OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets.
Version 2:
OntoMaton facilitates ontology search and tagging functionalities within Google Spreadsheets. It has been developed by the ISA Team at the University of Oxford's e-Research Centre.
Access the Open Access Bioinformatics article on OntoMaton here.
Eamonn Maguire, Alejandra González-Beltrán, Patricia L. Whetzel, Susanna-Assunta Sansone, and Philippe Rocca-Serra
OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets
Bioinformatics 2013 29: 525-527. doi: 10.1093/bioinformatics/bts718
Please, note that at the time of the publication, OntoMaton was powered by the NCBO BioPortal web services. Since then, we have made the following extensions:
For more information, see our blog posts on OntoMaton.
With the new add on infrastructure, installation is very easy.
You should get the following result:
Here you can click on the image and read more about OntoMaton:
You can access it through the 'Add On' menu option.
From OntoMaton, you can search three different services within one tool: the NCBO Bioportal, Linked Open Vocabularies and EBI Ontology Lookup Service, and insert the terms in your Google Spreadsheet directly. Full term provenance is recorded for you and later downstream analysis.
With OntoMaton, you can select a number of spreadsheet cells and then 'tag' them. This means that OntoMaton will take the terms in the cells and send them to BioPortal's Annotator service. The results will come back as a list of the free text terms, showing for each all matches in BioPortal.
From the settings screen, you can configure:
When you add a restriction using the 'Settings' panel for the first time, a 'Restrictions' sheet will be added automatically. This sheet will have the following column headers:
Column Name | Ontology | Branch | Version | Ontology Name | Service
. Then you may define for a particular column header in your spreadsheet what ontology should be searched (or list of ontologies) over what service (BioPortal, OLS or LOV). A restriction will only apply if using the corresponding service for search.
Additionally, within one ontology restriction, for BioPortal searches, you can restrict to a particular branch of an ontology, providing a way to further restrict the search space.
An example of a google spreadsheet with such functionality can be viewed here: https://docs.google.com/spreadsheet/ccc?key=0Al5WvYyk0zzmdDNLeEcxWHZJX042dS0taXJPNXpJMHc
Access the video tutorial showing how to install and use OntoMaton (version 1) here.
Templates can be found through accessing them on the google templates site. OntoMaton templates are here.
If you have any queries, please email us at link. For bug reports, please use the issue page here.
This work is licensed through a CPAL license, meaning that any derivitives should carry a powered by OntoMaton logo, shown here.
Fancy an OntoMaton t-shirt? We haven't got any to give away...yet! But...you can buy one of these rather snazzy t-shirts from Spreadshirts for just £15!