Category Archives: Uncategorized

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.

OntoMaton Add-on for Google Sheets

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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

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  • Select Get add-ons, search for OntoMaton

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  • By clicking on OntoMaton, you can find more information about it, including some screenshots.

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  • 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)

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  •  After that, you will be able to use OntoMaton functionality, accessible from the Add-ons menu

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  • 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.

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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!

BioSharing Profiles automatically assign data with publications

A while ago, we went along to the ORCID codefest at St. Anne’s College, Oxford.

In the day or two of coding, Alejandra won with her entry in adding ORCID functionalities to ISAcreator.

In my entry, I created a system that presented article impact metrics from ImpactStory and also automatically pulled ArrayExpress and PRIDE data links for  publications. The advantages being that users don’t have to go looking for the data for a publication across many repositories. Take this example from ArrayExpress, E-GEOD-31453 – from the submission, you’d never know that there were other data submissions directly related to this submission in ArrayExpress or elsewhere, e.g. E-GEOD-27713. The component developed for BioSharing, but could be used by anyone takes a PubMed ID or DOI and finds the data available in public repositories relating to that publication. It’s use is illustrated in one of the profiles for one of our latest BioSharing users, Sheng-Da Hsu. You can see a screenshot of his publications section below, or see it for yourself here.

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Screen Shot 2013-11-14 at 17.41.11

Getting up and running with the BII Web Application

In true Star Wars fashion, we are bringing you the prequel to the last blog post discussing how to set up data file access from your JBoss installation. In this post we’ll discuss how to set up the BioInvestigation web application, from build to deployment.

1. Getting Ready

  • First, you’ll need to have a Java installed.
  • Then you’ll need to download Maven, this is what automates the build process for the BII web application. A bit like Ant, but it adds dependency management, meaning no need for pesky lib directories. Why this version I hear you ask? Well for some silly reason, the Maven developers (as great as they are) thought that removing the ability to specify profiles in profiles.xml was a great idea. We don’t think it is. In Maven 3+ you can only specify profiles in the pom.xml file or in the settings.xml file under the .m2 directory on your system. So, use version 2.2.1. We’ll move on to configuring these profiles a little later.
  • Now you need Git which we’ll use to get the latest BII codebase from GitHub. If you haven’t heard of Git, you simply haven’t lived. Get out from underneath that SVN rock and join the Git revolution. It’s worth migrating just for the benefit of GitHub or some other funky equivalent (BitBucket or Launchpad).
  • Next, download JBoss 5.1.0 from http://sourceforge.net/projects/jboss/files/JBoss/JBoss-5.1.0.GA and move the JBoss directory to somewhere to your liking. For further examples, let’s say that’s /etc/jboss-5.1.0.GA/ for the rest of this post.
  • Finally, if you want to deploy properly, you’ll need a database. The BII works with Oracle, Postgres, MySQL or MariaDB. You can also run the application just for using the H2 database (we use this for testing). If your database of choice (apart from H2), you’ll need to create a database (we usually name it bioinvindex) and a user (it’s always a good idea to not just use root as the user) and grant that user all permissions to the database.

2. Grabbing the code

With everything in place, you need to ‘clone’ the BioInvIndex repository from GitHub. So navigate to a directory of your choosing, and via the command line type ‘git clone https://github.com/ISA-tools/BioInvIndex.git’. This will create a BioInvIndex directory for you with all the code inside.

3. Configure your profiles

I mentioned earlier about Maven and profiles. In the bioinvindex directory just created for you, you’ll see a profiles.xml file. Not to get too bogged down on details about what these profiles are for, I’ll give a brief explanation. The main pom.xml file (Project Object Model) for maven defines a number of dependencies, or libraries that are required for the application to run. Some of these dependencies are not always known in advance. For example, if I am running an application on MariaDB, why would I want to have Oracle and Postgres libraries in the final EAR (Enterprise Archive, the JBoss answer to WAR files in Tomcat)? The Profiles just allow us to automatically inject some properties in to the pom file on build depending on what the person building it wants to run. Some of these profiles also go towards creating the hibernate.properties file required by hibernate for connection to the database or in specifying to the application the whereabouts of the Lucene index (will talk more about that in a bit).

So now, given you have some context, open profiles.xml up and you’ll find a number of individual ‘profile’ elements for the various database installations and a few for the Lucene index locations.

First, find the profile matching your database and edit the username and password, database name (if not bioinvindex), URL and any version information, etc.

Then, modify the index profiles (named index_local and index_deploy) that specify where the Lucene index for the BII web app will reside. The Lucene index is used to speed up the web application, massively reducing the number of database queries that are required. The majority of the web application front end is based on the contents of the Lucene index. Make sure that the application has read/write access to that location.

4. Build!

Run the command mvn clean package -Dmaven.test.skip=true -Pdeploy,<your_database_profile>,<your_index_profile>

So, if I was deploying using mysql and using the index_deploy profiles, I would run

mvn clean package -Dmaven.test.skip=true -Pdeploy,mysql,index_deploy

Now watch the build succeed. When it completes, look in ear/target/ and you’ll see bii-x.y.ear where x and y are the major and minor versions respectively. The ear, or enterprise archive is what you’ll be deploying. Copy this file in to your JBoss directory, so given we’ve copied the JBoss installation files to /etc/jboss-5.1.0.GA/, we’d copy the ear to /etc/jboss-5.1.0.GA/server/default/deploy/

5. Run the web application

Finally, we want to actually run our application. The next step will rely solely on JBoss. navigate to /etc/jboss-5.1.0.GA/bin/ and you’ll see a number of scripts. The only one you need worry about is run.sh – to run JBoss using the default server (that’s where we copied the ear to), execute the following command – ./run.sh -c default -b 0.0.0.0 & the last bit will bind the server to address 0.0.0.0, so it’ll be visible to the outside world and will run on port 8080 by default. You can change the port by following the guidance in this Stackoverflow post.

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Hopefully everything will start running, and the bii ear will be deployed and you’ll be able to see it at http://localhost:8080/bioinvindex. You will see errors in the startup log, but that’s because nothing exists in our database yet…there are no tables present at this point. We’ll create the database next.

6. Set up the database

For this, you’ll need the BII Manager. You can download this from http://isatab.sourceforge.net/tools.html. The latest version (1.6.1) is available here.

Unzip it and you’ll have a BII-Data-Manager-x.y directory with some files in it. We’ll need to configure some things before we start:

  1. Firstly, the database connection information. Open up the hibernate.properties file under the config/ directory and copy in the same username, password, database URL, index location, etc. as you entered in the profiles.xml for the BII web application.
  2. Next, you may want to set up data-locations.xml. Data locations tell the manager tool where to copy data files and ISA-Tab files as well as the URL the web application will be able to access them from. More information on the set up of JBoss to point to these data directories is available in a previous blog post.

Now, we’re ready to go. If you are using MySQL, H2, MariaDB or Postgres, you’ll be able to run the application by just double clicking isa_deps.jar or executing ./run.sh from the command line.

If you are using Oracle, you will need to add the Oracle driver on the classpath. Edit the run.sh file to do this then when ready, from the command line, run ./run.sh.

When the application starts, you’ll be presented with a log in screen. At this point, create a curator account. When this is done for the first time and the database has no schema available, the application will automatically create the schema via Hibernate (a fantastic tool). So you’ve nothing to do. Then, when that’s completed successfully (if it doesn’t check your hibernate.properties entries), you’ll be able to log in and load content.

Finally, to make things a bit faster, open up your hibernate.properties file having used the data manager for the first time and delete the line

hibernate.hbm2ddl.auto=update

This will stop the checking of the schema every time a connection is opened.

That’s it! Let us know if we missed anything, and we’ll update this post.

Configuring Links to data files in the BII web app in JBoss 5.x

We have been getting asked a lot about general deployment within the ISA tools suite, particularly with respect to the web application, which can look a little complex. Here I’m going to describe one of the more perplexing tasks when setting up JBoss: how do I configure JBoss to serve up static content, i.e. my data files. I will also cover how to set up the URLs in data-locations.xml (for the BII Manager tool) to automatically place your files in this directory.

Setting up JBoss to serve out files

Probably the most annoying part of setting up JBoss is telling JBoss to serve out your data files from the web application. For instance, the BII data manager tool has sent the files to /tmp/data/bii/ on my file system and I want the URL http://localhost/data to point to that directory. There are a number of ways you can do this. You can use Apache or nginx to do this, you could change your data directory to be within the ROOT.war directory in your JBoss server directory, or you could do what I’m suggesting here and do everything through JBoss…which I think is a bit cleaner, and not so difficult when you know how.

1. The first thing to do is modify the profile.xml file found under the server/default/config/bootstrap folder in your JBoss installation.

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In profile.xml, there is a bean named BootstrapProfileFactory, you need to modify this and add a value element to the java.net.URI list element. Here, I’ve added a path to my Downloads directory.

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2. Next, we need to set up a folder in my Downloads directory, which has to have a series of folders following the deploy pattern of  /server/<profile>/deploy/ – so now, the directory /Users/eamonnmaguire/Downloads/server/default/deploy/ should exist. 

3. Within the deploy directory, create a data.war directory, and inside that create a WEB-INF directory. The name of the .war directory will dictate the URL, so data.war will correspond to http://localhost/data. In the WEB-INF directory, create an empty web.xml file. It’s contents will be <web-app></web-app> – Under the /Users/eamonnmaguire/Downloads/server/ I now have the following directory structure.

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4. Add your files

Finally, within your data.war directory, add the files you want to display. Here I’ve added a PDF for simplicity.

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Start up JBoss running ./run.sh -c default and navigate your browser to http://localhost:8080/data/Diagnosis.pdf and I get this lovely page.

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That’s it!

Now, to configure data-locations.xml. For out ISA-Tab for example, we simply set up the filesystem_path to be where, on our machine we want the files to be distributed. The web_url will be the URL we’ve just configured that has mapped data to that actual position in the file system.

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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 post, our YouTube video, some templates and the source code on Github.
Thanks again Trish for presenting OntoMaton at ICBO!

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.

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.

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.

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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.

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

The ISA team.