I2E 5.3

Improvements for I2E Pro Users

I2E 5.3 has a number of new features and improvements for creating queries, so that you can build your queries faster, with better precision and recall.

Most of the out-of-the-box I2E 5.3 Resources queries (such as finding all variations of subject-relation-object patterns, or gene-mutation-disease associations) can now be embedded within other queries, allowing you to further constrain your extracted relationships. An example would be to ensure that your relationships are found in only certain sections of your documents, or that certain terms do not occur in the same sentence as your chemical dosages.

In I2E 5.3, when you start typing in the class chooser, it will automatically suggest the top 20 classes with that prefix (Figure 1) across all of your terminologies. If you want more suggestions, you can “Resume” your search to match more terms. This new auto-suggestion feature also works for other applications that use the I2E server to suggest class matches.

Figure 1. Class Chooser Autocomplete for the prefix "foo"

You may see some new recommendations in the class chooser, with the improvements to the ontologies in the I2E OnDemand Indexes and available for download, including:

  • New Phenotypes in HPO
  • More Rare Diseases in Orphanet
  • More synonyms in drug product names
  • Improvements to Organizations by Sector, with more organizations, more synonyms, and improved consolidation

A new query-level feature in I2E 5.3 allows the user to easily “anchor” their terms to the Start or End of its parent container, for example to extract the First Inventor in a patent or to identify sentences in FDA Drug Labels the end with a certain keyword or concept.

Improvements for I2E Administrators

For fresh installations, I2E 5.3 servers are now configured to use SSL (TLS) by default, using a self-signed certificate. This ensures that all communication is encrypted and nothing, including user credentials, is sent through the network in the clear. The self-signed certificate can easily be replaced by a signed certificate for even greater security.

Administrators no longer need to install a version of Oracle Java on their Linux servers, as I2E now supports OpenJDK as an alternative Java provider.

Improvements for AMP Users 

The latest version of I2E includes some under-the-hood developments to make single document processing faster than ever. These improvements are enabled when you update to AMP v2.0: no other configuration changes are necessary.