Category Archives: ISAcreator

ISAcreator 1.7.11 now available

Today we announce the release of ISAcreator 1.7.11.

This release updates ISAcreator to work with Java 9.

You can download ISAcreator 1.7.11 from Github here: https://github.com/ISA-tools/ISAcreator/releases/tag/v1.7.11

If you’re an ISAcreator user, or use any of the other ISA-tools suite, please let us know and we can list you as being part of the ISAcommons community.

If you have any questions or any problems with using ISAcreator, please drop the ISA Team an email to isatools@googlegroups.com or to the ISA community forum.

ISAcreator 1.7.10 available now

Today we announce the release of ISAcreator 1.7.10.

Included in this release are several bug fixes primarily relating to Windows 10 file system issues that have been reported by the user community.

Above adapted from original photo by Robert Lee under Attribution-NonCommercial 2.0 Generic (CC BY-NC 2.0).

You can download ISAcreator 1.7.10 from Github here: https://github.com/ISA-tools/ISAcreator/releases/tag/1.7.10

If you’re an ISAcreator user, or use any of the other ISA-tools suite, please let us know and we can list you as being part of the ISAcommons community.

If you have any questions or any problems with using ISAcreator, please drop the ISA Team an email to isatools@googlegroups.com or to the ISA community forum.

ISAcreator 1.7.9 available now

Today marks the release of ISAcreator 1.7.9. It’s been a long time coming having been more than 2 years since the last update to the ISA framework’s flagship ISA-Tab creator and editor software.

Included in this release, we have addressed a range of bugs with fixes covering UI issues, file path handling errors, and cross-platform issues with bug reports from our Windows users. With this release, we want to demonstrate to our valued user community that development and maintenance of ISAcreator is still active and continues to be the de-facto editor for the ISA-Tab format.

You can download ISAcreator 1.7.9 from Github here:
https://github.com/ISA-tools/ISAcreator/releases/tag/1.7.9

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: Cytoscape, Galaxy, GenePattern, Genomica, Integrative 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’:

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):

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.

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

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:

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:

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):

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:

https://github.com/ISA-tools/ISAcreator/issues

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)

New developments: publication search UI improvements

I’ve never really liked the Publication locator utilities user interface much, so whilst at BioCurator, in the spare time I had, I redid the interface to make it clearer, faster and more informative to users. The result of the improvements are shown in the screenshots below!

Search by pubmed id – like the last version, only nicer 🙂

Publication information is now clearer, and you can easily access a previous search via the last result button in the top panel.

I might make some more improvements to the UI in the next few hours, but for now I think it’s much better than it was!

New developments: Transposed spreadsheet views in ISAcreator…

Some of our collaborators, especially those annotating samples with a lot of information told us that the standard spreadsheet view we presented in ISAcreator didn’t work so well when trying to annotate their data. So….we decided to add a transposed view to the spreadsheet, essentially flipping the spreadsheet around to make it easier for people to enter information.

Transposed Spreadsheet

Highlight the different types of data to be entered, making it easier to disseminate between different data entry fields.

The feedback we’ve received so far from users at GSC10 (http://gensc.org) and BioCurator have been extremely positive. This is yet another feature added from receipt of user feedback! Let us know what you think we’re missing and we’ll do our best to serve your needs providing there is enough interest from the community!

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!