Tinkering with OntoMaton

One of the primary challenges in open science is making the experiment data behind a paper easily accessible in a universally acceptable format.  A number of solutions have sprung up over the years to address parts of this problem; however, the primary challenge still remains — how can we make the data “universally” useable?

Imagine that you have been collecting gene expression data on an experiment in Microsoft Excel.  You want to be able to communicate to your colleagues that the data in the first column is gene symbols, the data in the second column is fold changes.  You also want to communicate experimental conditions like who performed the experiment, what tissue was used, what kind of instrument was used, what controls were used, and what protocol was used to arrive at the results.

Ultimately when someone looks at your data, they’ll want to be able to know if your results are correct and reproducible.  And they’ll want to compare your results with their own.

The problem lies in the fact that everyone inputs the data in their their spreadsheet differently.  Within a single lab you might be able to control this by insisting that people use a particular template.  Or perhaps by using a standard like MIAME.  But these standards don’t always exist.

Several years ago, the University of Manchester (long known for its semantic web program), created a tool called RightField to try and address this issue.  RightField allows you to “tag” cells in an Excel file with ontology references.  In effect, allowing you to say, “this column is a gene symbol (as unambiguously defined by this EDAM ontology reference: http://edamontology.org/data_1026)”.  If anyone wants to know what you meant by “gene symbol”, they simply follow the link.

This works well for people who are working with a single spreadsheet on their desktop, but what happens when your lab’s data exists in the cloud?  This is where OntoMaton from ISA Tools (@isatools on Twitter) comes into play.  As the video below shows, you can tag the cells in your Google Docs spreadsheet with ontology references from the National Center for Biomedical Ontology.  

But OntoMaton itself is only part of the picture.  ISA Tools has a whole suite of applications designed to help you collect, analyze and publish data.


About Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
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One Response to Tinkering with OntoMaton

  1. Pingback: Video Tip of the Week: OntoMaton productivity app | The OpenHelix Blog

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