Browser extension for accessing open data resources in the biomedical domain.
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.
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.
|EBI||Identifiers, ontology, GWAS, and chemical data|
|ExAC||Genomic variant annotation|
|IMPC||Mouse model phenotypes|
|NCBI||Literature, gene summaries, significance of genetic variation|
|MARRVEL||Disease associations, gene expression|
|STRING||Protein interaction networks|
|Wikimedia||Encyclopaedia and dictionary|
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
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.
Tools > Extensionsfrom the chrome menus; a new tab should appear listing all your installed extensions
Details; the view should change and display more details on the extension
- Scroll down to the setting
Allow access to file URLsand turn on the switch.
The extension has a dedicated page where you tune which data sources you would like displayed in the popups.
Tools > Extensionsfrom the chrome menu.
FAIR-biomedin the list of installed extensions and click
- Scroll down to the setting
Extension optionsand 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.
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.
In the news
FAIR-biomed was featured in the news!
- Using Europe PMC RESTful APIs, August 20 2019.
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.
Feedback and contributions are welcome. Please raise an issue in the github repository.
To incorporate a new data resource or plugin, see the documentation.