Mock sample for your project: OPTIMADE API

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OPTIMADE API

optimade.local

Version: 1.1.0


Use this API in your project

Speed up your application development by using "OPTIMADE API" ready-to-use mock sample. Mocking this API will allow you to start working in no time. No more accounts to create, API keys to provision, accesses to configure, unplanned downtime, just work.
It also improves your integration tests' quality and reliability by accounting for random failures, slow response time, etc.

Description

The Open Databases Integration for Materials Design (OPTIMADE) consortium aims to make materials databases interoperational by developing a common REST API.
This specification is generated using optimade-python-tools v0.16.0.

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ECHO Rest Services provide multiple service endpoints, each with specific capabilities, to search and retrieve data on facilities regulated as Clean Air Act (CAA) stationary sources, Clean Water Act (CWA) dischargers, Resource Conservation and Recovery Act (RCRA) hazardous waste generators/handlers, and Safe Drinking Water Act (SDWA) public water systems. Data of interest from other EPA sources, such as the Toxics Release Inventory, is also supplied for context.
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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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About CROssBAR & data
CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations
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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)
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Get all proteins from “/proteins” API endpoint which have a reactome pathway name equal to "WNT ligand biogenesis and trafficking".
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From the collection of targetchemblids collected from step 2 above, we query “/activities” API endpoint with pChEMBL value >=6, to obtain the ’moleculechemblid’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.
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