InterMine Data Browser Presentation Google Summer of Code 2018 Adrián Rodríguez-Bazaga

1. InterMine Data Browser
Google Summer of Code 2018
Adri´an Rodr´ıguez Bazaga
Organization: InterMine (University of Cambridge)
Mentors: Yo Yehudi, Rachel Lyne
Mail: adrianrodriguezbazaga@gmail.com
Twitter handle: @AdrianBZG
16th August 2018
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2. Outline
1 Overview
2 Tool Features
3 Demo
4 Future Work
5 References
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3. Overview
Problem Description
The existing query builder in InterMine requires some experience to
obtain the desired data in a mine, which can become overwhelming for
new users.
Challenge
For example, a query that given the human gene symbol “GATA1”
shows all genes interacting with it through a genetic interaction on
BioGRID dataset may sound simple-ish, but building it in our query
builder requires a strong familiarity with the data model.
Goal
The goal of this project is to implement a faceted search tool to display
the data from InterMine database, allowing the users to search easily
within the different mines available around InterMine, without the
requirement of having an extensive knowledge of the data model.
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4. Tool Features
1 Easily search over the different mines available within InterMine.
2 Filter the data with typeaheads and graphics in an intuitive way.
3 Leverage the query building and constraint handling tasks to the
server-side.
4 Plots and numeric counts of data to quickly show the data being
stored in a mine and understand it’s nature.
5 Alleviating the heterogeneity of the biological data feeding the
mines to the user, making it profit from the FAIR principles.
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5. Tool Features
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6. Demo time !
⇒ http://data-browser.apps.intermine.org/
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7. Future Work
Allow users to add their personal InterMine’s API tokens for each
mine.
Phenotypes filter.
Histogram plot to the top section about Gene length.
“Current class” filter added on the sidebar.
Refactor the per-mine filters to use path query.
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8. Join the development!
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9. References
GitHub repository
https://github.com/AdrianBZG/InterMine-Data-Browser-Tool
Heroku deployment
http://im-browser-prototype.herokuapp.com/
InterMine Apps deployment (may be outdated)
http://data-browser.apps.intermine.org/
Travis CI tracking
https://travis-ci.org/AdrianBZG/InterMine-Data-Browser-Tool
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10. Thank you for your attention...
...and waiting for your commits!
Contact:
Adri´an Rodr´ıguez Bazaga:
adrianrodriguezbazaga@gmail.com — linkedin.com/in/adrianbazaga/
Yo Yehudi: yo@intermine.org
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