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  • Eamonn Maguire 12:18 pm on May 24, 2013 Permalink | Reply  

    ORCID codefest 2013 

    Hi all,

    It’s been a while since we’ve updated you all. Yesterday and today, Alejandra and I participated in the ORCID codefest. ORCID, for those of you who don’t know about it, sets out to create a unique ID for every researcher. Gone will be the days of trying to find your articles online to list it on your web page!

    Eamonn's ORCID Profile page.

    Eamonn’s ORCID Profile page.

    So, what can our projects do with it? We had three ideas:

        1. Use ORCID as a source of information in BioSharing profile pages
        2. Use ORCID information to automatically fill out user profile information in ISAcreator – this won, and Alejandra will be going to CERN in October for the ODIN codefest!
        3. Use ORCIDs in ISA-Tab records to uniquely reference people involved in an investigaton

    1 and 2 were implemented in the last day. So, here’s a breakdown of what we did.

    1. Use ORCID as a source of information in BioSharing profile pages

    User profiles populated from ORCID information.

    User profiles populated from ORCID information in BioSharing.

    In the above image, we are showing my user profile in BioSharing. Any user can have a profile, and can import their ORCID profile by simply entering their ID. In addition to this, BioSharing profiles also include information about the standards, policies and biodbcore records maintained by the user.

    Publication information, with inferred data links and links out to article metrics - shown below.

    Publication information, with inferred data links and links out to article metrics – shown below.

    Aside from just showing the information from ORCID, we also do something which we think is really useful…automated retrieval of data records in public repositories for each publication. At the minute, we search on ArrayExpress, but can extend this to PRIDE, Metabolights and others soon.

    Impact story for an article is made available through the BioSharing interface.

    Impact story for an article is made available through the BioSharing interface.

    So what’s next? Well we’ll push these changes to the main BioSharing page pretty soon, once everything has undergone considerable testing!

    2. Use ORCID information to automatically fill out user profile information in ISAcreator

    Alejandra has been working on using ORCID to populate user profiles automatically when creating ISAcreator user profiles.

    User information automatically added from ORCID.

    User information automatically added from ORCID.

    Users can also search ORCID through an interface shown below if they do not know their ORCID.

    Search for an ORCID record via a dedicated interface.

    Search for an ORCID record via a dedicated interface.

    What’s next?

    We’ll be extending this, improving it and integrating it as a service for looking up contacts in ISAcreator too (point 3).

    Many thanks to the organisers for a great meeting! We really enjoyed this!

     
  • 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.

     
  • agbeltran 5:11 pm on November 23, 2012 Permalink | Reply  

    New paper on the Metabolights database! 

    A recent Nucleic Acids Research (NAR) paper features Metaboligths: the first general-purpose, open access repository for metabolomics studies, storing the studies raw experimental data and associated metadata. You can find the paper here. Metabolights is powered by the the open source ISA metadata framework, and thus is part of the ISA commons, and it is deployed at the European Bioinformatics Institute (EBI).

    Some of the characteristics of the database are: it is cross-species and cross-techniques, it covers metabolite structures and their reference spectra, their biological roles, locations, concentrations, and raw data from metabolic experiments.

    The paper describes the database content and technical architecture, the functionalities for searching and browsing the data, how to download data and get programmatic access to the database, and the data submission process, among other things.

     
  • agbeltran 10:18 am on October 5, 2012 Permalink | Reply  

    Risa is out! And available in the Bioconductor 2.11 release… 

    The ISA infrastructure now includes an R package, called Risa, to parse ISAtab datasets into R objects. The Risa package is included in BioConductor release 2.11.

    Risa provides functionality to read ISA-Tab datasets into R objects. These objects can then be used by downstream Bioconductor packages for data analysis and visualization (i.e, xcms). Currently, metadata associated to proteomics and metabolomics-based assays (i.e. mass spectrometry) can be processed into xcmsSet objects (from the xcms Bioconductor package). Risa also provides functionality to save the ISA-tab dataset, or each of its individual files, and to update assay files after analysis. For an example of using Risa for processing and analysis of metabolomics data, see https://github.com/sneumann/mtbls2.

    The source code and latest version can be found in the GitHub repository https://github.com/ISA-tools/Risa. Please, submit all ‘bugs’ and feature requests through https://github.com/ISA-tools/Risa/issues.

     
  • Eamonn Maguire 10:13 am on September 27, 2012 Permalink | Reply
    Tags: , , , , metabolights, metabolomics   

    New paper! MetaboLights: towards a new COSMOS of metabolomics data management 

    A new paper, featuring the ISA team as authors is now available to read on MetaboLights (EMBL-EBI metabolomics repository).

    MetaboLights, part of the ISA commons is the new European repository for metabolomic data held at the EBI. Their infrastructure is built upon the ISA software stack, utilising ISAcreator for data entry, ISA-Tab as the format then the BII data manager and database for persistence and storage respectively.

    Click here to access the MetaboLights repository.

     
  • Eamonn Maguire 4:41 pm on September 25, 2012 Permalink | Reply
    Tags: , mac osx, mountain lion, security   

    Running ISA tools in Mountain Lion, Maverick, or Yosemite 

    Since Mountain Lion came out, we’ve had some users unable to run ISA tools. The reason why is down to Apple’s change in security policies. Apple now try to restrict the applications run by default on Mac OS to those downloaded from the app store. 

    To change this, you need to access your security preferences. You can access this quickly through spotlight as shown below.

    Image

     

     

    You will then be faced with the security and privacy window and will see a section named “Allow applications downloaded from”. You need to change this from Mac App Store to Anywhere. If you are unable to change it, you first need to click on the lock icon to change it. In the end, your Security and Privacy screen should look like this.

    Image

     

    Apologies for any inconvenience caused. If you have any further queries, please email us at isatools@googlegroups.com

    The ISA team.

     
  • Eamonn Maguire 2:20 pm on September 12, 2012 Permalink | Reply
    Tags: biodiversity, digital research, Mobile apps   

    Eamonn wins the Digital Research 2012 Developer Challenge 

    Eamonn won the digital research 2012 developer challenge last night in an event held at the Oxford e-Research Center. His mobile app, called BioEye, of which a prototype was built in 1 day during the event helps in disseminating better the knowledge about biodiversity in our local environments. The app and idea won in a field of 6 other competitors. Further information about this app will come soon.

    For more information see: http://digital-research.oerc.ox.ac.uk/devchallenge

     
  • 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.

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