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  • 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 & 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.

  • Eamonn Maguire 9:26 am on June 8, 2012 Permalink | Reply
    Tags: Jobs, New starter   

    Alejandra Gonzalez-Beltran Joins the ISA team 

    The ISA team is very happy to announce that Alejandra has joined the ISA team as a software engineer. Alejandra will add a great deal to our team and we’re  especially looking forward to her contributions in our semantic web & linked data work.

    You can follow her on Github where Alejandra will be putting all of her code or on Twitter.

     
  • Eamonn Maguire 9:11 am on June 8, 2012 Permalink | Reply  

    My Data are your Data 

    “Encouraging more broad and inclusive data sharing in today’s world will involve concerted community efforts to overcome technical barriers and human foibles. Vivien Marx investigates.”

    A nice article by Vivien Marx is in Nature Biotechnology this month. He strongly mentions the ISA commons and BioSharing, two initiatives from our group and their importance in encouraging data sharing.

     
  • Eamonn Maguire 10:39 pm on May 15, 2012 Permalink | Reply  

    New Continuous Integration System for ISA tools 

    All of our tools are being ported over to Travis CI, so now you’ll be able to see the builds of the tools for ISAcreator, BII, etc. on every commit, and also see the current build status directly from each GitHub page.

    ISAcreator build status now more visible. This is happening now for all our tools incrementally over the next few weeks.

     
  • Eamonn Maguire 2:47 pm on May 3, 2012 Permalink | Reply
    Tags: mailing list,   

    We are close to releasing new versions of all the tools, with many features added and many things improved, including performance! Message coming soon via our isaforum mailing list (see http://isatab.sourceforge.net/contact.html for details on joining this list).

     
  • Eamonn Maguire 2:45 pm on May 3, 2012 Permalink | Reply  

    ^ *([\w_]+(?: *[\w/_\-\: ]+)? *) *(?:\[ *([\w_]+(?: *[\w/_\-\: ]+)? *)* *(?:\( *([\w_]+(?: *[\w/_\-\: ]+)? *|\b(((\S+)?)(@|mailto\:|(news|(ht|f)tp(s?))\://)\S+)\b) *\))?\])? *$

    Not my largest regex by any means, but it looks complicated :)

     
  • Eamonn Maguire 12:56 pm on March 25, 2012 Permalink | Reply
    Tags: Google, nescent, phylogenomics, summer of code   

    Google Summer of Code Project with Nescent and ISA-tools 

    Are you a student interested in evolutionary biology and open-source software development?

    PHYLOINFORMATICS SUMMER OF CODE 2012

    http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012

    The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program receive a stipend from Google (and the coveted T-shirt upon completion!), and work from their home, or home institution, for the duration of the 3 month program. You will have to opportunity to collaborate with our enthusiastic mentor community, and will have at least one dedicated mentor to help you complete your project. We are particularly targeting students interested in both evolutionary biology and software development.

    Our website, above, lists potential projects. Projects include many programming languages (e.g. C/C++, Java, Perl, R) and cover subjects ranging from visualization to algorithm implementation to data interoperability. You don’t need to be an expert in either evolutionary biology or software development – find a project idea that interests you, and we can work with you to develop a proposal that fits your skills. We also welcome novel project ideas apart from those already on the list.

    INTERESTED? Contact us phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. Admission is competitive, and we want plenty of time to work with you to develop a great project proposal.

    TO APPLY: Apply online at the Google Summer of Code website: http://www.google-melange.com/gsoc/homepage/google/gsoc2012 where you will also find GSoC program rules and eligibility requirements. The 14-day application period for students opens on Monday March 26th and runs through Friday, April 6th, 2012. Google Summer of Code FAQ: http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/faqs

     
  • Eamonn Maguire 9:31 am on February 15, 2012 Permalink | Reply
    Tags: MIT, Saliency,   

    What are the salient regions of my webpage? 

    I stumbled across Saliency from the Perceptual Science Group @ MIT.

    It identifies, given some web page, the important regions of your page, from what I can tell, it focuses on bright regions. The results are presented in a blacked out page, highlighting the ‘salient’ regions.

    Information about how the algorithm works is available from here.

     
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