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Posts from May 2018

Exome Sequencing in Rare Disease Research

Exome sequencing has become a very common tool in research of rare genetic diseases. The starting point is usually a family where several members share the same symptoms of an uncharacterized disease with presumably a genetic factor causing it. Once the exomes of a few affected individuals and their healthy parents, are sequenced, the data is ready to be analyzed, aiming to find the variant responsible for the disease phenotype. Many robust analysis tools and pipelines have been developed and are being used during the last decade or so. A typical analysis includes quality control filtration, alignment and variant calling which eventually yields a list of candidate variants, either tens or even many hundreds, which are then filtered to keep only the relevant ones.

Filtering Candidate Variants Demands Evidence

The next step, unravelling any significant biological associations for these gene variants, can be challenging.

Many approaches and criteria have been applied for the step of filtering variants, and accordingly different tools and software packages implement these approaches. For example, variants that show inconsistency between genotype and disease phenotype across samples are excluded, and ones who represent normal variability in the population regardless of disease (e.g. SNPs) are those that are filtered out. Also, significant alteration in protein structure or function based on the sequence variation is often used, or actual evidence of clinical effects (Polyphen and Clinvar respectively).

The latest release of Linguamatics AI Natural Language Processing (NLP) text mining software, I2E 5.3, has a number of new features and improvements for creating simple open queries to questions that use advanced linguistic analytics to reveal relevant results 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.

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, with our new auto-suggestion feature, you can “Resume” your search to match more terms.

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

For fresh installations, I2E 5.3 Enterprise is now configured to use SSL (TLS) by default. This ensures that all communication is encrypted and nothing, including user credentials, is sent through the network in the clear. 

Scientific search solution recognized as a breakthrough AI product that democratizes the power of NLP for pharma and biotech

Cambridge, England and Boston, USA — May 23, 2018 — Linguamatics, the leading natural language processing (NLP) text analytics provider, today announced that Bio-IT World has awarded Linguamatics the Best of Show Judges’ Prize for Linguamatics iScite 2.0, a software-as-a-service AI scientific search application that puts the power of text analytics directly into the hands of researchers and clinicians. iScite was one of 46 products considered for this prestigious award at last week’s Bio-IT World Conference & Expo in Boston.

Bio-IT World’s Best of Show Awards Program recognizes the most innovative product solutions for the life science industry, as judged by a panel of experts from academia, industry, pharma and biotech. During the May 16 awards ceremony, iScite was applauded as a product that had “blown away” the judges, by putting “big pharma power into the hands of the small guy”. Judges also recognized iScite for “the natural language processing power it delivers at a very affordable price point” and issued a challenge to the Bio-IT community to embrace the tool to “see what a whole community of really smart people can accomplish with it.”

The Philosophy of Yin and Yang

The idea itself is relatively simple - all things exist in a state of entanglement and contradiction to themselves. Like my favorite geeked out analogy - Star Wars with the light (Yin) and the dark side (Yang). If you recall - Luke (Yin) and Darth Vader (Yang) both always had one foot over the line that delineates the dark side from that of the light. Either character could have changed their sides but ultimately there must always be a balance in the Force.

Yin, Yang and Star Wars - What Does That Have to Do With Modern Healthcare?!

It’s about balance. Healthcare organizations are businesses. A business by its very nature needs to make a profit to continue its existence. Healthcare organizations just happen to be in the business of caring for people. It is a business that by all ethical principles should not be performing unnecessary procedures to stay out of the red and yet this is still done by some organizations.  

New release broadens ETL and enterprise workflow applications in healthcare and life science

Cambridge, England and Boston, USA — May 15, 2018 — Linguamatics, the leading natural language processing (NLP) text analytics provider, today announced the latest release of its I2E AMP platform to automate the discovery of critical insights from text using NLP.

The I2E Asynchronous Messaging Pipeline (AMP) platform delivers high-throughput, fault tolerant workflow management for real-time document and record processing, addressing the NLP text-mining and ETL (extract transform load) requirements for healthcare and life science organizations of all sizes by allowing users to plug I2E into enterprise workflows and rapidly process streams of data at scale.

I2E AMP 2.0 includes enhanced functionality to speed overall throughput and performance, sophisticated pre- and post-processing capabilities, a Web GUI to simplify the set-up of initial workflows, and new AMP Agents for smarter load balancing, easier deployment, and optimized I2E management.

 “I2E’s flexible NLP platform goes far beyond traditional entity mark-up, providing semantically enriched data that normalizes concepts and relationships based on the relevant context,” said David Milward, chief technology officer for Linguamatics. “With AMP, clients now have an enterprise class, high-throughput solution that provides secure, fault-tolerant, scalable, and real-time ETL from unstructured text to structured data.”

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