termite dealing with real world

SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456

Termite:

Dealing with real-world text:

Enhancing Enterprise Search

With Termite

July 2013

SciBite : Therapeutic Intelligence Systems

Red comments like this are for the slideshare version


SciBite: What we do

Therapeutic Intelligence

Platform

Therapeutic Intelligence

API

Text Mining Solutions

Ontology & Thesauri

Development

Launched March 2012

Visit us at SciBite.com


Termite, our text mining platform

Termite Search Engine

Termite Thesauri Modules

• Aim: Take scientific text and correctly identify the biomedical entities contained within

• “Semantic Normalisation” – we find “the thing” whatever the synonym used


Try Termite Now!

Go tohttp://scibite.com/site/p3/webconnect.html

Install Bookmarklet

Then find an article

http://www.ncbi.nlm.nih.gov/pubmed/23144792

See Termite In Action

http://scibite.com/site/p3/webconnect.html





How Is Termite Different? Ontologies are at our heart, not an afterthought:

Combine crowd-sourced and professional curation with experienced biomedical/pharma researchers

Thesauri are built to tackle real world text Integration-ready: We use public identifiers by default

Our text search engine Deals with multiple synonyms and multiple lexical variations

of biomedical terms Looks at the whole document, not just words or sentences Embraces ambiguity rather than ignoring it Augments and enhances existing enterprise search tools


Termite Architecture

Fast Text C Libraries

Termite Core

Command Line Service

Batch Processing Live Processing

PERL, PYTHON, JAVA

*nix Environment

{Entity “Thesauri”

[ n

GENERIC INTERFACE

Termite uses a combination of on-the-fly discovery and pre-built thesauri


Our Thesauri Products

.. And Now…Cell LineSpeciesInvestigative ProcedurePhenotype


Thesauri Management Combined, Continuous curation

Unique crowdsourced approach Curation team with >75 years Pharma experience

(combined!)

Quarterly Releases Provenance & Diffs >50,000 unit tests XML, RDF (skos), TSV delivery We add significant value to existing public

resources (so you don’t have to)


Synonyms Aren’t Easy.. Biomedical terms are very ambiguous

GSK (GlaxoSmithkiline or Glucose Synthase Kinase?) Hedgehog (Animal or developmental regulator protein?) Android (The FDA approved drug or the Phone OS?) Transgene (The company or the technique?) MCD (macular dystrophy (corneal) or malformations of

cortical development) Pacific (Pacific Biotechnology or the ocean?) EGFR (The kinase receptor or e-glomerular filtration rate?)


Ambiguity: Termites Strength Termite’s engine and thesauri understand which

synonyms are Fairly Dependable (e.g. Pfizer), Often Ambiguous (e.g. MCD) or correct but very dangerous (e.g. Pacific)

As a document is analysed, Termite uses both: Synonym Range: Which synonyms are used, how

ambiguous as a whole, not just one-by-one? Synonym Metrics: Frequency and position of synonyms,

relationship of abbreviations and full terms Document context: Does the document mention key

terms (but not synonyms) that increase or decrease the chances the ambiguous synonym is correct


Bottom Line

Termite allows you to use ambiguous synonyms in your

Thesauri to increase recall without returning a lot of

rubbish!


Augmenting Enterprise Search

DocRepositories

Extracted Files

StandardFormat

BatchTermite

SemanticMetadata

“Semantically Correct” User

Search Interface

Your search tool here


Termite: Some ExamplesA.k.a Does your existing search tool handle….


First, lets look at disease


Type 1 Diabetes Mellitus

Type I Diabetes Mellitus

Diabetes Mellitus, Type I

Type I Diabetes

Diabetes (1) Type

Many different lexical variants


Breast Cancer

Breast Cancers

Breast Neoplasm(s)

Breast Malignacy(ies)

Breast Tumor(s)

Breast Tumour(s)

Tumor, Breast

And more…


http://en.wikipedia.org/wiki/Ramsay_Hunt_syndrome


Commonly chosen, good starting point for text mining Around 45% of MeSH terms are of a “comma-permuted” form

(e.g. “Tumor, Breast”). These are restricted to searching the MeSH Qualifier and

MeSH descriptor tags in Medline records only, not general text Use might obtain an inaccurate match to D006331 (Heart

Diseases) via the synonym “disease, heart”.

“…while not affecting the heart, disease tissue was found…”,

Just flip commas? Yes, but… Amylo-1,6-Glucosidase Deficiencies acrocephaly, skull asymmetry, and mild syndactyly hand, foot and mouth disease

NLM MeSH as a Disease Thesaurus


100%Enrichment of high-precision

synonyms over the MeSH Disease Vocabulary

>11,000 New Synonyms

(and new indications)

Our Indication Thesaurus Offers


The new H7N9 bird flu strain continues to spread across China. Currently, more than 120 cases had been reported across 10 provinces, and 24 deaths. Yet no one knows where the virus started, which hampers efforts to contain it. But a promising new antiviral drug may help tackle this flu in the future.

When a non-specific term means something specific

Here they don’t mean generic flu, they mean H7N9 flu. Termite understands this


Empagliflozin Promising in Type 2 Diabetes

…..PHOENIX – The investigative sodium glucose cotransporter-2 (SGLT2) inhibitor empagliflozin appears to improve key diabetes parameters – and also seems to meaningfully reduce weight, researchers said here.

http://www.medpagetoday.com/MeetingCoverage/AACE/38946

Here they don’t mean generic diabetes , they mean type 2 diabetes. Termite understands this.

Its very common….


Picking The Right Pick’s Disease can be tricky

Pick's disease (Friedel J. Pick)D010494 Pericarditis, ConstrictiveSynonym: Pick(s) Disease

Pick's disease or syndrome II (Arnold Pick)D020774 Pick Disease Of BrainSynonym: Pick(s) Disease

Niemann-Pick disease (Ludwig Pick)D052536 Niemann-Pick Disease, Type ASynonym: Pick(s) Disease

Niemann-Pick disease (Ludwig Pick)D052537 Niemann-Pick Disease, Type BSynonym: Pick(s) Disease

Niemann-Pick disease (Ludwig Pick)D052556 Niemann-Pick Disease, Type CSynonym: Pick(s) Disease

Lubarsch-Pick syndrome (Ludwig Pick)Not in MESH DX90113 Lubarsch-Pick SyndromeSynonym: Pick(s) Disease

Pick's disease (Philipp Josef Pick)D008193 Lyme DiseaseSynonym: Pick(s) Disease

…this ”picks disease” parameters…

Paget’s

Kaposi’s

+ many more

Some engines find nothing as “pick” is a stopword

Termite can differentiate between these!


http://en.wikipedia.org/wiki/Epiphysis

Epiphysis


Search for “TBI”

transient brain ischemia

traumatic brain injury

TBI Pharmaceuticals

Termite understands which one is which.


Monitoring The Company “Transgene” Is Hard..But we can do it.


Hypens & Spaces & Drugs

AT-101 is an important drug

But don’t look for “AT 101”

PD-98059 has a hyphen..

But also valid as PD 98059

Termite knows which drugs we can substitute hyphens & spaces and which we should not


We all know proteins can be called all sorts of crazy things

http://en.wikipedia.org/wiki/Sonic_hedgehog


As if Hop wasn’t bad enough, its called p60 too

.. And p60 could mean anything….

Termite can find where these things really mean the Hop protein


β-actin

actin-β

b-actin

β actin

Beta actin

ß-actin

Actin, beta

b- actin

Got to handle the Greek characters

The German Sharp isnt beta but that doesn’t stop people using it

Including HTML Entity codes!


Examples Of Termite On Greek Chars

http://onlinelibrary.wiley.com/doi/10.1111/boc.201200077/abstract

http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature12205.html

Uses our Termite Highlight service to mark up HTML

Explore it yourself at: http://scibite.com/webconnect.html

http://scibite.com/webconnect.html





Muscarinic M1 Receptor(s)

Muscarinic (M1) Receptor

M1 Muscarinic Receptor

Muscarinic Receptor M1

Muscarinic Receptors M1

Muscarinic Receptor type M1

The usual variations….


But also…. Make sure you find both in:

M1/M2 muscarinic receptors

H1 and H2 Histamine Receptors

Kinases ERK1 and 2

ERK1/2


Ambiguous, Valid, SynonymsHere are 2 genes, both called “CD20”

CD20 is valid for both… so which one is your text about?

Termite uses document context to work out which one it really is


While iNos is a valid synonym for ISYNA1 (above), its *mostly* used for inducible nitric oxide synthase (below). Got to be able to call this correctly. (major pharma pathway)


Cox2 is Not Cox2, Its PDGS2

Cyclooxygenase 2 (COX2) is a major drug target. COX2 is a recognised symbol for this AND the cytochrome c oxidase II…

Like iNOS, got to get this one right!

This is Cox-2 but people don’t mean this!

They mean this!


There Are Simpler Issues…

The official gene names site gives “DUSP26” as a synonym of DUSP28

But DUSP26 is a different gene... Which has a synonym of DUSP24!

DUSP24 is actually STYXL1…

http://www.genenames.org/


>4.5 million

High-precision gene terms

(+ much more with dynamic matching)

Our Protein Thesaurus Offers


88%

7%5%

Accuracy Of Termite On Random Selection Of 400 Entries From Biocreative Gene-Mention

Task

CorrectDiasagreementIncorrect

http://biocreative.sourceforge.net/


In Addition To Our Known Drug Thesarus….


De-novo chemical recognition Plugin


Module Augmentation We provide thesauri covering critical areas of drug

discovery Can be augmented with your own internal terms

which never need to leave your firewall If you want symptoms as disease terms, you got it

Or we provide a curation service to enhance your searches

For example, Cryptococcal meningitis Cause: Cryptococcus neoformans / Cryptococcus gattii Pathology: infection of the meninges Symptoms: Headache


Try Termite Now!

Go tohttp://scibite.com/site/p3/webconnect.html

Install Bookmarklet

Then find an article


See Termite In Action






Conclusion Termite is built to provide high-precision recognition

of key biomedical terms For existing enterprise search installations, you can

use Termite to tag each document with semantically rich meta-data that augments your search and allows your users to find more relevant documents

We’re covering more & more entities, Cells, Adverse Events, Tests & Procedures, Get in touch to discuss your needs today at <info> at scibite.com!

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