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NLM Georgia Biomedical Informatics Course

NLM Georgia Biomedical Informatics CourseSeptember 14 20, 2014

What is informatics?

Concepts, actors, and interactions (Day 1)2What is biomedical informatics?The field that concerns itself with the cognitive, information processing and communication tasks of medical practice, education and research, including the information science and the technology to support these tasks.Greenes RA, Shortliffe EH.JAMA 1990 Feb 23; 263(8):1114-20.Forces propelling informatics toward increasing importance: health care costs, functional genomics, explosive growth of the literature, personal health records, mobile computing, privacy, translational research, public health disasters, social networking, big data3Burning Platform: Overwhelming ComplexitySets of Facts per Decision1000101005Human Cognitive Capacity2000201019902020SNPs, haplotypes, gene expression profiles, post-translational modificationDecisions by clinical phenotypeStead WW. Beyond expert-based practice. IOM (Institute of Medicine). Evidence-based medicine and the changing nature of health care: 2007 IOM annual meeting summary,(Introduction and Overview, p. 19). Washington, DC: The National Academies Press 2008.

Socio-cultural determinants of health4Todays PresentationMedical VocabulariesElectronic Health Records, Meaningful Use, and Health Information ExchangeSemantic MedlineData VisualizationOther TopicsFuture Research PrioritiesHow this applies to my/our work

Medical VocabulariesMeSHCPTDRGSNOMED-CTICD-10NDCRxNormLOINCFMAGONANDANICNOCGHHCCPCDSOmahaAORNICNPPSYMMXMDDBCSPHCDTDSM4LCHNCISEEROMIMQMRPDQVANDFULTSOPPPAC

Desiderata for Controlled VocabulariesCimino JJ. Desiderata for controlled medical vocabularies in the Twenty-First Century. Methods of Information in Medicine; 1998;37(4-5):394-403.

ContentConcept OrientationConcept PermanenceNonsemantic Concept IdentifiersPolyhierarchyFormal DefinitionsReject not otherwise classifiedUMLS A MetathesaurusThe purpose of the [Unified Medical Language System] is to improve the ability of computer programs to understand the biomedical meaning in user inquiries and to use this understanding to retrieve and integrate relevant machine-readable information for users.- Donald A.B. Lindberg, 1993UMLS A Metathesaurus

1999 82 source vocabularies; 1,358,891 strings; 626,893 concepts2014 148 (?) source vocabularies; 9,672,799 strings; 2,973,458 concepts9UMLS A MetathesaurusSome ways to use it

Reconstructing source terminologiesFinding additional synonyms for source termsAutomated translationInformatics Standards

Informatics StandardsStandards here already:Billing (ICD-9-CM, ICD-10-CM, CPT4, DRG)Data interchange (HL7)

Standards on the way:Health data (CDA)TerminologyInfobuttons

Office of the National Coordinator drives adoptionhttp://www.healthit.gov/sites/default/files/pdf/fact-sheets/onc-office-of-interoperability-and-standards.pdf

Electronic Health Records2004 President Bush announces goal to have every American covered by an EHR by 2014

2009 - Health Information Technology for Economic and Clinical Health Act (HITECH)

Earliest EHR system 1951 in California, involved punch cardsDevelopment continued through 70sEarly studies positive reduced medication errors, fewer things left out of the record, faster turnaround for orders

2008 only about 4% of doctors used any sort of HER

HITECH - Health Information Technology for Economic and Clinical Health13Incentive Payments14

Meaningful Use Stages15Stage 1Stage 2Stage 3

Sorry no source16

Whats Next?3 years: Ensure use, work on data standards, address policy/trust issues6 years: Incorporate patient-generated data, improve data aggregation/analytics, automate CDS and CQI10 years: the Learning Health SystemUsing the EHR for DiscoveryDe-identificationSynthetic Derivative~ 2 million recordsDe-identified DNA repository>170k samples

VanderbiltBioVUClinical NotesPhysicianOrdersPatient and StaffMessaging Billing codesLabs, Radiology, Test Results

Electronic Medical Record

18Health Information Exchange

Health Information ExchangeHealth information exchange (HIE) is the electronic movement of health-related information among organizations according to nationally recognized standards.-Health Resources and Services Administration20

Health Information ExchangeWhy early ones failedFunded with temporary investments and grant supportHealth systems perceive risk > benefitOld habits

ProcessTechPeoplenomatterwheremovie.com

EHRs Katrina: 2005 only about 25% of practices were using EHRs

Contrast with 2013 tornado in Moore, OK hospital took a direct hit, but records were securely backed up on servers hundreds of miles away22Semantic MedlineTypical search technologies rely on similarity

Semantic Medlinenot meaning.

Semantic MedlineThis isnt really about whether smoking causes asthma

Semantic MedlineLiterature-based discovery and the problem of mutually oblivious literatures

Medical literature as a potential source of new knowledge.Swanson DR.Bull Med Libr Assoc. 1990 Jan;78(1):29-37.PMID: 2403828 26

These literatures never cite each other.Semantic MedlineSemRep extracts meaningful predicationsTamoxifenBreast carcinomatreatsCDKN1A geneBreast carcinomaassociated_withAromatase Inhibitors Breast carcinomatreatsCDKN1A geneBARD1 genestimulates

Semantic MedlineUseful for discovering mechanistic links

Semantic MedlineSuccesses so far

A closed literature-based discovery technique finds a mechanistic link between hypogonadism and diminished sleep quality in aging men [Miller et al., Sleep 2012, PMID 22294819]

Semantic MEDLINE for discovery browsing: using semantic predications and the literature-based discovery paradigm to elucidate a mechanism for the obesity paradox [Cairelli et al., AMIA Annu Symp Proc 2013, PMID 24551329]

Try it yourselfRequest a license to access the UMLS Metathesaurus Browser, Semantic Medline, and more

https://uts.nlm.nih.gov/home.htmlData VisualizationFrom data to insight

TwinListhttps://www.youtube.com/watch?v=YXkq9hQppOw

Other TopicsGenomicsMathematical ModelingNLM ResourcesClinical Research InformaticsBig Data and the CloudConsumer Health/Social MediaDisaster InformaticsPublic Health InformaticsTelehealth and ImagingOrganizational Issues

Marching OrdersNatural language understandingInteractive publicationsClinical TrialsReproducibility of results

Apply now for 2015 sessionsSpring dates: April 12-18Fall dates: September 27 October 3

To apply:http://gru.edu/library/greenblatt/informaticscourse/apply.php