OntoMaton and an update on development

[Eamonn Maguire]

Hi all,

For those of you at ISMB, we hope you're having a great time! :) Susanna and Philippe are there so if you want to meet with them, dorp an email to isat...@googlegroups.com where they'll both pick up the messages.

We have some updates for you all:

1) OntoMaton - ontology search & tagging right within google spreadsheets

We've just released OntoMaton an ontology search and tagging tool powered by the NCBO bioportal. You can access it via the script gallery located under the tools menu in google spreadsheets. Search for ontology or ontomaton, both will lead you to the tool for installation. Full information can be found in the related blog post here: http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/

2) New member to the team - Alejandra Gonzalez-Beltran

Alejandra Gonzalez-Beltran has joined our team as a developer. Alejandra used to work at UCL and has focused her research largely around linked data. She has already made great strides with Philippe on creating a converter between ISA and OWL and is also working on completion of the R ISA-Tab module for inclusion in the next release of Bioconductor. The Github repository for that is available here https://github.com/ISA-tools/isa2owl - code will be added here, so 'follow' the repository to keep up to date on its development. 

More updates coming soon as well as news about our newest releases of all the tools!

Have a great weekend,

Eamonn Maguire

(on behalf of the ISA team)

[Bob MacCallum]

Hi Eamonn et al,

OntoMaton looks awesome, but I'm having some trouble taking it for a test drive via the example document here
https://docs.google.com/spreadsheet/ccc?key=0Al5WvYyk0zzmdDNLeEcxWHZJX042dS0taXJPNXpJMHc#gid=2

I've tried FF on Linux and FF and Chrome on Mac.

Each time I execute a script from the OntoMaton menu the mini popup dialogue "Running script ontologySearch Dismiss" stays there and never goes away (and no ontology lookup magic occurs).  IIRC the OntoMaton menu wasn't even there in Chrome.

Is there something else I need to do?

cheers,
Bob.


On Saturday, 14 July 2012 18:10:25 UTC+1, Eamonn Maguire wrote:

Hi all,

... 

1) OntoMaton - ontology search & tagging right within google spreadsheets

We've just released OntoMaton an ontology search and tagging tool powered by the NCBO bioportal. You can access it via the script gallery located under the tools menu in google spreadsheets. Search for ontology or ontomaton, both will lead you to the tool for installation. Full information can be found in the related blog post here: http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/

... 

[Eamonn Maguire]

Hi Bob,

We have not encountered this error and i've just opened the OntoMaton utility there now, just to ensure there were no problems with google.

I would guess (if it was just one browser doing it), that you have some popup blocker which is maybe stopping it from running, but even this is a guess. How long did you leave it before you gave up? It is supposed to give the message "Running script ontologySearch Dismiss", but that should quickly turn to finished, then should give you the tool in a window.

Thanks and happy new year! :)

Eamonn

-- Eamonn Maguire Oxford e-Research Centre & Computer Science Department University of Oxford 7 Keble Road, Oxford, OX1 3QG T: 01865 (2) 610788 M: 07526 924483

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[Bob MacCallum]

Just to say that Eamonn and I figured out that OntoMaton may only work if you install it in your own spreadsheet (a three click procedure) and authorize it (another click).  YMMV with the demo sheet.

cheers,
Bob.

[Bob MacCallum]

Also wanted to add that my colleague here in my office can use the OntoMaton scripts on the aforementioned spreadsheet after clicking "OK" to the security warning that the scripts are by me and not google.  So no worries, it really does work collaboratively!

I've changed the column headings it looks for to "Term Source REF" and "Term Accession Number" by the way.

Now, what to do with these purls...

[Eamonn Maguire]

Thanks Bob,

It seems we made an mistake with those column headers. Will modify this asap. PURLs are semi-awesome when they resolve to a useful place :) 

Thanks,

Eamonn

-- Eamonn Maguire Oxford e-Research Centre & Computer Science Department University of Oxford 7 Keble Road, Oxford, OX1 3QG T: 01865 (2) 610788 M: 07526 924483