1 Workshop on Infectious Disease Ontology Influenza Informatics in the BioHealthBase Bioinformatics Resource Center Richard H. Scheuermann, Ph.D. Department.

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  • Workshop on Infectious Disease Ontology

    Influenza Informatics in the BioHealthBase Bioinformatics Resource Center

    Richard H. Scheuermann, Ph.D.Department of PathologyU.T. Southwestern Medical Center

  • BioHealthBase BRCBioinformatics Resource Centers for Biodefense and Emerging/Re-emerging Infectious Diseases program funded by NIAID (www.brc-central.org)8 centers fundedBioHealthBase (www.biohealthbase.org) is an integrated resourceInterrelates data from NCBI, UniProt, Pfam, and other sourcesDirect summary and visualization of integrated dataLinkouts to source data sites for additional data detailsAllows one-stop shopping for science researchersBioHealthBase provides value-added, pre-computed dataValuable processed data not available elsewhereProtein structural and functional predictionsSequence alignment and polymorphism analysisPredicted immunological epitopesBioHealthBase provides a forum for displaying collaborative dataPathways with Reactome; epitopes with Immune Epitope DatabaseBioHealthBase emphasizes host-pathogen interactionsPathogen effects on host cellular pathwaysImmune response to pathogen infectionSupport of research related to vaccine, therapeutic and diagnostic development

  • BHB Flu - Home Page & Data Summarywww.biohealthbase.org

  • BHB Flu - Query & Detail Record

  • BHB Flu - Sequence Conservation

  • BHB Flu - Immune Epitopes

  • BHB Flu - Reactome

  • 3D Visualization302 Flu structures702 Mtb structures

  • CEIRSMotivationlay the groundwork for the development of new and improved control measures understanding how influenza viruses evolve, adapt and transmitidentifying immunological factors that determine disease outcomeResearch AreasResearch Area 1: Animal Influenza Surveillance Conduct prospective international and/or domestic animal influenza surveillance for the rapid detection and characterization of influenza viruses with pandemic potential.Research Area 2: Pathogenesis and Host Response Research Conduct research to enhance understanding of the molecular, ecological, and/or environmental factors that influence pathogenesis, transmission, and evolution of influenza viruses; and characterize the protective immune response.

  • IDO scales of granularityHost-pathogen interactions occurs at a variety of scalesEcosystemOrganismOrganCellMoleculeSurveillancePathogenesis

  • IDO scales & termsEcosystem - transmission, geographic location, population density, routes of migration, specimen isolation procedure, specimen isolation source, vector, carrier, reservoir, environment, prevalenceOrganisms - latency, reactivation, disease progression, innate immune response, adaptive immune response, cytokine storm, symptoms (consumption, night sweats, fever, weight loss, wasting, immunosuppression), sterile eradication, delayed-type hypersensitivity, vaccine, surrogate markers of protection, viral load, animal model, pathogenesis, route of treatment, protection, resistance, sensitive, tuberculosis, human immunodeficiency syndrome, infective endocarditisOrgan - granuloma, caseous necrosis, inflammation, endocarditis, lung, peripheral blood, cavity, pericavitary tissue, distant lung, immune system, mucosa, gut lumen, lymph node, inductive site, effector site, tissue damage, Cell - phagocytosis, pathogen sensing, cytotoxicity, T cells, B cells, macrophages, dendritic cells, bacterium, antibiotic drug, antiviral drug, cell autonomous apoptosis, bystander apoptosis, antigen presentation, infected, activatedMolecules - transport/binding proteins, cell wall synthesis, two component systems, chaperones, detoxification (glyoxalase), DNA repair, lipid biosynthesis, fatty acid degradation, cell surface variable proteins, methylglyoxal, advanced glycation end products, reactive oxygen intermediates (ROIs)

  • IDO scales & branches

    ScaleIndependent ContinuantDependent ContinuantOccurrentEcosystemspecimen isolation source, environmentvector (role), carrier (role), population density, routes of migration (?), host (role), pathogen (role), source (?), temperaturetransmission, migration, specimen isolation process, specimen isolation eventOrganismNCBI taxonomy, vaccine preparation,healthy, sick, animal model (role), viral load, latent (state), sterile eradication (state), symptoms (quality), immunogen (role), adjuvant (role), pathogen (disposition), resistant (disposition)pathogenesis, reactivation, progression, immune response, vaccinationOrganFMA (mucosal organ - lung, secondary lymphoid organ - lymph node), pericavitary tissue, abssessviral load (quality), inductive site (role), effective site, inflamed (quality), granuloma (quality), caseous necrosis (quality)inflammation, tissue damage, necrosisCellT cell, dendritic cellInfected (quality), activated, susceptible (disposition)antigen presentation, proliferation, phagocytosis, cytoxicity, apoptosisMoleculeGlyoxalase, catalase, recAdetoxification (role), DNA lesion recognition, DNA repair, transportcatalysis, binding, transport

  • Relationship between experiments and biological knowledgePrimary isolateAmplified specimenAmplified specimensManipulated variableAnalyte levelsResponding variableVariablesCorrelation/cause-and-effectOBI:biomaterialtransformationOBI:assayOBI:datatransformation

  • AcknowledgmentsU.T. SouthwesternBurke SquiresVictoria HuntShubhada GodboleRoger ChangJyothi NoronhaFeng LuoCathy SprangerKevin McIverLANLCatherine MackenMira DimitrijevicCo-investigatorsBarbara Mann (UVA)Adolfo Garcia-Sastre (MSSM)Hillary Morrison (MBL)Louis Weiss (Albert Einstein)Ellen Vitetta (UTSW)AmarX. WeiDavid DengDMID/NIAIDValentina DiFrancescoNorthrop GrummanEd KlemKevin BiersackCarey GireJason LucasSharmila VattikutiSanjeev KumarPaul ShrabsteinSurabhi SharmaTammie AjayiAihui WangZuoming DengJianjun WangDeWayne EjikemeVecnaJames WolowiczChris LarsenAl RamseyReactomeMarc GillespiePeter D-EustachioLincoln SteinMITREJoanne LucianoLynette Hirschman

    Upper left screenshot is protein shown as a ball-and-stick configuration

    Upper right screenshot is the same protein with the backbone shown as secondary structure and the B chain highlighted with 75% space-fill

    Center screenshot shows a subsequence from amino acid 10 to 20 highlighted as yellow spheres

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