OPS REST services

Created: 2013-07-06 07:49:19

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Library of REST services developed for the Open Pharmacological Space (OPS) by the OpenPHACTS project.

Usage:

Copy-paste a service into your workflow
Add an output to responseBody
Run the workflow (this will produce output in XML)
Copy the XML output
Go back to the design window and add the XPath widget to the canvas
Link the responseBody output to the XPath widget input
Paste the XML output to the example window in the XPath configure window
Select the desired elements from the example XML
Generate the XPath query and test it
Add a workflow output and link it to the XPath output.

Preview

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Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3644/download?version=1
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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (0)

Processors (11)

Name	Type	Description
Chemical_Structure_Exact_Search	rest	https://dev.openphacts.org/docs#operation/0 Description Returns a ChemSpider URL corresponding to an input SMILES string. Driven by ChemSpider. Parameter Value Description app_id Your access application id app_key Your access application key searchOptions.Molecule A SMILES string. E.g. CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl searchOptions.MatchType 0: ExactMatch ; 1: AllTautomers ; 2: SameSkeletonIncludingH ; 3: SameSkeletonExcludingH ; 4: AllIsomers commonOptions.Complexity (Not supported at the moment) 0: Any ; 1: Single ; 2: Multi commonOptions.Isotopic (Not supported at the moment) 0: Any ; 1: Labeled ; 2: NotLabeled commonOptions.HasSpectra (Not supported at the moment) Boolean commonOptions.HasPatents (Not supported at the moment) Boolean resultOptions.Limit Integer resultOptions.Start Integer resultOptions.Length Integer. How many results should be returned starting from Start index. Default value: -1. _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Chemical_Structure_Similarity_Search	rest	https://dev.openphacts.org/docs#operation/29 Description Returns a set of ChemSpider compound URLs, similar to the input molecule according to the specified algorithm and threshold. Driven by ChemSpider. Parameter Value Description app_id Your access application id app_key Your access application key searchOptions.Molecule A SMILES string. E.g. CC(=O)Oc1ccccc1C(=O)O searchOptions.SimilarityType 0: Tanimoto ; 1: Tversky ; 2: Euclidian searchOptions.Threshold Double <= 1.0 commonOptions.Complexity (Not supported at the moment) 0: Any ; 1: Single ; 2: Multi commonOptions.Isotopic (Not supported at the moment) 0: Any ; 1: Labeled ; 2: NotLabeled commonOptions.HasSpectra (Not supported at the moment) Boolean commonOptions.HasPatents (Not supported at the moment) Boolean resultOptions.Limit Integer. Search limit. Specefy how many results return back during the search. Default value: -1 . resultOptions.Start Integer. Return results starting the index. Default value: 0 resultOptions.Length Integer. How many results should be returned starting from Start index. Default value: -1. _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Get_concept_description	rest	https://dev.openphacts.org/docs#operation/67 Description Get the description of a concept, based on a concept URL. Driven by ConceptWiki. Parameter Value Description app_id Your access application id app_key Your access application key uuid UUID of the concept; required. E.g. 8e3a87ae-345d-4c25-bd7a-5b3221c6e3fa branch The search results will be filtered by this source authority; optional. Possible values: 1 = Community, 2 = UMLS, 3 = SwissProt, 4 = ChemSpider, 5 = ConceptWiki _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Free_text_to_conceptURL_withtype	rest	Search for a set of concept URLs based on free text and an input tag, which specifies the semantic type. Driven by ConceptWiki. Parameter Value Description app_id Your access application id app_key Your access application key q Query; required. Minimum length is 3 characters. E.g. water limit Limits the number of results; optional. Minimum value is 1, maximum value is common sense. Default value is 10. uuid UUID of the tag concept; required. Specifies the 'semantic type' required for the search results. E.g. 07a84994-e464-4bbf-812a-a4b96fa3d197 branch The search results will be filtered by this source authority; optional. Possible values: 1 = Community, 2 = UMLS, 3 = SwissProt, 4 = ChemSpider, 5 = ConceptWiki _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Free_text_to_conceptURL	rest	Search for a set of concept URLs based on free text. Driven by ConceptWiki. Parameter Value Description app_id Your access application id app_key Your access application key q Query; required. Minimum length is 3 characters. E.g. water limit Limits the number of results; optional. Minimum value is 1, maximum value is common sense. Default value is 10. uuid branch The search results will be filtered by this source authority; optional. Possible values: 1 = Community, 2 = UMLS, 3 = SwissProt, 4 = ChemSpider, 5 = ConceptWiki _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Map_URL	rest	Returns a set of URLs associated to the input URL. Parameter Value Description app_id Your access application id app_key Your access application key URL An input URL to be mapped. targetURISpace List of URI spaces separated by '\|' characters. Restricts the results to targets in this/these URISpace(s). The URI space of a URL is the one defined when the mapping is loaded. E.g. http://www.conceptwiki.org/concept/ _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Get_target_information	rest	Returns information about a single target that corresponds to {uri}. Parameter Value Description uri A target URI. e.g.: http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291 app_id Your access application id app_key Your access application key _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Get_pathway_information	rest	Returns information about a single pathway that corresponds to {uri}. https://dev.openphacts.org/docs#operation/305 Parameter Value Description uri A Pathway URI. e.g.: http://rdf.wikipathways.org/WP1019_r48131 app_id Your access application id app_key Your access application key _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Get_activity_types	rest	A list of activities type which have been normalised. https://dev.openphacts.org/docs#operation/305 Parameter Value Description app_id Your access application id app_key Your access application key _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Get_compound_information	rest	Returns information about a single compound that corresponds to {uri}. https://dev.openphacts.org/docs#operation/172 Parameter Value Description uri A compound URI. e.g.: http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5 app_id Your access application id app_key Your access application key _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.
Get_activity_paginated	rest	A page of items corresponding to acitivity values in the LDC for a given target. https://dev.openphacts.org/docs#operation/348 Parameter Value Description uri A target URI. e.g.: http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291 app_id Your access application id app_key Your access application key assay_organism A literal organism in ChEMBL. target_organism A literal target organism in ChEMBL. activity_type One of the activity types listed at /pharmacology/filters/activities activity_value Return activity values equal to this number. min-activity_value Return activity values greater than or equal to this number. minEx-activity_value Return activity values greater than this number. max-activity_value Return activity values less than or equal to this number. maxEx-activity_value Return activity values less than this number. activity_unit The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed valued. For e.g. IC50: /pharmacology/filters/units/IC50 _page A number; the page that should be viewed _pageSize The desired page size. Set to all to retrieve all results in a single page. _orderBy The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending _format The desired result format. _callback For JSONP _metadata Additional metadata to be included with response.