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README.md

@datafire/bridgedb

Client library for bridgedb webservices

Installation and Usage

npm install --save @datafire/bridgedb
let bridgedb = require('@datafire/bridgedb').create();

.then(data => {
  console.log(data);
});

Description

Actions

organism.attributeSearch.query.get

Returns a list of xrefs and associated attributes that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source, or by the type of attribute. See possible attribute types via /{organism}/attributeSet.

bridgedb.organism.attributeSearch.query.get({
  "organism": "",
  "query": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • query required string: Text to find in attributes
    • limit integer: Number of results
    • attrName string: Restrict search by attribute name (case sensitive). Use GET /{organism}/attributeSet to find out which attributes are supported.

Output

Output schema unknown

organism.attributeSet.get

Returns the supported attributes to the given Organism.

bridgedb.organism.attributeSet.get({
  "organism": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.

Output

Output schema unknown

organism.attributes.systemCode.identifier.get

Returns the attributes for a given identifier, data source, organism. Optionally display only a specified attribute

bridgedb.organism.attributes.systemCode.identifier.get({
  "organism": "",
  "systemCode": "",
  "identifier": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • systemCode required string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): System
    • identifier required string: Identifier
    • attrName string: Type of attribute

Output

Output schema unknown

organism.isFreeSearchSupported.get

Returns true or false based on whether or not /{organism}/search/{query} is supported for a given organism.

bridgedb.organism.isFreeSearchSupported.get({
  "organism": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.

Output

Output schema unknown

organism.isMappingSupported.sourceSystemCode.targetSystemCode.get

Returns true or false based on whether or not /{organism}/xrefs/{systemCode}/{identifier} would possibly return a {targetSystemCode} result given a {sourceSystemCode} query. This function basically combines the results of /{organism}/sourceDataSources and /{organism}/targetDataSources into a single boolean result.

bridgedb.organism.isMappingSupported.sourceSystemCode.targetSystemCode.get({
  "organism": "",
  "sourceSystemCode": "",
  "targetSystemCode": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • sourceSystemCode required string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): System code for source (input/query) data source
    • targetSystemCode required string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): System code for target (output/result) data source

Output

Output schema unknown

organism.properties.get

Returns the list of properties available for a given organism

bridgedb.organism.properties.get({
  "organism": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.

Output

Output schema unknown

organism.search.query.get

Returns a list of xrefs with identifiers that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source.

bridgedb.organism.search.query.get({
  "organism": "",
  "query": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • query required string: Identifier query
    • limit integer: Number of results per data source

Output

Output schema unknown

organism.sourceDataSources.get

Returns a list of data sources available as xref sources for a given organism.

bridgedb.organism.sourceDataSources.get({
  "organism": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.

Output

Output schema unknown

organism.targetDataSources.get

Returns a list of data sources available as xref targets for a given organism.

bridgedb.organism.targetDataSources.get({
  "organism": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.

Output

Output schema unknown

organism.xrefExists.systemCode.identifier.get

Returns true or false based on whether or not an xref exists in the database given an identifier, data source, and organism.

bridgedb.organism.xrefExists.systemCode.identifier.get({
  "organism": "",
  "systemCode": "",
  "identifier": ""
}, context)

Input

  • input object
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • systemCode required string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): Source (input) data source system code
    • identifier required string: Identifier

Output

Output schema unknown

organism.xrefs.systemCode.identifier.get

Returns a list of xrefs that map to a given identifier, data source, and organism.

bridgedb.organism.xrefs.systemCode.identifier.get({
  "organism": "",
  "systemCode": "",
  "identifier": ""
}, context)

Input

  • input object
    • dataSource string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): (Optional) Restrict results by data source system code
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • systemCode required string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): Source (input) data source system code
    • identifier required string: Identifier

Output

Output schema unknown

organism.xrefsBatch.post

Returns a list of xrefs, per identifier, that maps to a given list of identifiers an data source given an organism.

bridgedb.organism.xrefsBatch.post({
  "organism": "",
  "body": ""
}, context)

Input

  • input object
    • dataSource string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): (Optional) Restrict results by data source system code
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • body required string

Output

Output schema unknown

organism.xrefsBatch.systemCode.post

Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism.

bridgedb.organism.xrefsBatch.systemCode.post({
  "organism": "",
  "systemCode": "",
  "body": ""
}, context)

Input

  • input object
    • dataSource string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): (Optional) Restrict results by data source system code
    • organism required string (values: Human, Homo sapiens, Tuberculosis, Mycobacterium tuberculosis, Mosquito, Anopheles gambiae, Zebra fish, Danio rerio, Arabidopsis thaliana, Rice, Oryza sativa, Sea Squirt, Ciona intestinalis, Barley, Hordeum vulgare, Frog, Xenopus tropicalis, Soybean, Glycine max, Fruit fly, Drosophila melanogaster, Horse, Equus caballus, Rhesus Monkey, Macaca mulatta, Wine Grape, Vitis vinifera, Yeast, Saccharomyces cerevisiae, Tomato, Solanum lycopersicum, Rat, Rattus norvegicus, Cow, Bos taurus, Western Balsam Poplar, Populus trichocarpa, Chimpanzee, Pan troglodytes, Indian Rice, Oryza indica, Dog, Canis familiaris, Maize, Zea mays, Pig, Sus scrofa, Worm, Caenorhabditis elegans, Platypus, Ornithorhynchus anatinus, Chicken, Gallus gallus, Fusarium graminearum, Gibberella zeae, Bacillus subtilis, Escherichia coli, Black mold, Aspergillus niger, Mouse, Mus musculus): Organism Latin name or short name.
    • systemCode required string (values: En, Cs, X, E, Rh, Ck, Eco, Cg, Ch, Il, Uc, Rf, Pd, U, Ma, Lm, Wd, Wi, Cpc, Mb, Rk, Ce, S, L, Wg, Om, T, Mc, Ik, H, Re, Ag, Q, Ca, Up, Cks): Source (input) data source system code
    • body required string

Output

Output schema unknown

Definitions

This integration has no definitions