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bionode-quickgo\n\nAcess EBI QuickGO REST API with promises and streams.\n\n## API Documentation\n\nAccess EBI QuickGO REST API with promises and streams.\n\n\n* [bionode-quickgo](#module_bionode-quickgo)\n    * _static_\n        * [.GAnnotationAsync(fields)](#module_bionode-quickgo.GAnnotationAsync) ⇒ \u003ccode\u003ePromise\u003c/code\u003e\n        * [.GAnnotation(fields)](#module_bionode-quickgo.GAnnotation) ⇒ \u003ccode\u003eStream\u003c/code\u003e\n        * [.GTerm(fields)](#module_bionode-quickgo.GTerm) ⇒ \u003ccode\u003eStream\u003c/code\u003e\n        * [.GTermAsync(fields)](#module_bionode-quickgo.GTermAsync) ⇒ \u003ccode\u003ePromise\u003c/code\u003e\n    * _inner_\n        * [~format](#module_bionode-quickgo..format) : \u003ccode\u003eString\u003c/code\u003e\n        * [~limit](#module_bionode-quickgo..limit) : \u003ccode\u003eString\u003c/code\u003e\n        * [~gz](#module_bionode-quickgo..gz) : \u003ccode\u003eString\u003c/code\u003e\n        * [~goid](#module_bionode-quickgo..goid) : \u003ccode\u003eString\u003c/code\u003e\n        * [~aspect](#module_bionode-quickgo..aspect) : \u003ccode\u003eString\u003c/code\u003e\n        * [~relType](#module_bionode-quickgo..relType) : \u003ccode\u003eString\u003c/code\u003e\n        * [~termUse](#module_bionode-quickgo..termUse) : \u003ccode\u003eString\u003c/code\u003e\n        * [~evidence](#module_bionode-quickgo..evidence) : \u003ccode\u003eString\u003c/code\u003e\n        * [~source](#module_bionode-quickgo..source) : \u003ccode\u003eString\u003c/code\u003e\n        * [~ref](#module_bionode-quickgo..ref) : \u003ccode\u003eString\u003c/code\u003e\n        * [~with](#module_bionode-quickgo..with) : \u003ccode\u003eString\u003c/code\u003e\n        * [~tax](#module_bionode-quickgo..tax) : \u003ccode\u003eString\u003c/code\u003e\n        * [~protein](#module_bionode-quickgo..protein) : \u003ccode\u003eString\u003c/code\u003e\n        * [~qualifier](#module_bionode-quickgo..qualifier) : \u003ccode\u003eString\u003c/code\u003e\n        * [~db](#module_bionode-quickgo..db) : \u003ccode\u003eString\u003c/code\u003e\n        * [~q](#module_bionode-quickgo..q) : \u003ccode\u003eString\u003c/code\u003e\n        * [~col](#module_bionode-quickgo..col) : \u003ccode\u003eString\u003c/code\u003e\n        * [~id](#module_bionode-quickgo..id) : \u003ccode\u003eString\u003c/code\u003e\n        * [~format](#module_bionode-quickgo..format) : \u003ccode\u003eString\u003c/code\u003e\n        * [~annotationRequest(fields)](#module_bionode-quickgo..annotationRequest) ⇒ \u003ccode\u003eObject\u003c/code\u003e\n        * [~termRequest(fields)](#module_bionode-quickgo..termRequest) ⇒ \u003ccode\u003eObject\u003c/code\u003e\n\n\u003ca name=\"module_bionode-quickgo.GAnnotationAsync\"\u003e\u003c/a\u003e\n### bionode-quickgo.GAnnotationAsync(fields) ⇒ \u003ccode\u003ePromise\u003c/code\u003e\nQuickGO Annotation service\n\n**Kind**: static method of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n\n| Param | Type | Description |\n| --- | --- | --- |\n| fields | \u003ccode\u003eObject\u003c/code\u003e | valid query fields |\n\n\u003ca name=\"module_bionode-quickgo.GAnnotation\"\u003e\u003c/a\u003e\n### bionode-quickgo.GAnnotation(fields) ⇒ \u003ccode\u003eStream\u003c/code\u003e\nQuickGO Annotation service\n\n**Kind**: static method of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n\n| Param | Type | Description |\n| --- | --- | --- |\n| fields | \u003ccode\u003eObject\u003c/code\u003e | valid query fields |\n\n\u003ca name=\"module_bionode-quickgo.GTerm\"\u003e\u003c/a\u003e\n### bionode-quickgo.GTerm(fields) ⇒ \u003ccode\u003eStream\u003c/code\u003e\nGO term information\n\n**Kind**: static method of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n\n| Param | Type | Description |\n| --- | --- | --- |\n| fields | \u003ccode\u003eObject\u003c/code\u003e | valid query fields, id required |\n\n\u003ca name=\"module_bionode-quickgo.GTermAsync\"\u003e\u003c/a\u003e\n### bionode-quickgo.GTermAsync(fields) ⇒ \u003ccode\u003ePromise\u003c/code\u003e\nGO term information\n\n**Kind**: static method of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n\n| Param | Type | Description |\n| --- | --- | --- |\n| fields | \u003ccode\u003eObject\u003c/code\u003e | valid query fields, id required |\n\n\u003ca name=\"module_bionode-quickgo..format\"\u003e\u003c/a\u003e\n### bionode-quickgo~format : \u003ccode\u003eString\u003c/code\u003e\nDownload file format\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003egaf\u003c/code\u003e  \n**Example**  \n```js\ngaf, gpa, gene2go, proteinList, fasta, tsv\n```\n\u003ca name=\"module_bionode-quickgo..limit\"\u003e\u003c/a\u003e\n### bionode-quickgo~limit : \u003ccode\u003eString\u003c/code\u003e\nDownload limit (number of lines). Note that the default limit is\n10,000 rows, which may not be sufficient for the data set that you are\ndownloading. To bypass this default, and return the entire data set,\nspecify a limit of -1.\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\n9001, -1\n```\n\u003ca name=\"module_bionode-quickgo..gz\"\u003e\u003c/a\u003e\n### bionode-quickgo~gz : \u003ccode\u003eString\u003c/code\u003e\ngzips the downloaded file\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003efalse\u003c/code\u003e  \n**Example**  \n```js\nfalse, true\n```\n\u003ca name=\"module_bionode-quickgo..goid\"\u003e\u003c/a\u003e\n### bionode-quickgo~goid : \u003ccode\u003eString\u003c/code\u003e\nGO identifiers either directly or indirectly (descendant GO\nidentifiers) applied in annotations\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nGO:0002080\n```\n\u003ca name=\"module_bionode-quickgo..aspect\"\u003e\u003c/a\u003e\n### bionode-quickgo~aspect : \u003ccode\u003eString\u003c/code\u003e\nUse this to limit the annotations returned to a specific ontology or\nontologies (Molecular Function, Biological Process or Cellular Component)\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nF, P, C\n```\n\u003ca name=\"module_bionode-quickgo..relType\"\u003e\u003c/a\u003e\n### bionode-quickgo~relType : \u003ccode\u003eString\u003c/code\u003e\nBy default, QuickGO will display annotations to GO terms that are\nrelated to that specified in the goid parameter by is_a, part_of and\noccurs_in relations; this parameter allows you to override that behaviour.\nSee [Ontology Relations](http://geneontology.org/page/ontology-relations).\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003eIPO=\u003c/code\u003e  \n**Example**  \n```js\n? (ancestor)\n= (indentity)\nI (is_a)\nP (part_of)\nO (occurs_in)\nR (regulates)\n+ (positively_regulates)\n- (negatively_regulates)\n```\n\u003ca name=\"module_bionode-quickgo..termUse\"\u003e\u003c/a\u003e\n### bionode-quickgo~termUse : \u003ccode\u003eString\u003c/code\u003e\nIf you set this parameter to slim, then QuickGO will use the\nsupplied set of GO identifiers as a slim and will map the annotations up\nto these terms. See [here](http://www.ebi.ac.uk/QuickGO/GMultiTerm) for\nmore details. The default behaviour (termUse=ancestor) is to not perform\nthis mapping.\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003eancestor\u003c/code\u003e  \n**Example**  \n```js\nancestor, slim\n```\n\u003ca name=\"module_bionode-quickgo..evidence\"\u003e\u003c/a\u003e\n### bionode-quickgo~evidence : \u003ccode\u003eString\u003c/code\u003e\nAnnotation evidence code (Ev) category\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nIDA, IC, ISS, IEA\n```\n\u003ca name=\"module_bionode-quickgo..source\"\u003e\u003c/a\u003e\n### bionode-quickgo~source : \u003ccode\u003eString\u003c/code\u003e\nAnnotation provider\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nUniProtKB, HGNC\n```\n\u003ca name=\"module_bionode-quickgo..ref\"\u003e\u003c/a\u003e\n### bionode-quickgo~ref : \u003ccode\u003eString\u003c/code\u003e\nPubMed or GO reference supporting annotation. Can refer to a specific\nreference identifier or category (for category level, use * after ref type)\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nPUBMED:*, GO_REF:0000002, 16262699\n```\n\u003ca name=\"module_bionode-quickgo..with\"\u003e\u003c/a\u003e\n### bionode-quickgo~with : \u003ccode\u003eString\u003c/code\u003e\nAdditional supporting information supplied in IEA, ISS, IPI, IC\nevidenced annotations; see:\n[GO documentation](http://www.geneontology.org/GO.evidence.shtml).\nCan refer to a specific identifier or category (for category level, use *\nafter with type)\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nEC:2.5.1.30, IPR000092, HAMAP:*\n```\n\u003ca name=\"module_bionode-quickgo..tax\"\u003e\u003c/a\u003e\n### bionode-quickgo~tax : \u003ccode\u003eString\u003c/code\u003e\nNCBI taxonomic identifer of annotated protein\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\n9606\n```\n\u003ca name=\"module_bionode-quickgo..protein\"\u003e\u003c/a\u003e\n### bionode-quickgo~protein : \u003ccode\u003eString\u003c/code\u003e\nSpecifies one or more sequence identifiers or accessions from\navailable database(s) (see DB filter column)\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nMm.363225, P99999\n```\n\u003ca name=\"module_bionode-quickgo..qualifier\"\u003e\u003c/a\u003e\n### bionode-quickgo~qualifier : \u003ccode\u003eString\u003c/code\u003e\nTags that modify the interpretation of an annotation\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nNOT, colocalizes_with, contributes_to\n```\n\u003ca name=\"module_bionode-quickgo..db\"\u003e\u003c/a\u003e\n### bionode-quickgo~db : \u003ccode\u003eString\u003c/code\u003e\nProtein database (identifier type)\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\nUniProtKB, UniGene, Ensembl\n```\n\u003ca name=\"module_bionode-quickgo..q\"\u003e\u003c/a\u003e\n### bionode-quickgo~q : \u003ccode\u003eString\u003c/code\u003e\nAdvanced query. Used to customize GO annotation sets using Boolean\noperators. See [Advanced Annotation Search](http://www.ebi.ac.uk/QuickGO/reference.html#advanced_annotation)\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;\u0026#x27;\u003c/code\u003e  \n\u003ca name=\"module_bionode-quickgo..col\"\u003e\u003c/a\u003e\n### bionode-quickgo~col : \u003ccode\u003eString\u003c/code\u003e\nThis parameter, which is currently only applicable to the tsv\ndownload format, allows you to specify a comma-separated list of columns\nthat you want to be included in the returned data set. The list below shows\nthe available column names; clicking on the name of a column will take you\nto the description of the column in the QuickGO help file. The default set\nof columns is shown in bold text.\n* [**proteinDB**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinDB)\n* [**proteinID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinID)\n* [**proteinSymbol**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSymbol)\n* [**qualifier**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-qualifier)\n* [**goID**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goID)\n* [**goName**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-goName)\n* [**aspect**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-aspect)\n* [**evidence**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-evidence)\n* [**ref**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-ref)\n* [**with**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-with)\n* [**proteinTaxon**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxon)\n* [**date**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-date)\n* [**from**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-from)\n* [**splice**](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-splice)\n* [proteinName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinName)\n* [proteinSynonym](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinSynonym)\n* [proteinType](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinType)\n* [proteinTaxonName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-proteinTaxonName)\n* [orginalTermID](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalTermID)\n* [originalGOName](http://www.ebi.ac.uk/QuickGO/reference.html#annotation-column-originalGOName)\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003e\u0026#x27;proteinDB,proteinID,proteinSymbol,qualifier,goID,goName,aspect,evidence,ref,with,proteinTaxon,date,from,splice\u0026#x27;\u003c/code\u003e  \n**Example**  \n```js\n'proteinDB,proteinID,goID,goName,aspect'\n```\n\u003ca name=\"module_bionode-quickgo..id\"\u003e\u003c/a\u003e\n### bionode-quickgo~id : \u003ccode\u003eString\u003c/code\u003e\nGO identifier\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003enone\u003c/code\u003e  \n**Example**  \n```js\nGO:0003824\n```\n\u003ca name=\"module_bionode-quickgo..format\"\u003e\u003c/a\u003e\n### bionode-quickgo~format : \u003ccode\u003eString\u003c/code\u003e\n| Format                                                                   | Description                                                       |\n|:-------------------------------------------------------------------------|:------------------------------------------------------------------|\n| [mini](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824\u0026format=mini)     | Mini Mini HTML, suitable for dynamically embedding in popup boxes |\n| [obo](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824\u0026format=obo)       | OBO format snippet                                                |\n| [oboxml](http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0003824\u0026format=oboxml) | OBO XML format snippet                                            |\n\n**Kind**: inner property of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Default**: \u003ccode\u003eobo\u003c/code\u003e  \n\u003ca name=\"module_bionode-quickgo..annotationRequest\"\u003e\u003c/a\u003e\n### bionode-quickgo~annotationRequest(fields) ⇒ \u003ccode\u003eObject\u003c/code\u003e\ngenerate an annotation request object\n\n**Kind**: inner method of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Returns**: \u003ccode\u003eObject\u003c/code\u003e - {{method, uri, form} object for request}  \n\n| Param | Type | Description |\n| --- | --- | --- |\n| fields | \u003ccode\u003eObject\u003c/code\u003e | valid query fields |\n\n\u003ca name=\"module_bionode-quickgo..termRequest\"\u003e\u003c/a\u003e\n### bionode-quickgo~termRequest(fields) ⇒ \u003ccode\u003eObject\u003c/code\u003e\ngenerate an term request object\n\n**Kind**: inner method of \u003ccode\u003e[bionode-quickgo](#module_bionode-quickgo)\u003c/code\u003e  \n**Returns**: \u003ccode\u003eObject\u003c/code\u003e - {{method, uri, form} object for request}  \n\n| Param | Type | Description |\n| --- | --- | --- |\n| fields | \u003ccode\u003eObject\u003c/code\u003e | valid query fields |\n\n\n## License\n\nMIT [http://jmazz.mit-license.org](http://jmazz.mit-license.org)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionode%2Fbionode-quickgo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbionode%2Fbionode-quickgo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionode%2Fbionode-quickgo/lists"}