Introducing I2E 5.6
I2E 5.6 includes a number of improvements, these include updated Charting functionality, updates to the way you prioritize multiple query terms and updates to our multilingual functionality. Along with the changes below, there are the usual bug fixes and under-the-hood improvements.
Our latest release of Charting - Version 3 is included with I2E 5.6 and is designed to improve the usability of the Chart output from I2E (see figure 1).
We've moved some elements of the charts around to make them easier to read and move results higher up the page. Charts now display the first few items (rather than filling the space available) and hide rows in the charts that, after filtering, match zero documents.
Prioritization of items in alternatives
I2E 5.6 has introduced a new way to prioritize multiple query terms within a search, so that results are streamlined and easier to review. Alternatives with Prioritization of children set to Within container or Same span (figure 2) will now prefer matches from the top child and only try to match child further down the list if it hits nothing before.
This is a very powerful new feature in I2E with a lot of potential use cases. For example, you may want to tag a document as being related to Humans and only tag a document as being related to Animals if Humans are not mentioned. Or you may want to prioritize one ontology (e.g. Linguamatics Diseases) but ensure that you capture all of the missed hits by using other ontologies (e.g. MeSH, Orphanet, MedDRA).
As part of our continual multi-lingual improvements within I2E, version 5.6 will now treat the dot symbol as a thousands separator in European languages and find numerical ranges in German, French, Italian, Spanish and Dutch (as well as English). These ranges can be found in the Numerics, Measurements and Duration & Frequency pattern ontologies.
The Mutations ontology has been improved to match additional constructions and more consistent identify and normalization different substitution patterns.
As part of our quarterly ontology update, sources for ChEBI, CPC, Diseases, Entrez Gene, HPO, NCI, MedDRA and RxNorm have been updated to later versions.
I2E OnDemand: Index Updates
There is also a new Document Identifier shadow region, which is included in all of the I2E OnDemand indexes. Queries that extract the identifier from your documents can run against any OnDemand index: simply replace the existing source-specific region (e.g. PMID) with the new Document Identifier shadow region.
Better Management of Large Indexes and Restrictions
Index Restrictions were introduced as an API-only feature in I2E 5.4.1. In I2E 5.6, they have been made accessible via the I2E Administration view. This, along with the introduction of the Document Identifier shadow region, greatly simplifies their creation and use.
Index Restrictions can be created, read and deleted via the I2E Administration view and both types -- include and exclude – are supported. Earlier versions of index restrictions could have lists of both documents to include and exclude, but this functionality has been removed and those older restrictions cannot be displayed.
These combinations of indexes and their restrictions are defined in virtual indexes written into files that live on the I2E server (as distinct from virtual indexes created within Index Trees). These file-based virtual indexes have traditionally been used within I2E to support command-line index management, but in I2E 5.6 they have been added to the I2E Administration view.
Virtual Indexes can be created in the I2E Administration view and, once displayed, Indexes and Published Indexes can be dragged into them. Index Restrictions can similarly be dragged in from their location in the tree.