Updates from June, 2010 Toggle Comment Threads | Keyboard Shortcuts

  • Eamonn Maguire 7:42 pm on June 16, 2010 Permalink | Reply
    Tags: Flash, MIBBI, , Standards   

    MICheckout and how it’ll make your life easier 

    MICheckout is a new service from the MIBBI project. It allows one to select the concepts needed to describe an experiment and then produce XML, XSD, TAB and eventually (soon) ISAcreator configurations.

    Some screenshots of the tool are below.

    Selecting concepts in MICheckout is easy.

    Export to XSD, XML or Tab delimited files with the click of a button.

    information about related projects and contact details.

    The really nice thing is that everything is backup up by a nice web service which given certain accessions and information about what you want to produce, will create the checklist for you, without any need for a user interface!


    or, to view a checklist as a HTML table/list:



    Very neat!

  • Eamonn Maguire 4:29 pm on June 15, 2010 Permalink | Reply  

    Browse & search OLS and BioPortal Seamlessly with ISAcreator and ISAcreator configurator 

    For browsing and querying OLS and BioPortal seamlessly, ISAcreator and it’s associated configurator have done much to make life easier for it’s users.

    ISAcreator configurator and it’s use for ontologies

    ISAcreator Configurator is a tool used by community experts or curators to detail the Minimum Information (via MIBBI for instance) that users should enter to describe their experiment. As part of this, curators can define which fields (e.g. Sample Name) are required, whether or not they require ontology terms and if so, which ontologies (and parts of the ontologies) users should be pointed to.

    ISAcreator Configurator - allows curators to define 'checklists': these are the fields required to describe an experiment from start to finish.

    The ISAcreator configurator provides both the ability to browse ontologies and to search them, so as to allow curators to select which ontologies and which parts of these ontologies should be suggested to users whenever they annotate a field in the ISAcreator.

    Browsing ontologies

    Users can browse ontologies in OLS and BioPortal via an easy to use GUI. The browsing is done on the fly by accessing hierarchy web services from both the OLS and BioPortal. An extensible code base means that other ontology resource (should they become available) can be added at any point.

    Browse ChEBI from OLS

    Browsing OBI (Ontology for Biomedical Investigations) from BioPortal

    Search within ontologies

    Search within ontologies

    Users can search within ontologies and then locate the ontology in the entire ontology hierarchy. This functionality is provided to aid curators in finding the appropriate branch of an ontology to restrict users to.

    ISAcreator and how it makes ontology selection easier for users

    ISAcreator is a tool used by the community who often don’t know much about ontologies or the minimum information required to describe an experiment. The ISAcreator configurator produces XML describing the minimum information and the ontologies to use so that users need not worry about what to enter.

    ISAcreator's main menu

    The user interface needs to be easy to use, and ontology selection should be seamless. The user needs not know which ontology resource they are browsing, but ontologies should be presented to them in a way which makes selection straightforward. ISAcreator achieves this by automatically prompting users for ontology terms whenever they are set to be required by the ISAcreator configurator.

    Users are automatically prompted for Ontology terms

    Users are presented with the full search result from both OLS and Bioportal in a standard form.

    In summary, the functionalities inside both ISAcreator and it’s associated configurator make browsing and searching both OLS and BioPortal much simpler for users! An API with many advanced functionalities, building upon BioPortal and OLS services will be released soon as well as a standalone ontology browser and searcher!

    Download ISAcreator and the ISAcreator configurator now from the ISAtab sourceforge site!

  • Eamonn Maguire 12:37 pm on June 15, 2010 Permalink | Reply  


    As part of our ongoing attempts to improve our communication to our community we’ve set up this blog to not only describe what’s going on with development, but explain some of the features of the tools which you may not be aware of!

    You can also follow us on twitter at http://twitter.com/isatools

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