Search Results for: ontomaton Toggle Comment Threads | Keyboard Shortcuts

  • agbeltran 10:41 am on November 14, 2014 Permalink | Reply  

    OntoMaton Add-on for Google Sheets 

    ontomaton-fig5

    This is a very delayed blog post about the OntoMaton Add-on version we released earlier in the year. But better late than never: here we describe the new features we incorporated in the latest OntoMaton version.

    OntoMaton is a widget bringing together ontology lookup and tagging within the collaborative environment provided by Google Spreadsheets. The original motivation for creating OntoMaton was to support users to create well-annotated experimental metadata in biosciences in a collaborative way, while keeping track of different versions. Google Spreadsheets provide such facilities for collaboration and versioning, so we combined them with ontology search and tagging functionality offered by the NCBO BioPortal web services. BioPortal is a web-based repository for biomedical ontologies/terminologies with functionality  for searching and visualizing the ontologies and support ontology-based annotations.

    For more information about OntoMaton and its motiviation, see our publication in Bioinformatics and our previous blog posts.

    After our initial version of OntoMaton,

    Consequently, we upgraded OntoMaton to the latest versions of these services.

    We also took the opportunity to incorporate searches across the Linked Open Vocabularies repository. Linked Open Vocabularies (LOV) is a repository of (RDFS or OWL) vocabularies used in the Linked Data Cloud, and thus, not restricted to bio-ontologies. This addition allows OntoMaton to be used for other use cases, relying on vocabularies outside the bio-domain.

    For this new version, the installation procedure with Google Add-ons is as follows:

    • Open a Google Spreadsheet and select the Add-ons menu

    ontomaton-fig1

    • Select Get add-ons, search for OntoMaton

    ontomaton-fig2

    • By clicking on OntoMaton, you can find more information about it, including some screenshots.

    ontomaton-fig8

    • Then you can install OntoMaton (by clicking over the Free button) or if it is already installed, you can manage the installation by clicking on the Manage button.
    • You will need to authorise OntoMaton to view and manage your spreadsheets (as the Add-on will search over terms from your spreadsheets and incorporate links, etc) and connect to an external service (the REST services that OntoMaton relies upon)

    ontomaton-fig3

    •  After that, you will be able to use OntoMaton functionality, accessible from the Add-ons menu

    ontomaton-fig4

    • And that’s it! You can start using OntoMaton for searching and tagging… The functionality is as before, except that when searching you need to select if you want to search BioPortal or LOV.

    ontomaton-fig6

    ontomaton-fig7

    In the Bioinformatics publication, we shown some of the use cases for OntoMaton. More recently, OntoMaton has been:

    If you are interested in the OntoMaton source code, you can find it in its GitHub repository.

    Finally, if you have questions or comments about OntoMaton, contact us (the ISA team) at isatools <AT> googlegroups.com (replacing <AT> for @!). We would love to hear about how you are using OntoMaton!

    Advertisements
     
  • agbeltran 9:26 am on August 3, 2013 Permalink | Reply  

    OntoMaton at the International Conference on Biomedical Ontology (ICBO) 

    The 4th International Conference on Biomedical Ontology (ICBO 2013) took place in Montreal, Canada, on 8th and 9th July 2013. It was held jointly with the Canadian Semantic Web Symposium (CSWS 2013) and Data Integration in the Life Sciences (DILS 2013) in what was called the Semantic Trilogy 2013.

    The members of the core ISA team could not be present this time, but our collaborator and co-author Trish Whetzel was there to present OntoMaton in the Highlight Track entitled OntoMaton: Google spreadsheets meet NCBO BioPortal services. We take this opportunity to thank Trish for her presentation, which was very well received. We have had many new users from the Biomedical Ontology community since ICBO.

    The presentation was about our publication “OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets” available (open access) in Bioinformatics. 2013 February 15; 29(4): 525–527.

    OntoMaton is a script for Google Spreadsheets that relies on NCBO Bioportal Web Services to provide searching and tagging with ontology terms, using those ontologies registered in Bioportal. These functionality for ontology-based annotation of spreadsheets can be used collaboratively among distributed parties. Also, Google Spreadsheets provide version control.

    This is the link to the publication in Bioinformatics: http://bioinformatics.oxfordjournals.org/content/29/4/525 and this is in PubMed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3570217/.

    And the slides that Trish presented are here:

    If you are interested in OntoMaton, apart from the publication and slides, you can also see our previous blog postour YouTube video, some templates and the source code on Github.
    Thanks again Trish for presenting OntoMaton at ICBO!
     
  • agbeltran 7:29 am on January 22, 2013 Permalink | Reply  

    New year, new paper, new features! 

    Happy New Year to all!

    Our first post of the year is about a few announcements about OntoMaton, our tool for ontology searches and ontology tagging in Google Spreadsheets introduced back in July (see our previous blog post here and the initial video tutorial here). OntoMaton relies on NCBO web services to provide the tagging and searching functionalities based on ontologies, which are available through National Center for Biomedical Ontologies (NCBO) BioPortal.

    First, we would like to announce that our OntoMaton paper has been published in Bioinformatics! The paper is entitled “OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets”, it is open access and a collaboration between the ISA team and Trish Whetzel on behalf of the NCBO, Stanford University, USA. The paper can be found following this link.

    Second, we would like to describe some extensions of the OntoMaton functionality that we produced since we first announced the tool. This new version is already available through the Google Apps Scripts Gallery.

    The new functionality includes:

      1. a new ‘Settings’ menu (see a screenshot below), which allows you to:
        •  select between two options for where to place the term name and accession: in the same column or in different columns (see screenshot). The default value is “Place term name and accession in same column.”
        • restrict the search space for columns, by selecting the ontologies sources for the terms in that column. These restrictions are added to a ‘Restrictions’ spreadsheet. While this functionality was already available in the initial version, the ‘Restrictions’ spreadsheet had to be created manually. In fact, currently the ‘Settings’ options allow you just to select ontologies to restrict the search space of particular columns, but by manually modifying the ‘Restrictions’ spreadsheet you can also restrict to specific versions and branches of the ontologies.

    OntoMaton-Settings-popupwindow                  OntoMaton-links

    1.  both ontology tagging and searching functionalities, now provide a ‘Details’ option, which allows you to see the term ID and definitions of the terms you are considering (see screenshot below), so that you can make a more informed decision on the appropriateness of the term for your annotation.

    OntoMaton-details

    If you have already installed OntoMaton in a Google Spreadsheet, you will need to reinstall it to have the new functionality. If you are installing it for the first time in a Google Spreadsheet, you need to follow the same instructions as before (see our previous blog post here).

    The code updates are available in the GitHub repo, and if you have any feature requests or bug reports, please leave us a note in the Issue tracker.

     
  • Eamonn Maguire 9:18 am on July 24, 2012 Permalink | Reply  

    OntoMaton tutorial video now available 

    Prepared by Philippe!

     
  • Eamonn Maguire 7:41 am on July 18, 2012 Permalink | Reply
    Tags: , , templates   

    Blank Google Spreadsheet Template with OntoMaton 


    Template

    We’ll be adding more templates shortly in the ISA format, making it even easier for you to use OntoMaton within Google docs.

     
  • Eamonn Maguire 5:50 pm on July 13, 2012 Permalink | Reply
    Tags: Google docs, , ISA-Ta, , ,   

    Introducing OntoMaton – Ontology Search &amp;amp;amp; Tagging for Google Spreadsheets 

    We are happy to announce the release of OntoMaton, a tool which allows users to search for ontology terms and tag free text right in Google Spreadsheets. This post will serve to introduce you to the tool, how it works and how it can make it easier for users to use ontologies in a pervasive, powerful and collaborative environment, complementing existing work from our team in the creation of ISAcreator.

    How it looks

    OntoMaton is available from the Google Script Gallery and when installed provides a menu as shown below.

    From the menu you may access two resources part of OntoMaton: ontology search and ontology tagging. There is also an ‘about’ option.

    Ontology Search

    Ontology Tagging

    Behind the scenes: restricting the ontology search space

    If a sheet named “restrictions” is in your spreadsheet, OntoMaton will consult it to determine if the currently selected column/row name has a narrowed ontology search space. This makes it quicker to search BioPortal, allows for restriction of the user’s result space to make easier the process of selecting a term.

    Behind the scenes: extra information about the terms you select

    For every term you select, it’s full details are recorded in a “terms” sheet. This makes it possible to use OntoMaton in any spreadsheet and all provenance information (including URIs, ontology source and version) for selected ontology terms will be immediately available for use when exposing your records to the linked data world!

    Installing

    To install, create a new google spreadsheet, then go to the menu tools > script gallery. In the script gallery, search for ontology or ontomaton and you’ll get the following result pane.

    Click on ‘install’ and this will install the scripts inside your spreadsheet. Then there is one more and final step to follow for installation. You have to click again on tools > script manager and you’ll be presented with something like that shown in the image below.

    OntoMaton contains lots of functions, but the only one you need to worry about in order to run the program is the onOpen function. Click this then click on run and the OntoMaton menu will be installed in your menu bar. From here you’ll be able to access the ontology search and ontology tagging functions.

    Let us know what you think! New releases will come soon to fix any problems you may identify, please submit all ‘bugs’ and feature requests through https://github.com/ISA-tools/OntoMaton/issues

    OntoMaton inherently supports ISA-Tab files too. So if you have an investigation file it will automatically add ontology sources to the ONTOLOGY SOURCE REFERENCE block. Also, if you have Term Source Ref and Term Source Accession after a column, OntoMaton will automatically populate these columns for you.

    Also, the following table provides a quick review of available tools attempting to mix spreadsheets and access to vocabulary servers:

    domain

    automated

    annotation

    ontology search/lookup

    versioning*

    collaboration

    RightField

    general

    ISA creator

    multiomics

    Proteome Harvest PRIDE

    proteomics

    Annotare

    transcriptomics

    OntoMaton

    general

    • by versioning we refer to managing of user edits throughout the annotation process.

    We hope you enjoy this new feature!

    The ISA team

    Addendum:

    Safari 6 users, be aware you will have to activate the ‘developer menu’ from the Advanced Item in the Safari ‘Preferences’ menu item. Once activated, go to menu ‘Develop’ and navigate to ‘User Agent’ item and select ‘Safari 5.1.7’ for enabling the browser to work with Google Spreadsheet. (Thanks to rpyzh for reporting the issue, see here)

     
    • Michel Dumontier 6:16 pm on July 14, 2012 Permalink | Reply

      Can you provide more details setting the list of allowed ontologies for the “restrictions” tab?

    • Geordie Pele 6:45 pm on July 14, 2012 Permalink | Reply

      Superschlagen! Looks canny lad, gut!

    • Eamonn Maguire 9:02 am on July 16, 2012 Permalink | Reply

      Ta pet 🙂 Canny.

    • Alan Ruttenberg 6:43 pm on November 5, 2012 Permalink | Reply

      No definitions!
      I notice that there is a pop up saying what Ontomaton is, when I’m selecting it from the list of scripts. Our ontology terms deserve the same treatment! Please also include the definition with the other “provenance” information that can be inserted into the spreadsheet too. (you know I was going to say this, right?)

      • Eamonn Maguire 6:46 pm on November 5, 2012 Permalink | Reply

        Michel had a similar comment. We want to have the definition, however the query time on bioportal increases a lot. We will speak with the bioportal tea and see if this can be solved. If so, having definitions will be no problem.

    • Alan Ruttenberg 6:58 pm on November 5, 2012 Permalink | Reply

      A slow tool that lets you pick the right ontology tool is better than a fast tool that helps you make mistakes.

c
Compose new post
j
Next post/Next comment
k
Previous post/Previous comment
r
Reply
e
Edit
o
Show/Hide comments
t
Go to top
l
Go to login
h
Show/Hide help
shift + esc
Cancel
%d bloggers like this: