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@biothings-explorer/annotator
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A nodejs package providing batch annotating features for biomedical entities
A nodejs module to annotate biomedical entities in batch for BioThings Explorer
npm i @biothings-explorer/annotator
Import and Initialize
const annotate = require("@biothings-explorer/annotator")
Annotate Gene IDs
const gene_ids = {
"NCBIGene:4888": {
"db_ids": {
"NCBIGene": [
"4888"
],
"HGNC": [
"7959"
],
"SYMBOL": [
"NPY6R"
],
"UMLS": [
"C1417819"
]
}
},
"NCBIGene:4597": {
"db_ids": {
"NCBIGene": [
"4597"
],
"ENSEMBL": [
"ENSG00000167508"
],
"HGNC": [
"7529"
],
"SYMBOL": [
"MVD"
],
"UMLS": [
"C1417507"
]
}
}
}
let res = await annotate("Gene", gene_ids);
console.log(res);
// {"NCBIGene:4888": {"genomic_position": ..., "generif": ..., "biological_process": ...},"NCBIGene:4597": {"genomic_position": ..., "reactome": ..., "wikipathways": ...}}
Annotate ChemicalSubstance IDs
const chemical_ids = {
"CHEBI:8863": {
"id": {
"label": "RILUZOLE",
"identifier": "CHEBI:8863"
},
"db_ids": {
"CHEBI": [
"CHEBI:8863"
],
"CHEMBL.COMPOUND": [
"CHEMBL744"
]
}
},
"CHEBI:133809": {
"id": {
"label": "ANISINDIONE",
"identifier": "CHEBI:133809"
},
"db_ids": {
"CHEBI": [
"CHEBI:133809"
],
"CHEMBL.COMPOUND": [
"CHEMBL712"
]
}
}
};
let res = await annotate("ChemicalSubstance", chemical_ids);
console.log(res);
// {"CHEBI:133809": {"max_phase": ..., "molecular_weight": ..., "molecular_type": ...}, "CHEBI:8863": {"max_phase": ..., "enzymes": ..., "targets": ...}}
npm run test
👤 Jiwen Xin
Contributions, issues and feature requests are welcome!
Feel free to check issues page.
Give a ⭐️ if this project helped you!
FAQs
A nodejs package providing batch annotating features for biomedical entities
The npm package @biothings-explorer/annotator receives a total of 5 weekly downloads. As such, @biothings-explorer/annotator popularity was classified as not popular.
We found that @biothings-explorer/annotator demonstrated a not healthy version release cadence and project activity because the last version was released a year ago. It has 1 open source maintainer collaborating on the project.
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