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.

 

 

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.

 

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

The ISA team.

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)

ISA tools web page updated

We’ve revamped the ISA tools website to try and clean things up a bit. The old site wasn’t exactly great! In any case, please check out the new site. Here are some screen shots! 🙂

 

Tools page

 

People page

Big improvements to the BII web application (version 1.4)

Performance improvements

A few weeks ago, we started loading the InnoMed datasets in the EBI instance of the BioInvestigation Index and we started to notice performance problems, especially when accessing the detailed study pages (it was taking almost 70 seconds it to render the pages). We found two problems: the growing number of annotations in the database (1.6 million) were increasing the query space considerably; and 2) the inefficiencies present in Hibernate queries resulted in larger scope queries than we really wanted .

So, we improved the Lucene index which was generated from the loader and already consumed by the web application to generate the browse view and made it capable of holding all of the assays, factors, characteristics, publications, contacts & their respective content so that we would remove the inefficient queries necessary to generate the study page and therefore make things quicker. Now, everything is quicker and there is no real latency in the page load process. Plus, we’ve also adding server-side caching to further reduce lag. So now, pages such as this one http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-8 load almost instantly, compared to the 90 seconds it took beforehand (obviously completely unacceptable).

Interface improvements

If you visit the EBI or Harvard Stem Cell Discovery Engine instances of the BII, you’ll immediately see the improvements to the web application look and feel. We’ve made considerable improvements to clean up the interface and make browsing the content much easier.

The browse study view

Log in/register view

Detail information view

We still have some plans to even further enhance the web application, so watch this space for version 1.5! You can download version 1.4 from here…you’ll need maven 2.2.1 and JBoss 5 installed first though! There are instructions on our GitHub pages about how to build!

In ISAcreator 1.4 we have made a very…

In ISAcreator 1.4, we have made a very significant release, improving many aspects of the codebase, solving many of the problems encountered in previous releases, adding new functionality and further improving the user interface. We won’t go into everything here, but will list the major changes:

Better performance: We’ve tweaked the code, refactored and improved performance and memory load drastically.

Light mode and advanced mode. Now you can run the creator without the added complication of the wizard or mapper functionalities. If you need them, they are there, but if you don’t then just use the light version.

New error display: remember the ugly list of errors you had when the ISAtab wasn’t valid? Well, that’s gone, here’s what the new version looks like.

New ontology lookup interface and the ability to browse within restricted ontologies (e.g. a Label should come from ChEBI) either on the entire ontology level (if no branch of the ontology is specified) or on a specific branch so that the users selections are more targeted.

Automated annotation of your free text with ontology terms using the NCBO Annotator service.

You can download it for Mac, Linux and Windows.