@datafire/ebi_ac_uk

v3.0.0

Published

3 years ago

DataFire integration for CROssBAR Data API

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@datafire/ebi_ac_uk

Client library for CROssBAR Data API

Installation and Usage

npm install --save @datafire/ebi_ac_uk

let ebi_ac_uk = require('@datafire/ebi_ac_uk').create();

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

Description

About CROssBAR & data

CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations CROssBAR is a comprehensive system that integrates large-scale biomedical data from various resources e.g UniProt, ChEMBL, Drugbank, EFO, HPO, InterPro & PubChem and stores them in a new NoSQL database, enrich these data with deep learning based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to the user via easy to interpret, interactive and heterogeneous knowledge graphs. CROssBAR platform exposes a set of 12 endpoints to query data stored in the CROssBAR database. These endpoints help the user to find data of interest using different parameters provided by the API endpoint. For example, https://www.ebi.ac.uk/tools/crossbar/proteins?accession=A0A023GRW5 -> will provide protein information about accession 'A0A023GRW5' including its interactions, functions, cross-references, variations and more. https://www.ebi.ac.uk/tools/crossbar/activities?moleculeChemblId=CHEMBL465983 -> will provide ChEMBL bio-interactions related information including targets and bio-activity measurements associated with molecule chembl id 'CHEMBL465983'

Knowledge graphs Another use case of CROssBAR's API endpoints is in building knowledge graphs. These endpoints can be weaved together (output from one API endpoint fed as input to another API endpoint) programmatically to link nodes like protein, disease, drugs etc. as nodes of the graph. The endpoints are designed to be independent from each other which allows users the flexibility to drive biological networks from any facet e.g drug-centric, disease-centric, gene-centric etc. Our service for knowledge graph construction is available at https://crossbar.kansil.org. An example for the part of the background queries on the CROssBAR API during the construction of a knowledge graph, (with the aim of keeping the example simple, we have only included the processes related to pathways, genes/proteins and drugs/compounds) In this example, we would like to find bio-active compounds (with a pChEMBL value threshold of at least 6.0) & drugs targeting all proteins belonging to "WNT ligand biogenesis and trafficking" pathway (based on Reactome pathway annotations). This can be achieved by using endpoints listed on this swagger documentation as illustrated in following steps- Find bio-active compounds (with a pChEMBL value threshold of at least 6.0) & drugs targeting all proteins belonging to "WNT ligand biogenesis and trafficking" pathway (based on Reactome annotations) This can be achieved by using endpoints listed on this swagger documentation as illustrated in following steps-

Get all proteins from “/proteins” API endpoint which have a reactome pathway name equal to "WNT ligand biogenesis and trafficking".
From the collection of uniprot protein accessions collected from step 1 above, we query “/targets” API endpoint to obtain the ‘target_chembl_id’s of these proteins.
From the collection of target_chembl_ids collected from step 2 above, we query “/activities” API endpoint with pChEMBL value >=6, to obtain the ’molecule_chembl_id’s of the molecules that we need.
From the collection of uniprot protein accessions collected from step 1 above, we find out Drug names and ids from the “/drugs” API endpoint that targets our proteins.
From the collection of ’molecule_chembl_id’s obtained in step3, we query “/molecules” endpoint to get the compounds that are interacting with the genes/proteins belonging to the “WNT ligand biogenesis and trafficking” pathway.

Actions

getActivitiesUsingGET

Get ChEMBL activities

ebi_ac_uk.getActivitiesUsingGET({}, context)

Input

input object
- assayChemblId array: assayChemblId
- limit integer: limit
- moleculeChemblId array: moleculeChemblId
- page integer: page
- pchemblValue number: pchemblValue
- targetChemblId array: targetChemblId

Output

output Activities

getAssaysUsingGET

Get ChEMBL assays

ebi_ac_uk.getAssaysUsingGET({}, context)

Input

input object
- assayChemblId array: assayChemblId
- assayOrg array: assayOrg
- assayType array: assayType
- limit integer: limit
- page integer: page
- targetChemblId array: targetChemblId

Output

output Assays

getDrugsUsingGET

drugs collected from Drugbank

ebi_ac_uk.getDrugsUsingGET({}, context)

Input

input object
- accession array: accession
- chemblId array: chemblId
- identifier array: identifier
- limit integer: limit
- name array: name
- page integer: page
- pubchemCid array: pubchemCid

Output

output Drugs

getEFOUsingGET

Get EFO diseases data

ebi_ac_uk.getEFOUsingGET({}, context)

Input

input object
- doid array: doid
- label array: label
- limit integer: limit
- mesh array: mesh
- oboId array: oboId
- omimId array: omimId
- page integer: page
- synonym array: synonym

Output

output EFOEntities

getHpoUsingGET

Get HPO phenotypes data

ebi_ac_uk.getHpoUsingGET({}, context)

Input

input object
- genesymbol array: genesymbol
- hpotermname array: hpotermname
- limit integer: limit
- page integer: page
- synonym array: synonym

Output

output HpoEntities

getMoleculesUsingGET

Get ChEMBL molecules

ebi_ac_uk.getMoleculesUsingGET({}, context)

Input

input object
- canonicalSmiles array: canonicalSmiles
- inchiKey array: inchiKey
- limit integer: limit
- moleculeChemblId array: moleculeChemblId
- page integer: page

Output

output Molecules

getProteinsUsingGET

Proteins collected from Uniprot for selective tax ids HUMAN(9606), MOUSE(10090), RAT(10116), BOVINE(9913), ESCHERICHIA_COLI(83333), SUS_SCROFA(9823), MYCOBACTERIUM_TUBERCULOSIS(83332), ORYCTOLAGUS_CUNICULUS(9986), SACCHAROMYCES_CEREVISIAE(559292), CVHSA(694009) & SARS2(2697049)

ebi_ac_uk.getProteinsUsingGET({}, context)

Input

input object
- accession array: accession
- ec array: ec
- fullName array: fullName
- gene array: gene
- go array: go
- interpro array: interpro
- limit integer: limit
- omim array: omim
- orphanet array: orphanet
- page integer: page
- pfam array: pfam
- reactome array: reactome
- taxId array: taxId

Output

output Proteins

getBioassaysUsingGET

Get pubchem bioassays

ebi_ac_uk.getBioassaysUsingGET({}, context)

Input

input object
- accession array: accession
- assayPubchemId array: assayPubchemId
- limit integer: limit
- ncbiProteinId array: ncbiProteinId
- page integer: page

Output

output Bioassays

getBioassaysUsingGET_1

Get pubchem bioassays associated to particular substance ids (sid) & outcome

ebi_ac_uk.getBioassaysUsingGET_1({}, context)

Input

input object
- limit integer: limit
- outcome string: outcome
- page integer: page
- sids array: sids

Output

output Bioassays

getCompoundsUsingGET

Get pubchem compounds

ebi_ac_uk.getCompoundsUsingGET({}, context)

Input

input object
- canonicalSmiles array: canonicalSmiles
- cid array: cid
- inchiKey array: inchiKey
- limit integer: limit
- page integer: page

Output

output PubchemCompounds

getSubstancesUsingGET

Get pubchem substances

ebi_ac_uk.getSubstancesUsingGET({}, context)

Input

input object
- cid array: cid
- limit integer: limit
- page integer: page
- sid array: sid

Output

output PubchemSubstances

getTargetsUsingGET

Get ChEMBL targets

ebi_ac_uk.getTargetsUsingGET({}, context)

Input

input object
- accession array: accession
- limit integer: limit
- page integer: page
- targetIds array: targetIds

Output

output Targets

Definitions

Activities

Activities object
- activities array
  - items Activity
- pageMeta PageMeta

Activity

Activity object
- assay_chembl_id string
- data_validity_comment string
- molecule_chembl_id string
- pchembl_value number
- standard_flag boolean
- standard_relation string
- standard_units string
- standard_value number
- target_chembl_id string

Assay

Assay object
- assay_chembl_id string
- assay_id string
- assay_organism string
- assay_type string
- confidence_score number
- target_chembl_id string

AssayData

AssayData object
- standard_type string
- standard_units string
- standard_value number

AssayOrganism

AssayOrganism object
- db_object_id integer
- tax_name string

Assays

Assays object
- assays array
  - items Assay
- pageMeta PageMeta

BioAssay

BioAssay object
- activity integer
- assay_organisms array
  - items AssayOrganism
- assay_pubchem_id integer
- assay_type string
- chembl_xref string
- protein_name string
- source string
- target_info array
  - items TargetInfo
- target_type_info array
  - items TargetType

BioAssayMetaData

BioAssayMetaData object
- bioAssay BioAssay
- sidRelatedData array
  - items SidRelatedData

Bioassays

Bioassays object
- bioassays array
  - items BioAssayMetaData
- pageMeta PageMeta

CrossReferences

CrossReferences object
- ensembl array
  - items Ensembl
- go array
  - items Go
- interpro array
  - items Interpro
- kegg array
  - items Kegg
- omim array
  - items Omim
- openTargets array
  - items OpenTargets
- orphanet array
  - items Orphanet
- pdBe array
  - items PDBe
- pfam array
  - items Pfam
- reactome array
  - items Reactome

CrossbarDrug

CrossbarDrug object
- alogp number
- canonical_smiles string
- chembl_id string
- full_mwt number
- identifier string
- inchi_key string
- kegg_cid string
- molecule_type string
- name string
- pathway array
  - items Pathway
- pb_structures array
  - items string
- polar_surface_area number
- pubchem_cid string
- pubchem_sid string
- standard_inchi string
- targets array
  - items Target
- uniprot_accession string

CrossbarFeature

CrossbarFeature object
- begin FeaturePosition
- category string
- description string
- end FeaturePosition
- ftId string
- type string

CrossbarMolecule

CrossbarMolecule object
- alogp number
- canonical_smiles string
- chirality number
- full_mwt number
- heavy_atoms_count integer
- inchi_key string
- molecular_species string
- molecular_type string
- molecule_chembl_id string
- parent_chembl_id string
- prodrug number
- standard_inchi string
- xrefs array
  - items Xref

CrossbarPCCompound

CrossbarPCCompound object
- alogp number
- atom_chiral_count integer
- atom_chiral_def_count integer
- bond_chiral_count integer
- bond_chiral_def_count integer
- bond_chiral_undef_count integer
- canonical_smiles string
- cid integer
- covalent_unit_count integer
- finger_print string
- full_mwt number
- heavy_atoms_count integer
- inchi_key string
- isotope_atom_count integer
- polar_surface_area number
- standard_inchi string
- tautomers_count integer

CrossbarProteinVariation

CrossbarProteinVariation object
- alternativeSequence string
- association array
  - items VariationAssociation
- begin FeaturePosition
- clinicalSignificances string
- description string
- end FeaturePosition
- evidences array
  - items VariationEvidence
- ftId string
- somaticStatus integer
- sourceType string
- wildType string
- xrefs array
  - items VariationXref

CrossbarTarget

CrossbarTarget object
- accession string
- target_chembl_id string

Drugs

Drugs object
- drugs array
  - items CrossbarDrug
- pageMeta PageMeta

EFO

EFO object
- description array
  - items string
- doid array
  - items string
- icd9 array
  - items string
- label string
- mesh array
  - items string
- ncit array
  - items string
- obo_id string
- omim array
  - items string
- short_form string
- snowmed array
  - items string
- synonyms array
  - items string
- umls array
  - items string

EFOEntities

EFOEntities object
- diseases array
  - items EFO
- pageMeta PageMeta

Ensembl

Ensembl object
- geneId string
- id string
- isoform string
- proteinSequenceId string

FeaturePosition

FeaturePosition object
- ceil integer
- floor integer
- uncertain boolean
- unparsed string

Features

Features object
- active_site array
  - items CrossbarFeature
- binding_site array
  - items CrossbarFeature
- chain array
  - items CrossbarFeature
- domain array
  - items CrossbarFeature
- mutagen array
  - items CrossbarFeature
- region array
  - items CrossbarFeature
- top_dom array
  - items CrossbarFeature
- variant array
  - items CrossbarFeature

Fragment

Fragment object
- from integer
- to integer
- type string

Gene

Gene object
- id string
- symbol string

Go

Go object
- evidences array
  - items GoEvidence
- id string
- term string

GoEvidence

GoEvidence object
- source_id string
- source_name string

HPOEntity

HPOEntity object
- db_references array
  - items string
- gene array
  - items Gene
- hpo_id string
- synonyms array
  - items string
- term_name string

HitPosition

HitPosition object
- from integer
- to integer

HpoEntities

HpoEntities object
- hpo array
  - items HPOEntity
- pageMeta PageMeta

Interpro

Interpro object
- entry_id string
- entry_name string
- entry_type string
- fragments array
  - items Fragment
- hit_position HitPosition

Kegg

Kegg object
- id string

Molecules

Molecules object
- molecules array
  - items CrossbarMolecule
- pageMeta PageMeta

Omim

Omim object
- _id string
- type string

OpenTargets

OpenTargets object
- id string

Orphanet

Orphanet object
- disease string
- id string

PDBe

PDBe object
- chains string
- id string
- method string
- resolution string

PageMeta

PageMeta object
- currentElements integer
- currentPage integer
- limit integer
- totalElements integer
- totalPages integer

Pathway

Pathway object
- category string
- name string

Pfam

Pfam object
- entryName string
- id string

Protein

Protein object
- accession string
- chromosome string
- crossreferences CrossReferences
- ec_numbers array
  - items string
- features Features
- full_name string
- genes array
  - items string
- interactions array
  - items ProteinInteraction
- length number
- mass number
- tax_id integer
- variations array
  - items CrossbarProteinVariation

ProteinInteraction

ProteinInteraction object
- id string
- interaction_type string
- interactors array
  - items string

Proteins

Proteins object
- pageMeta PageMeta
- proteins array
  - items Protein

PubchemCompounds

PubchemCompounds object
- compounds array
  - items CrossbarPCCompound
- pageMeta PageMeta

PubchemSubstances

PubchemSubstances object
- pageMeta PageMeta
- substances array
  - items Substance

Reactome

Reactome object
- id string
- pathwayName string

SidRelatedData

SidRelatedData object
- assay_data array
  - items AssayData
- assay_pubchem_id integer
- outcome string
- sid integer
- standard_relation string

Substance

Substance object
- chembl_cmpd_xref string
- cids array
  - items integer
- sid integer

Target

Target object
- accessions array
  - items string
- action array
  - items string
- id string
- name string
- organism string

TargetInfo

TargetInfo object
- ncbi_protein_id integer
- target_chembl_id string
- uniprot_accession string

TargetType

TargetType object
- molecule_type string
- value integer

Targets

Targets object
- pageMeta PageMeta
- targets array
  - items CrossbarTarget

VariationAssociation

VariationAssociation object
- description string
- evidences array
  - items VariationEvidence
- name string
- xrefs array
  - items VariationXref

VariationEvidence

VariationEvidence object
- source VariationEvidenceSource

VariationEvidenceSource

VariationEvidenceSource object
- id string
- name string

VariationXref

VariationXref object
- id string
- name string

Xref

Xref object
- id string
- source string

Published

Vulnerabilities

Links

Maintainers

Keywords

Readme

@datafire/ebi_ac_uk

Installation and Usage

Description

About CROssBAR & data

Actions

getActivitiesUsingGET

Input

Output

getAssaysUsingGET

Input

Output

getDrugsUsingGET

Input

Output

getEFOUsingGET

Input

Output

getHpoUsingGET

Input

Output

getMoleculesUsingGET

Input

Output

getProteinsUsingGET

Input

Output

getBioassaysUsingGET

Input

Output

getBioassaysUsingGET_1

Input

Output

getCompoundsUsingGET

Input

Output

getSubstancesUsingGET

Input

Output

getTargetsUsingGET

Input

Output

Definitions

Activities

Activity

Assay

AssayData

AssayOrganism

Assays

BioAssay

BioAssayMetaData

Bioassays

CrossReferences

CrossbarDrug

CrossbarFeature

CrossbarMolecule

CrossbarPCCompound

CrossbarProteinVariation

CrossbarTarget

Drugs

EFO

EFOEntities

Ensembl

FeaturePosition

Features

Fragment

Gene

Go

GoEvidence

HPOEntity

HitPosition

HpoEntities

Interpro

Kegg

Molecules