Uses of Informatics to Solve Real World Problems in Veterinary Medicine
Post on 07-Feb-2017
Embed Size (px)
Uses of Informatics to Solve Real World Problemsin Veterinary Medicine
Suzanne L. Santamaria n Kurt L. Zimmerman
ABSTRACTVeterinary informatics is the science of structuring, analyzing, and leveraging information in an effort to advance animalhealth, disease surveillance, research, education, and business practices. Reference and terminology standards arecore components of the informatics infrastructure. This paper focuses on three current activities that use referencestandards in veterinary informatics: (1) the construction of a messaging standard in a national animal health laboratorynetwork, (2) the creation of breed and species terminology lists for livestock disease surveillance, and (3) the develop-ment of a standardized diagnoses list for small animal practices. These and other endeavors will benefit from researchconducted to identify innovative and superior tools, methods, and techniques. The authors believe there are manyareas requiring study and special focus in order to advance veterinary informatics, and this paper highlights some ofthe needs and challenges surrounding these areas.
Key words: veterinary informatics, reference standards, terminology standards
INFORMATICS IS THE SCIENCE OF INFORMATIONInformatics, by strict definition, is the study of the scienceof information. Medical informatics is the science ofstructuring and analyzing information and data to im-prove problem solving and decision making in healthcare.1 Informatics provides the basis by which mean-ingful advancements toward evidence-based veterinarymedicine can be made, and standardized references andterminology are core components of the informatics in-frastructure,2 as demonstrated by their use in electronicmedical records for patient diagnosis and procedures.This helps with the management of patient informa-tion and enables clinicians to aggregate such informationfor epidemiological surveillance, to perform retrospectivestudies, and to drive evidence-based medical decisionmaking. For example, suppose a state health monitoringagency needs to monitor the number of cases of lowerrespiratory disease seen in the past 10 days. Viral orbacterial pneumonia, decreased respiratory function, andbronchioloalveolar adenocarcinoma, among others, areall classified as types of lower respiratory disorders inthe standardized terminology hierarchy. However, stand-ardized terminology could provide the means by whichto gather more specific types of lower respiratory dis-orders. Medical informatics encompasses a wide varietyof topics beyond terminology standards; however, itis too broad of a discipline to fully discuss these otheraspects of medical informatics in a single article. Thegoal of this paper is therefore to highlight the use ofstandardized medical terminology3 in veterinary medi-cine by examining how use of these standards haveaddressed three different problems: (1) the constructionof a messaging standard in a national animal health labo-ratory network, (2) the creation of breed and speciesterminology lists for livestock disease surveillance, and(3) the development of a standardized diagnoses list forsmall animal practice. Finally, this paper will also discuss
some of the challenges and necessary research within thearea of veterinary medical informatics terminology.
REFERENCE STANDARDS IN INFORMATICSReference standards are an integral part of informaticsas they enable unambiguous communication betweendisparate users and systems in order to ensure that twousers derive the same meaning from the same bit ofinformation. The need for reference standards is evidentin all areas of medicine such as in meta-analyzing pub-lished biomedical results, relating phenotypical findingsto clinical microscopic and molecular data, naming thedisorders, and even in describing the patients in terms ofbreeds, reproductive status, and so forth.411 Using refer-ence standards allows for the compilation and compari-son of large amounts of data from multiple sources. Forexample, a common terminology language is used totransmit and store diagnoses from eight veterinary teach-ing hospitals to a large data repository at Veterinary Medi-cal Databases (VMDB).12 This data repository can then besearched as a whole and compared to other data sets.13Typically, reference standards either provide the message/report (laboratory report) or the terminology to fit inthe message/report (test performed). A description of onemessage standard and two terminology standards usedin medical informatics follows.
HL7 Standard for MessagesHealth Level Seven (HL7)14 is an international standardthat promotes and enables interoperability in health careby providing a mechanism for electronic informationtransfer within and among clinics. It provides a structureand rules for when a message is instigated (patientadmitted to a hospital), the actual message composition(patients name), and how the message is encoded (thefirst and last name are separated by a certain symbol in
doi:10.3138/jvme.38.2.103JVME 38(2) 6 2011 AAVMC 103
the message).15 In some parts of the message, a form ofstandardized terminology may provide the value (patientdiagnosis is recorded using medical terminology). HL7is fee-based and members vote on changes. It is widelyused in human health care. The American VeterinaryMedical Association (AVMA) endorsed HL7 as an officialinformatics standard for veterinary medicine.1624
LOINC Terminology for Laboratory TestsLogical Observations Identifiers Names and Codes(LOINC),25 a medical terminology managed by the non-profit Regenstrief Institute at Indiana University,26 con-tains over 30,000 terms and numeric codes for laboratorytests and clinical documents (e.g., Over The Counteranimal drug label). Each LOINC term is divided intofive or six parts, including the component or analytetested, its property, timing aspect, the body systemtested, and the scale and method used. For example, theLOINC term for a heartworm serum antigen test (its longname is Dirofilaria immitis Ag [Presence] in Serum and itscode is 318014) contains the following parts: componentof Dirofilaria immitis with the subcomponent Antigen,property of Arbitrary Concentration, time of Point in time,Serum system, and Ordinal scale. The terminology can besearched and downloaded online without charge. LOINCis endorsed for use by numerous federal agencies and theAVMA.24,2729
SNOMEDCT Terminology for MedicineThe Systematized Nomenclature of MedicineClinicalTerms (SNOMEDCT)30 is a large, international standar-dized medical terminology managed by the non-profitInternational Health Terminology Standards DevelopmentOrganization of Copenhagen, Denmark.31,32 SNOMEDCT attempts to describe the whole discipline of medicinethrough its 19 interrelated hierarchies of concepts: clini-cal finding, procedure, observable entity, body structure,organism, substance, pharmaceutical/biologic product,specimen, special concept, linkage concept, physical force,event, environment or geographic location, social context,situation with explicit context, staging and scales, physicalobject, qualifier value, and record artifact.33 SNOMEDCTconcepts have numeric identifiers and computable defini-tions created through the use of attribute-value triplesand inheritance from parental concepts.31,32,34-40 For ex-ample, the computable definition of the concept viralkeratitis includes a causative agent of virus, pathologicalprocess of infectious process, morphology of inflammation,and a finding site of the cornea. Figure 1 provides a
graphical representation of this concept. SNOMEDCTcontains over 300,000 medical concepts and 900,000 syn-onyms or alternate descriptions. SNOMEDCT has beenadopted by numerous federal agencies, the AVMA, andother veterinary organizations.24,41 It is free to usersin the United States and available for download, butit requires users to consent to a licensure agreement.41SNOMEDCT has an extension mechanism31 wherebyorganizations can create concepts and descriptions fortheir specific needs which still fit into the SNOMED frame-work. The Veterinary Terminology Services Laboratoryat Virginia Tech maintains an extension of SNOMEDCT to house additional veterinary content.42
TERMINOLOGIES IN ACTIONDescriptions of three examples of cases where standardswere used to overcome a challenge in veterinary medi-cine follow. Information on the stakeholders, their needs,and the solution are discussed.
Common Structure for Individual LaboratoriesReporting to the National Veterinary Laboratory
The ChallengeThe National Veterinary Services Laboratory (NVSL), adivision of the US Department of Agriculture, Animaland Plant Health Inspection ServicesVeterinary Services(USDA, APHISVS), is a national, regional, and interna-tional veterinary diagnostic reference laboratory.43 TheNVSL protects US animal health, public health, and inter-national trade through disease surveillance and emer-gency response. State veterinary diagnostic laboratoriessubmit laboratory test results to the NVSL, which thencompiles the reports to detect and analyze emerginganimal-health events. Efficient categorization and analysisof the laboratory reports have proven difficult for multiplereasons. One problem has been that different structures,different terms, and paper submissions provided inade-quate turn-around time during emergencies. Other chal-lenges included the lack of a reliable Internet connectionand insufficiently configured computers at some labo-ratories. Also, many laboratory personnel do not haveknowledge or experience in informatics.
The SolutionThe National Animal Health Laboratory Network(NAHLN)44 was created to coordinate the NVSL withinthe existing infrastructure of state and university labora-
Figure 1: Concept map of a SNOMED-CT concept. Viral keratitis and its associated defining relationships areshown. Each concept has a numeric identifier and defining parental relationships (these are omitted herefor brevity). Created using CmapTools (http://cmap.ihmc.us/).
104 JVME 38(2) 6 2011 AAVMC
tories. The state laboratories are equipped with Internetconnections and adequate computers to transmit relevantinformation. A standardized, structured message formatwas created by (1) analyzing the common, necessary in-formation for the laboratory reports (e.g., each reporthas a submitting organization, specimen type, test per-formed, and so forth); (2) creating a new Health LevelSeven (HL7) message structure to support the requiredtypes of information and their organization by consultingthe guidance documents and collaborating with users; (3)developing subsets of multiple terminology standardsto provide values for the HL7 elements (LOINC subset oflaboratory tests, SNOMEDCT subset of breeds, etc.). Ter-minology from the standards was identified through theuse of mapping tools (RELMA25 for LOINC) or browsers(SNOMEDCT) to identify the qualifying terminologycontent.
This standard message enables NVSL to compile all labo-ratory reports submitted from the various state laboratoriesand to use sophisticated data analytics to aid in the de-tection of emerging animal-health events. This solutioncreates a unified electronic laboratory reporting systembetween the state diagnostic laboratories and the federalorganization responsible for ensuring agriculture animalhealth. A representation of part of the NAHLN labora-tory message might appear as follows:
Identifier 235663Text VSNJV Ab Ser QI EIAName of coding system LOINC Terminology
The HL7 element OPU_R25.ACCESSION.SPECIMEN.ORDER identifies that the information that follows con-cerns the test order. The identifier 235663 correspondsto a Vesicular stomatitis virus New Jersey antibody ELISAtest on the serum in the LOINC reference terminology.
In addition, necessary informatics training and support wasprovided to pertinent laboratory personnel for mappingtheir existing reports and term lists onto the NAHLNmessage. The laboratory message and terminology valuesare available to all via an open Web site, and an onlineforum connects and assists NAHLN users and adminis-trators.45
Enhanced Intra- and Inter-agency Communicationand Analytic Possibilities with StandardizedTerminology
The ChallengeThe mission of the USDA Animal and Plant Health In-spection ServicesVeterinary Services (VS) is to protectthe health of animals and animal products in the US.46The judicious monitoring of animal health and identifica-tion of and response to disease outbreaks are critical tothe mission. VS consists of multiple internal centers andprograms that work with over 600 field animal-healthworkers to perform animal-health initiatives. In order tosafeguard animal health, it is necessary for VS to collabo-rate with multiple stakeholders including other federal
agencies, state veterinary offices, and industry and foreigngovernments. Information in support of specific programswithin VS was recorded in different formats and could notbe analyzed expediently during disease outbreaks. In fact,VS stated that the lack of standardization of data ele-ments and integration within U.S. animal health data sys-tems is the most significant challenge today in conduct-ing successful animal trace back and controlling animaldisease.47 VS is currently creating a unified data manage-ment system that will improve the collection and analysisof animal-health events. This system includes a commondatabase repository with many of the data values draw-ing from standardized terminology subsets. This discus-sion focuses on the issue of representing animal typeand taxonomy in this centralized database.
Terminologies to identify the kind of animal by breed,Linnaean classification, or common grouping had beendeveloped independently by various programs within VSto suit a particular programs needs. The use of differenttaxonomic lists by different programs precluded readycomparison of data or integration with other data sets. Acomputer could not reconcile that a Hampshire breed pigfrom one record was a subtype of Sus scrofa in anotherrecord, nor could it understand how a record of swinewould encompass both of these terms. Therefore, thisconsistent type of taxonomic information is necessary tocompile and analyze records from the multiple animal-health programs.
The SolutionVeterinary Services funded the Veterinary TerminologyServices Laboratory (VTSL) to align (that is, to map) eachindividual program taxonomy list (breed, species, etc.)with a standardized terminology, SNOMEDCT. The tax-onomy lists were mapped in a Microsoft Excel spread-sheet. Candidate SNOMEDCT concepts were identifiedusing the VTSL browser41 of the Veterinary Adaptationof SNOMEDCT. Difficult terms and maps were dis-cussed via conference calls and/or electronic communi-cation. The resulting list of SNOMEDCT concepts wasuploaded with tools developed by VTSL into its data-base. Subsets of the various kinds of information werecreated for ease of use at the USDA (see Table 1 for anexa...