Human feces 342 Human urine 322 marine sediment 318 seawater 232 Industry 192 From soil 188 spacecraft-associated clean room class ISO 8, Herschel Space Observatory 187 Human sputum 181 sediment 175 leaf of Arabidopsis thaliana, wild-type genotype 166 Seawater 165 human faeces 163 forest soil 155 Human wound 152 roots of Arabidopsis thaliana ecotype Shakdara (Sha) 121 Environment,industry 115 soil with lime pebbles and plant residues 114 hot spring 112 soil with plant residues and lime pebbles 112 Human cerebrospinal fluid 111 Water 109 garden soil 105 soil sample 104 activated sludge 103 Human sputum,cystic fibrosis 101 faeces of rabbit