Tuesday, 20 August 2019

Using Europe PMC RESTful APIs

What is FAIR-biomed?

FAIR-biomed is a browser extension that aims to facilitate investigative research in biomedicine. It connects users to information stored in specialized databases. For example, when reading an online report, with simple clicks, FAIR-biomed can help you find all the relevant information on biological entities present in that report. For example, a gene, its description, along with its biological functions and interactors. It also provides links to the sources where this gene was mentioned from the biomedical literature. 
FAIR-biomed retrieves this information from several relevant data sources including Europe PMC, NCBI, ChEMBL, Uniprot and etc. Thus, this browser extension can query entities such as genes, chemicals, pathways, authors, titles of journal articles, and other relevant and useful biomedical terms. FAIR-biomed is available on the Chrome web store and its source code is available on GitHub. This tool was developed by Tomasz Konopka from Queen Mary University of London.

As an example scenario, imagine reading a page describing a work where the development of Plasmodium parasites stopped in female mosquitoes treated with an antimalarial drug. So, if you would like to know what is new in the domain of antimalarial compounds, FAIR-biomed would allow you to access relevant published articles without needing you to switch browser tabs or even searching explicitly in the Google. Just with few clicks, select the text “antimalarial compounds”, open a context menu and select the extension with a right-click, or press Ctrl+Shift+Z on the keyboard. Voila, a pop-up window will appear, displaying all the relevant data resources, including publications from Europe PMC.


How is Europe PMC API integrated in FAIR-biomed?

FAIR-biomed sends a request to the Europe PMC servers via their  RESTful API. The top 8 results including links to the article as well as the full search results are then retrieved from Europe PMC APIs, seamlessly and very easily. Integrating this functionality was straightforward as the API endpoints at Europe PMC have an intuitive structure. The documentation is very well written and concise providing easy-to-use examples with code snippets for integration.


The browser extension is optimised to display a small set of relevant hits and therefore uses some non-default settings such as “resultType=lite” and adjusting the “pageSize=8”. All these optimised settings from Europe PMC, along with the API documentation with concise descriptions for all advanced options made the integration with FAIR-biomed a very easy task.


Try it yourself! This is the Europe PMC API query used for finding relevant information on the “antimalarial compounds”: https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=antimalarial%20compounds&format=json&pageSize=8&resultType=lite 
Technically this query is a combination of strings. The API url string is stored within the extension code, and the user query is inserted in between “search?query=” and “format=json”.
The extension displays the exact API call on the “</>” icon in the bottom toolbar. So the results are reproducible! This is handy if you want to use similar API calls in your own code without reading through documentation pages. 


The extension converts JSON data from the API response into HTML paragraphs. It uses the following fields: “title”, “authorString”, “journalTitle”, “pubYear”, “pubType”. Below, is an example of the output obtained from the Europe PMC API.


By using Europe PMC APIs, FAIR-biomed allows readers to explore biomedical publications such as recent preprints, as well as peer-reviewed articles, and thus provides up-to-date information on the current literature on any biomedical topic.

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