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

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 to
http://scibite.com/site/p3/webconnect.html
Install Bookmarklet
Then find an article
http://www.ncbi.nlm.nih.gov/pubmed/23144792
See Termite In Action

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
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 Line
Species
Investigative Procedure
Phenotype

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
Doc
Repositories
Extracted
Files
Standard
Format
Batch
Termite
Semantic
Metadata
“Semantically
Correct” User
Search Interface

Termite: Some Examples
A.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, Constrictive
Synonym: Pick(s) Disease
Pick's disease or syndrome II (Arnold Pick)
D020774 Pick Disease Of Brain
Niemann-Pick disease (Ludwig Pick)
D052536 Niemann-Pick Disease, Type A
D052537 Niemann-Pick Disease, Type B
D052556 Niemann-Pick Disease, Type C
Lubarsch-Pick syndrome (Ludwig Pick)
Not in MESH
DX90113 Lubarsch-Pick Syndrome
Pick's disease (Philipp Josef Pick)
D008193 Lyme Disease
…this ”picks disease” parameters…
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

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, Synonyms
Here 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
Correct
Diasagreement
Incorrect
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

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!

Termite dealing with real world

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