Mock sample for your project: CROssBAR Data API
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CROssBAR Data API
ebi.ac.uk
Version: 1.0
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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 â/proteinsâ 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 â/targetsâ API endpoint to obtain the âtargetchemblidâs of these proteins.
From the collection of targetchemblids collected from step 2 above, we query â/activitiesâ API endpoint with pChEMBL value >=6, to obtain the âmoleculechemblidâs 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 â/drugsâ API endpoint that targets our proteins.
From the collection of âmoleculechemblidâs obtained in step3, we query â/moleculesâ endpoint to get the compounds that are interacting with the genes/proteins belonging to the âWNT ligand biogenesis and traffickingâ pathway.
Other APIs in the same category
U.S. EPA Enforcement and Compliance History Online (ECHO) - Clean Water Act (CWA) Rest Services
CWA Rest Services provides multiple service endpoints, each with specific capabilities, to search and retrieve data on facilities regulated under the Clean Water Act (CWA) and managed under the National Pollutant Discharge Elimination System (NPDES) program. The returned results reflect data drawn from EPA's ICIS-NPDES database.
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The getfacilities, getmap, getqid, and getdownload end points are meant to be used together, while the enhanced getfacilityinfo end point is self contained.
The getfacilityinfo end point returns either an array of state, county or zip clusters with summary statistics per cluster or an array of facilities.
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The recommended use scenario for getfacilities, getqid, getmap, and getdownoad is:
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1) Use getfacilities to validate passed query parameters, obtain summary statistics and to obtain a queryid (QID). QIDs are time sensitive and will be valid for approximately 30 minutes.
2) Use get_qid, with the returned QID, to paginate through arrays of facility results.
3) Use get_map, with the returned QID, to zoom in/out and pan on the clustered and individual facility coordinates that meet the QID query criteria.
4) Use get_download, with the returned QID, to generate a Comma Separated Value (CSV) file of facility information that meets the QID query criteria.
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Use the qcolumns parameter to customize your search results. Use the Metadata service endpoint for a list of available output objects, their Column Ids, and their definitions to help you build your customized output.
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Additional ECHO Resources: Web Services, About ECHO's Data, Data Downloads