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Browser extension for accessing open data resources in the biomedical domain
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README.md

FAIR-biomed

Browser extension for accessing open data resources in the biomedical domain.

Introduction

Vasts amounts of biomedical data are stored in open databases and knowledge-bases. Data in these resources are intended to be findable, accessible, interoperable, and reusable (FAIR). However, the data is distributed across many resources and integrating relevant parts within a specific project can be a challenge.

FAIR-biomed is a browser extension (for chrome) that brings open data resources directly to specific research situations. Consider, for example, reading a report in your browser. With FAIR-biomed, you can access additional information on any part of the report without leaving the page.

To make use of the extension, first highlight some text, for example, a gene name. Press Ctr+Shift+Z on the keyboard (alternatively right-click > FAIR-biomed search with the mouse). A new box should appear prompting you to choose a data source to query.

Clicking on one of the options triggers a query to the corresponding data service and displays a summary of results.

Search results provide summaries of the data resource, details of how the data query was executed, and a link to further data.

Data sources

The FAIR-biomed app is composed of core components and a library of plugins. Each of the plugins provides access to a data resource and a specific query type.

The current plugin library provides access to a small but varied set of data sources.

Data source Plugins
ClinGen Allele registry
EBI Identifiers, ontology, GWAS, and chemical data
Europe PMC Literature
ExAC Genomic variant annotation
Genomics England PanelApp
HGNC Gene nomenclature
IMPC Mouse model phenotypes
NCBI Literature, gene summaries, significance of genetic variation
MARRVEL Disease associations, gene expression
Reactome Pathways
STRING Protein interaction networks
Uniprot Knowledgebase
Wikimedia Encyclopaedia and dictionary

Practical Issues

Installation

The extension is available from the chrome web store. Select the extension in the web store, click Add to chrome, and read any information boxes. Once installed, highlight text on a web page and press Ctrl+Shift+Z to perform searches.

To install the FAIR-biomed extension manually using code from this repository, see the develper's documentation

Local URLs

The extension is automatically active on all pages that you accesss via urls starting with 'http' or 'https'. You can also use the extension with reports stored on your own computer, but this functionality is disabled by default by the chrome browser. To use this feature, you must enable it manually.

  • Select Tools > Extensions from the chrome menus; a new tab should appear listing all your installed extensions
  • Find FAIR-biomed and click Details; the view should change and display more details on the extension
  • Scroll down to the setting Allow access to file URLs and turn on the switch.

Options

The extension has a dedicated page where you tune which data sources you would like displayed in the popups.

  • Select Tools > Extensions from the chrome menu.
  • Find FAIR-biomed in the list of installed extensions and click Details.
  • Scroll down to the setting Extension options and click on the link.
  • On the page that appears, use the switches to turn individual plugins on or off. Use the rating systems to mark which plugins you find most useful.

Privacy

Once installed, the extension records a small amount of information to personalize its usage to each user. This data pertains to which plugins are active (see previous section on Options), how many times each plugin is used, and whether each plugin is rated/bookmarked. This information remains on each user's computer and can be adjusted through the Options page. This information is not shared with outside services.

The extension does not record performed searches. Note, however, that the extension sends queries to external APIs. Some of these services may record activity for their own purposes (for example, to demonstrate their relevance to the science community). See the privacy policies of those services for details.

When installing the extension from the chrome web store, Google collects some user information. See their privacy policy for details.

In the news

FAIR-biomed was featured in the news!

Notes and References

The idea of augmenting web pages with additional information has a long history.

  • Reflect was an early implementation of a browser extension aimed at biomedical research. This extension sent a whole web-page to a server for annotation.

  • Dynamic linking outlined an idea to infer links to specialist sources by scanning the context of web pages.

  • GIX described an extension for retrieving information on gene products.

Get involved

Feedback and contributions are welcome. Please raise an issue in the github repository.

To incorporate a new data resource or plugin, see the documentation.

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