planteome-demo.json

{
    "encodeur" : "sentence-transformers/all-MiniLM-L6-v2",
    "threshold_similarity_tag_chunk" : 0.70,
    "threshold_similarity_tag" : 0.80,
    "batch_size" : 32,

    "populate_owl_tag_embeddings" : {
        "prefix" : {
            "rdf" : "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
            "rdfs" : "http://www.w3.org/2000/01/rdf-schema#",
            "owl" : "http://www.w3.org/2002/07/owl#"
        },
        "ontologies": {
            "planteome_link" : {
                "peco": {
                    "url": "http://purl.obolibrary.org/obo/peco.owl",
                    "prefix": "http://purl.obolibrary.org/obo/PECO_",
                    "format": "xml",    
                    "label" : "rdfs:label",
                    "properties": ["obo:IAO_0000115","rdfs:comment","owl:annotatedTarget"]
                },
                "po": {
                    "url": "http://purl.obolibrary.org/obo/po.owl",
                    "prefix": "http://purl.obolibrary.org/obo/PO_",
                    "format": "xml",
                    "label" : "rdfs:label",
                    "properties": ["obo:IAO_0000115","rdfs:comment","owl:annotatedTarget"]
                },
                "pso": {
                    "url": "http://purl.obolibrary.org/obo/pso.owl",
                    "prefix": "http://purl.obolibrary.org/obo/PSO_",
                    "format": "xml",
                    "label" : "rdfs:label",
                    "properties": ["obo:IAO_0000115","rdfs:comment","owl:annotatedTarget"]
                },
                "to": {
                    "url": "http://purl.obolibrary.org/obo/to.owl",
                    "prefix": "http://purl.obolibrary.org/obo/TO_",
                    "format": "xml",
                    "label" : "rdfs:label",
                    "properties": ["obo:IAO_0000115","rdfs:comment","owl:annotatedTarget"]
                }
            }
        }
    },
    "populate_abstract_embeddings" : {
        "abstracts_per_file" : 500,
        "from_ncbi_api" : {
            "ncbi_api_chunk_size" : 200,
            "debug_nb_ncbi_request" : -1,
            "retmax" : 2000,
            "selected_term" : [
                "Crops%2C+Agricultural%2Fmetabolism%5BMeSH%5D"
            ]
        }
    }
}