Video Tip of the Week: OntoMaton productivity app

This week’s tip highlights not a whole database or big resource like we generally do–it presents a small productivity app that help you in many types of investigations once you’ve got data from a big mining effort or from a project you are working on, and want to curate it, consider OntoMaton to help you out.

OntoMaton is just one of a whole bunch of handy little tools of this type, though. It comes from the Isa-Tools team, where they are working to create helpful and flexible features that you can use in spreadsheets like Google spreadsheets, and for other types of analysis, validation, conversion, or other tasks. So you might have a big list of genes or regions or variants that you are investigating in more detail. Using OntoMaton could catalog lists of items using standard term lists from the NCBO BIoPortal ontology collections. And even within your own project you would want to standardize the way you annotate or describe these tools–and if you are working with others it’s only more complicated. But you could all use these apps to describe the features using standardized terminology. I can see this being a great model for citizen science sorts of projects too.

And when your data got toward the publication and submission stages, it will make your life easier to already have your data curated with standardized terms and ontologies that databases and publishers might require.

I found out about this from a post by Mark Fortner on Google+, but you should go to his blog and read the longer version of his look at OntoMaton: Tinkering with OntoMaton. And I’ve been working on a number of projects that involved a Google doc curation project with multiple folks–I’m certain this kind of standardized terminology would have been a real benefit across a team that’s hacking away at a project of this sort. This Google widget is a neat idea, and a good model for other types of cloud-based shared projects as well.

There’s a short paper that describes OntoMaton that I’ve linked below. The embedded video is for the OntoMaton features. But I’ve also included the publication for the wider ISA software suite of projects. You should go over to their site Isa-Tools and click the “Software Suite” navigation to examine a whole lot more of these.

Quick link:



Rocca-Serra P., Brandizi M., Maguire E., Sklyar N., Taylor C., Begley K., Field D., Harris S., Hide W. & Hofmann O. & (2010). ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level, Bioinformatics, 26 (18) 2354-2356. DOI:

Maguire E., Gonzalez-Beltran A., Whetzel P.L., Sansone S.A. & Rocca-Serra P. (2013). OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets, Bioinformatics, 29 (4) 525-527. DOI: