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  • 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!

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  • agbeltran 12:31 pm on October 6, 2014 Permalink | Reply  

    We are hiring! 

    The ISA and BioSharing team is hiring!

    We are seeking to appoint a Software Developer based in the Life, Natural and Biomedical team within the Oxford e-Research Centre at the University of Oxford. In this varied, interesting and challenging role the successful candidate will provide technical knowledge, software engineering and leadership ability for (i) the ELIXIR UK node of the ELIXIR programme, and (ii) a growing portfolio of data and knowledge management projects.

    The position requires a software engineer/research associate with both technical and social ability, and also experience and skills to manage more than one project, plan and monitor project deadlines, assist in writing reports and communicate with geographical distributed collaborators. The successful candidate will liaise with end users and collaborators (e.g. at the European Bioinformatics Institute, Stanford University, Manchester University, Imperial College), members of community-driven initiatives (e.g. working groups in the Research Data Alliance) and developers of data publication platforms journals (e.g. at Nature Publishing Group and BioMedCentral). The candidate will work closely with the team and contribute towards the enhancement of relevant components of the ISA software suite (see the ISA commons community) and of the BioSharing registry, embedded into a large number of UK, EU and NIH funded projects.

    This post is fixed-term for 3 years.

     

    For more information and to apply, visit this link.

     
  • 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 5:05 pm on June 18, 2013 Permalink | Reply  

    ISAcreator available in GenomeSpace 

    ISAcreator has supported access to GenomeSpace since release 1.7.0. and it is now also available through the GenomeSpace online interface.

    GenomeSpace is a framework supporting cloud-based interoperability of genomics analysis tools. By providing access to multiple tools through their interface, and supporting file transfers in the cloud, GenomeSpace provides a bridge among the tools, allowing users    Some of the tools available through GenomeSpace are: CytoscapeGalaxyGenePatternGenomicaIntegrative Genomics Viewer (IGV), and the UCSC Genome Table Browser. Find out more about what is GenomeSpace and what GenomeSpace can do for you.

    I will now describe the functionality ISAcreator supports for GenomeSpace.

    You can launch ISAcreator from your desktop or you can launch it once you are logged in to GenomeSpace (after registering to their service). For launching ISAcreator from within GenomeSpace, just hover over the ISAcreator icon and select ‘Launch’:

    GS-8

    If you launch ISAcreator from GenomeSpace, you will be prompted to download ISAcreator and will see the following pop-up window (after you accept to download the file):

    GS-10

    When running ISAcreator (either from your desktop or following the GenomeSpace route), you will notice that it now has a third mode of operation (apart from the previously available light and normal modes) that corresponds to GenomeSpace. With this third method of operation, ISAcreator supports opening ISA-TAB files stored on the cloud environment provided by GenomeSpace and also, saving files into GenomeSpace storage facilities.

    GS-7

    If you choose the GenomeSpace mode, you will have to enter your GS user credentials in the ISAcreator login page:

    GS-3

    Then you will load the configuration files, as usual, and get to the main menu where you can choose to load an existing ISA-TAB file. If it is not the first time you are loading files, you will see the previously loaded files and also have the option to search GenomeSpace for more files:

    GS-11

    As an example, you can find the publicly available BII-I-1 ISA-TAB dataset in GenomeSpace under Public/agbeltran/ISA-TAB-datasets, and select it to load:

    GS-12

    After loading an ISA-TAB dataset, you can save it to GenomeSpace (even if it is a local dataset that you want to store in GenomeSpace):

    GS-13

    GenomeSpace also provides documentation about ISAcreator in this page and a guide about using ISAcreator in this other page.

    As always, send us comments or questions contacting:

    • the ISA team at isatools [at] googlegroups [dot] com, 
    • the ISA user forum at isaforum [at] googlegroups [dot] com

    or send us feature requests or bug reports through the issue tracker in Github:

     
  • 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.

     
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