termite dealing with real world
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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. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
SciBite: What we do
Therapeutic Intelligence
Platform
Therapeutic Intelligence
API
Text Mining Solutions
Ontology & Thesauri
Development
Launched March 2012
Visit us at SciBite.com
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Our Thesauri Products
.. And Now…Cell LineSpeciesInvestigative ProcedurePhenotype
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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)
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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?)
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Bottom Line
Termite allows you to use ambiguous synonyms in your
Thesauri to increase recall without returning a lot of
rubbish!
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Augmenting Enterprise Search
DocRepositories
Extracted Files
StandardFormat
BatchTermite
SemanticMetadata
“Semantically Correct” User
Search Interface
Your search tool here
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Termite: Some ExamplesA.k.a Does your existing search tool handle….
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
First, lets look at disease
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Type 1 Diabetes Mellitus
Type I Diabetes Mellitus
Diabetes Mellitus, Type I
Type I Diabetes
Diabetes (1) Type
Many different lexical variants
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Breast Cancer
Breast Cancers
Breast Neoplasm(s)
Breast Malignacy(ies)
Breast Tumor(s)
Breast Tumour(s)
Tumor, Breast
And more…
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
http://en.wikipedia.org/wiki/Ramsay_Hunt_syndrome
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
100%Enrichment of high-precision
synonyms over the MeSH Disease Vocabulary
>11,000 New Synonyms
(and new indications)
Our Indication Thesaurus Offers
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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….
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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!
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
http://en.wikipedia.org/wiki/Epiphysis
Epiphysis
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Search for “TBI”
transient brain ischemia
traumatic brain injury
TBI Pharmaceuticals
Termite understands which one is which.
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Monitoring The Company “Transgene” Is Hard..But we can do it.
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
We all know proteins can be called all sorts of crazy things
http://en.wikipedia.org/wiki/Sonic_hedgehog
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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!
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
Muscarinic M1 Receptor(s)
Muscarinic (M1) Receptor
M1 Muscarinic Receptor
Muscarinic Receptor M1
Muscarinic Receptors M1
Muscarinic Receptor type M1
The usual variations….
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
But also…. Make sure you find both in:
M1/M2 muscarinic receptors
H1 and H2 Histamine Receptors
Kinases ERK1 and 2
ERK1/2
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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)
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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!
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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/
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
>4.5 million
High-precision gene terms
(+ much more with dynamic matching)
Our Protein Thesaurus Offers
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
88%
7%5%
Accuracy Of Termite On Random Selection Of 400 Entries From Biocreative Gene-Mention
Task
CorrectDiasagreementIncorrect
http://biocreative.sourceforge.net/
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
In Addition To Our Known Drug Thesarus….
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
De-novo chemical recognition Plugin
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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
SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456
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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