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How to use the Open PHACTS API
- 1. How to usethe Open PHACTS API Ian Dunlop Ian.dunlop@manchester.ac.uk
- 2. Go to https://dev.openphacts.org Signup, sign in or use the app ID/app Keys available from: http://goo.gl/z3rWwZ
- 3. Use the APIfrom the documentation View results in a browser Write some code What shall we do?
- 4. Anatomy of anAPI 1 Required elements with a single value Optional elements with a single value Optional elements with a single value or array
- 5. Anatomy of anAPI 2 URI identifying the item you are interested in Application ID created at https://dev.openphacts. org Application Key for the application ID created at https://dev.openphacts.org
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- 8. Compound Pharmacology List (page1, 10 results) https://beta.openphacts.org/1.3/compound/pharmacology/pages?uri=htt p%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f- 4a4e-a46a- 4ed1d7bdf9d5&app_id=a921aad5&app_key=1be1aa775de4126dab09 d54ef95e5832&_format=json http://goo.gl/nw4YFQ
- 9. Compound Pharmacology Filters Howmany results are there with an IC50 less than or equal to 1500nM?
- 10. Compound Pharmacology Filters Answer:146 https://beta.openphacts.org/1.3/compound/pharmacology/count?uri=http%3A% 2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a- 4ed1d7bdf9d5&app_id=a921aad5&app_key=1be1aa775de4126dab09d54ef95 e5832&activity_type=IC50&max- activity_value=1500&activity_unit=nanomolar&_format=json activity_type=IC50 max-activity_value=1500 activity_unit=nanomolar http://goo.gl/BbHmKN
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- 13. Write some code Openup zip (available from http://goo.gl/NaN5BJ) Start with an empty HTML page – Open compound.html in your browser (file:///….) Not much to see here – Loads OPS.js and jQuery
- 14. Write some code Openthe HTML in your favourite text editor Add some magic (http://goo.gl/JvE4mt) inside the JavaScript code block appID = "a921aad5"; appKey = "1be1aa775de4126dab09d54ef95e5832"; var searcher = new Openphacts.CompoundSearch("https://beta.openphacts.org/1.3", appID, appKey); var callback = function(success, status, response) { var compoundResult = searcher.parseCompoundResponse(response); $("#compound-info").append("I am " + compoundResult.prefLabel + " with molecular weight " + compoundResult.fullMWT); }; searcher.fetchCompound('http://www.conceptwiki.org/concept/389325 52-111f-4a4e-a46a-4ed1d7bdf9d5', null, callback); Refresh your browser
- 15. Open PHACTS widgets Collaborationwith Biojs http://openphacts.github.io/ops-html-widgets/ https://github.com/biojs/biojs
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Editor's Notes
- #3 The app id and key is used to measure number of uses of the API, not who is using it. The actual API calls used are wiped from the logs.
- #4 All the API calls are documented at https://dev.openphacts.org/1.3/docs and can be run from within that page
- #5 Response format is described in RDF triple format. Green means that the element will be present in the response and will have a single value. Yellow means that the element may or may not be in the response and will have a single value Orange means that the element may or may not be in the response and can have a single value or multiple values wrapped inside an array (ie list) Purple means that the element will be present in the response and can have a single value or multiple values wrapped inside an array (ie list)
- #6 Most API calls follow the same format of https://beta.openphacts.org/API_VERSION/API_CALL?uri=URI&app_id=YOUR_APP_ID&app_key=YOUR_APP_KEY&_format=CHOSEN_FORMAT _callback parameter is for JSONP _metadata parameter adds additional info to the response eg formats returns the mime types available Click the ‘Send Request’ button to see the call executed inside the page which returns a response along with the actual API call sent in CURL format
- #7 Each version of the API has a number and starting with 1.3 the URL contains the API verison number ie https://beta.openphacts.org/1.3 followed by the path to the call itself eg /compound. Each call must contain a valid app_id and app_key parameter created at dev.openpahcts.org.
- #10 Various filters and extra parameters can be added to the API calls.
- #13 The default page is 1 and page size is 20 but you can change these to suit your applications. Set the _pageSize parameter to ‘all’ to retrieve all the results in one API call.
- #14 Template has a JavaScript code block that is called when the page loads. Loads the OPS.js library which can be used to call the Open PHACTS API and flatten the results. This library is used by the Open PHACTS Explorer ‘2’.
- #16 There are currently 2 Open PHACTS widgets in the Biojs codebase. Compound Info and Target Info. They will eventually end up on http://www.ebi.ac.uk/Tools/biojs/registry/ They allow the addition of Open PHACTS UI components on any web page with minimal coding, only a couple of lines of JavaScript.
- #17 Note: the explorer 2 demo on jupiter.cs.man.ac.uk is liable to change or move at any time. It will be hosted under an openphacts IP address in the near future.