InterMine 4.1.0

InterMine team has just released InterMine 4.1.0.

The new release includes a better integration with Galaxy: we can import data into Galaxy from any InterMine of our choice (either starting from InterMine or Galaxy), and we can export a list of identifiers from Galaxy to any InterMine of our choice through the InterMine registry. No need to configure anything any more: all the Galaxy properties have been moved to InterMine core. No need to create a mine-specific Galaxy tool anymore, use the NEW intermine tool instead. Please read here for more details. A simple InterMine tutorial will be published soon in the Galaxy Training Material, under the Data Manipulation topic.

This release offers the integration with ELIXIR AAI (Authentication and Authorisation Infrastructure) allowing the researchers to log in the InterMine instances using their ELIXIR profile. You will need:

  1. an ELIXIR identity
  2. register the InterMine client in order to obtain the client-id and the client-secret which must be set in the mine properties file.

More details here in the OpenAuth2 Settings section of the documentation.

Also new in this version is the gradle wrapper 4.9, which is compatible with Java11. This only effects the users which compile/install InterMine code.

Thank you so much to our contributor Joe Carlson for improving the generateUpdateTriggers task.

The release contains also a few bug fixes.

Bug Fixes

  • Solved the error caused by obsolete terms in the gene ontology
  • Fasta query result: CDS translation option + extra view parameter
  • The ONE OF constraint works properly when editing a template
  • The default queries configuration have been migrated to json
  • The task generateUpdateTriggers has been improved

See the release notes for the complete list and detailed information.

This is a non-disruptive release. To update your mine with these new changes, see the upgrade instructions.

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InterMine 4.0 – InterMine as a FAIR framework

We are excited to publish the latest version of InterMine, version 4.0.

It’s a collection of our efforts to make InterMine more “FAIR“. As an open source data warehouse, InterMine’s raison d’être is to be a framework that enables people to quickly and easily provide public access to their data in a user friendly manner. Therefore InterMine has always strived to make data Findable, Accessible, Interoperable and Reusable and this push is meant to formally apply the FAIR principles to InterMine.

What’s included in this release?

  1. Generate globally unique and stable URLs to identify InterMine data objects in order to provide more findable and accessible data.
  2. Apply suitable ontologies to the core InterMine data model to make the semantic of InterMine data explicit and facilitate data exchange and interoperability
  3. Embed metadata in InterMine web pages to make data more findable
  4. Improve accessibility of data licenses for integrated sources via web interface and REST web-service.

More details below!

How to upgrade?

This is a non-disruptive release, but there are additions to the data model. Therefore, you’ll want to increment your version, then build a new database when upgrading. No other action is required.

However, keep reading for how to take advantages of the new FAIR features in this release.

Unique and stable URLs

We’ve added a beautiful new user-friendly URL.

Example: http://beta.flymine.org/beta/gene:FBgn0000606

Currently this is used only in the “share” button in the report pages and in the web pages markup. In the future, this will be the only URL seen in the browser location bar.

For details on how to configure your mine’s URLs, see the docs here.

See our previous blog posts on unique identifiers.

Decorating the InterMine data model with ontology terms

InterMine 4.0 introduces the ability to annotate your InterMine data model with ontology terms.

While these data are not used (yet), it’s an important feature in that it’s going to facilitate cross-InterMine querying, and eventually cross-database analysis — allowing us to answer questions like “Is the ‘gene’ in MouseMine the same ‘gene’ at the EBI?”.

For details on how to add ontologies to your InterMine data model, see the docs here.

Embedding metadata in InterMine webpages

We’ve added structured data to web pages in format of JSON-LD to make data more findable, and these data are indexed by Google data search. Bioschemas.org is extending Schema.org with life science-specific types, adding required properties and cardinality on the types. For more details see the docs here.

By default this feature is disabled. For details on how to enable embedding metadata in your webpages, see the docs here.

Data licences

In our ongoing effort to make the InterMine system more FAIR, we have started working on improving the accessibility of data licences, retaining licence information supplied by the data sources integrated in InterMine, and making it available to humans via our web application and machines via queries.

See our previous blog post on data licences.

For details on how to add data licences to your InterMine, see the docs.

Future FAIR plans

  1. Provide a RDF representation of data stored, lists and query results, and the bulk download of all InterMine in RDF form, in order to allow the users to import InterMine resources into their local triplestore
  2. Provide an infrastructure for a SPARQL endpoint where the user can perform federated queries over multiple data sets

Upcoming Releases

The next InterMine version will likely be ready in the Fall/Winter and include some user interface updates.

Docs

To update your mine with these new changes, see upgrade instructions. This is a non-disruptive release.

See release notes for detailed information.

InterMine 3.1.2 – patch release

We’ve released a small batch of bug fixes and small features. Thank you so much to our contributors: Sam Hokin, Arunan Sugunakumar and Joe Carlson!

Features

  • Templates can be tagged by any user, not just the super user. (Via webservice only – for now)

Fixes

  • When searching our docs, some times the “.html” extension was dropped. This was fixed by our beautiful documentation hosters – readthedocs.org
  • Installing the “bio” project via Gradle does not fail if you do not have the test properties file.
  • Gradle logs error fixed
  • Removed old GAF 1.0 code
  • Fixed XML library issue:  java.lang.ClassCastException for org.apache.xerces
  • Set converter.class correctly
  • Updated the protein atlas expression graph
  • Handle NULL values returned by NCBI web services
  • Updated Solr to support new Solr versions
  • Removed unneeded Gretty plugin
  • Better error handling for CHEBI web services
  • Publication abstract is longer than postgres index
  • Removed phenotype key, it’s not in the core model and has conflicting key
  • Updated ObjectStoreSummary to handle ignored fields consistently.

Upcoming Releases

InterMine 4.0 is scheduled for release the week of 7 May 2019.

Docs

To update your mine with these new changes, see upgrade instructions. This is a non-disruptive release.

See release notes for detailed information.

InterMine 3.1.1 – patch release

We’ve released a small batch of bug fixes and small features. Thank you so much to our contributors: Sam Hokin, Paulo Nuin and Joel Richardson!

Features

  • Added access to the GFF header in the GFF parser
  • GFF sequence handler has access to feature now
  • Added DOES NOT CONTAIN constraint
  • Added a few end points for BlueGenes

Fixes

  • InterPro source handles DTD correctly
  • Updated to new GitHub URL for Gretty Plugin
  • Fixed OMIM link outs
  • NCBI going to update their GFF files (at our request! Thanks Wayne!)
    • fix spelling on feature “DNaseI_hypersensitive_site” i
    • change “recombination_region” to “recombination_feature”
  • Updated external links on enrichment widget
  • Handle NULL search index correctly
  • Fix publication with NULL title
  • Fixed log library dependency conflict
  • Removed deprecated Yahoo login link
  • Fixed Panther source to handle proteins

Upcoming Releases

  • 3.1.2 – More small bug fixes
  • 4.0.0 – FAIR release

Docs

To update your mine with these new changes, see upgrade instructions. This is a non-disruptive release.

See release notes for detailed information.

InterMine 3.1 – Extending the Core InterMine Data Model with Multiple Genome Versions, Strains

Advances in sequencing technologies mean that genome sequence and annotation data for multiple strains of a species are now often available. An update to the InterMine core data model was decided that would allow addition of Strain data should it be available without affecting InterMines which do not have this data.

It was decided that the addition of a new class, Strain, which is referenced by Organism and Sequence feature and vice versa, would allow both the flexibility required and allow for addition of further data and expansion if required.

strains

The Strain class has the following features/advantages:

  • SequenceFeature entities, such as Genes, would continue to reference Organism, but would also reference the new Strain class, allowing for queries returning SequenceFeatures for a specific strain.
  • Providing strain information as a separate class allows individual InterMine’s to reference other information as required, such as Genotype and Stocks.
  • The Strain class extends BioEntity so will include strain-relevant attributes such as PrimaryIdentifier and Name and will reference other collections such as synonym.
  • Minimal changes to the user interface will be required as, to our knowledge, SequenceFeatures in individual strains always have a unique identifier. With the help of templates if necessary, users will be able to identify particular SequenceFeatures and which strain they originate from.

To update your mine with these new changes, see upgrade instructions. This is a non-disruptive release.

See release notes and the notes from the community call for more details. Please join our community calls if you’d like to be part of future data model decisions! (Details of upcoming calls are available via our developer mailing list).