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Termite dealing with real world
 

Termite dealing with real world

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This presentation is based on one i've given to a few different groups and tries to explain why our text-mining engine, Termite, is a little bit different to others that are out there.

This presentation is based on one i've given to a few different groups and tries to explain why our text-mining engine, Termite, is a little bit different to others that are out there.

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    Termite dealing with real world Termite dealing with real world Presentation Transcript

    • 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
    • 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 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
    • 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 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 Line Species Investigative Procedure Phenotype
    • 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 Doc Repositories Extracted Files Standard Format Batch Termite Semantic Metadata “Semantically Correct” User Search Interface
    • SciBite. Drug Discovery, Now. © 2013 SciBite Limited. Reg. No. 7778456 Termite: Some Examples A.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, Constrictive Synonym: Pick(s) Disease Pick's disease or syndrome II (Arnold Pick) D020774 Pick Disease Of Brain Synonym: Pick(s) Disease Niemann-Pick disease (Ludwig Pick) D052536 Niemann-Pick Disease, Type A Synonym: Pick(s) Disease Niemann-Pick disease (Ludwig Pick) D052537 Niemann-Pick Disease, Type B Synonym: Pick(s) Disease Niemann-Pick disease (Ludwig Pick) D052556 Niemann-Pick Disease, Type C Synonym: Pick(s) Disease Lubarsch-Pick syndrome (Ludwig Pick) Not in MESH DX90113 Lubarsch-Pick Syndrome Synonym: Pick(s) Disease Pick's disease (Philipp Josef Pick) D008193 Lyme Disease Synonym: Pick(s) Disease …this ”picks disease” parameters… 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, 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
    • 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 Correct Diasagreement Incorrect 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 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
    • 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!