Nanomedicine Informatics
1Nanomedicine informaticsDennis G. Thomas, Pacific Northwest National LabAlan Chappell, Pacific Northwest National LabElaine Freund, 3rd MillenniumSharon Gaheen, SAICStacey Harper, Oregon State UniversityJuli D. Klemm, NIH/NCIDavidS.Paik, Stanford UniversityNathanA.Baker, Pacific Northwest National Lab, nathan.baker@pnnl.gov
Pacific Northwest National LaboratoryNCI Nano Alliance - Nano WG July 5, 2012National Cancer Institute caBIG Nanotechnology Working GroupGovernmentNational Institutes of HealthNCI, NHLBI, NIBIB, NCLCenter for Disease ControlFood and Drug AdministrationEnvironmental Protection AgencyAcademiaWashington UniversityPacific Northwest National LabOregon StateStanfordMITGeorgia TechUCLAIndustryIntelPennsylvania NanoSystems
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Standards organizationsASTM E56ISO TC229Alliances and organizationsInternational Alliance for NanoEHS HarmonizationOregon Nanoscience and Microtechnologies InstituteNational Nanotechnology InitiativeNational Nanomanufacturing NetworkNCI Nano Alliance
Working Group Scope3
Shaw et al., 2008. PNAS, 105: 7387.Nano WG current areas of focusNano-TAB development (enabling)Nanotechnology data sharing standardsWorking draft readyCommunity engagedNeed to focus on applications and standardsNPO support and expansion (enabling)Standard vocabulary and ontology for nanomedicineFoundation establishedCommunity engagedNeed to focus on support for nano-TAB and other annotation projectsNano-QSAR (applying)Structure-activity relationships for nanomaterial-biological interactionsCommunity engaged; participants identifiedMany potential areas of focus
Nanotechnology informatics challenges5What is the problem? Unrealized potential due to combinatorial complexityNanomaterials are small and diverseThe promise:High densityImproved biodistributionMulti-modal applicationsThe problems:Combinatorial diversityDifficult characterizationAn important challenge!6
McNeil SE. J Leukoc Biol, 2005. 78(3): p. 585-94.doi:10.1189/jlb.0205074
Size distribution dataSurface morphology dataTissue biodistributionDrug loading dataAnti-tumor activityIn vitro drug releaseZeta PotentialPreparationChemical composition of nanoparticle formulationSource: Chawla JS et al, Int J Pharm, 249, 127-38 (2002), Son YJ et al, J Control Release, 91, 135-145 (2003)What is the problem? Diversity of dataAll data taken from journal resourcesSelected few sample data sets representative of data sets that we look for.What is the problem? Disconnected resources and users8
9Nanomedicine informatics needsThe nanomedicine community has an immediate need for nanomaterial informatics:Understand nanomaterial toxicity and other biological propertiesSearch for existing data on nanoparticle synthesis and propertiesSystematically represent nanomaterial structure and compositionExchange nanomaterial chemical, physical, and biological dataDesign nanoparticles, and other materials with custom properties for specific biological applications
Nanotechnology ontology10Ontology enables resource integration11
NanoParticle Ontology (NPO)Capture knowledge underlying nanomaterialPreparationChemical compositionPhysiochemical characterizationBiological function/behaviorBasic Formal Ontology structureInitial focus on cancer diagnosis and therapyCurrent growth to include a broader range of nanotechnology conceptsSupported by the caBIG Nano WGAvailable through Bioportalhttp://purl.bioontology.org/ontology/NPO
http://www.nano-ontology.org/Thomas DG, Pappu RV, Baker NA. NanoParticle Ontology for Cancer Nanotechnology Research. J Biomed Inform, in press. doi:10.1016/j.jbi.2010.03.001
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Example view into the NPO
13A more detailed view of nanoparticle composition using the NPO
14Nanotechnology Resource Integration15NCBO + NPO enable resource integration16
Bioportal, NCBO Resource Index, & PubNano
Nanotechnology data sharing17Protocol ReferenceSample Identifiers
Study Factors
Assay MeasurementsAssay FilesAssay NameData RepositoriesNTP (NIEHS)NCL (NCI, FDA, NIST)NBI (ONAMI)InterNano (NNN)NIL (NIOSH)STANDARDIZEDSTANDARDIZEDGoal of nano-TABDevelop a specification to facilitate the import/export of data on nanomaterials and their characterizations to/from nanotechnology resources18Insert slides from Nanoinformatics 2010What is nano-TAB?A standard tab-delimited format for describing data related toInvestigationsNanomaterialsSpecimensAssays Leverages and extends the Investigation/Study/Assay (ISA-TAB) formatStandard tab-delimited file formatDeveloped by the European Bioinformatics Institute (EBI) for representing a variety of assays and technology typesExample: MAGE-TABNano-TAB supports ontology-based curationNanomaterials and concepts from the NanoParticle Ontology (NPO) as well as other ontologiesnano-TAB structure1. Describe the Investigation and Studies2. Identify Study Samples3. Record Assay Conditions and Measurementsi_xxx.txtm_xxx.txts_xxx.txta_xxx.txtInvestigation FileStudy File(s)Material File(s)Assay File(s)nano-TAB structure1. Describe the Investigation and Studies2. Identify Study Samples3. Record Assay Conditions and Measurementsi_xxx.txtm_xxx.txts_xxx.txta_xxx.txtInvestigation FileStudy File(s)Material File(s)Assay File(s)ISA-TAB-Nano Investigation FileDescribes:Primary investigationAssociated studies, assays, and protocolsDescriptive information about the study includes:Design descriptors and factorsPublicationsAssays and protocolsContacts Vertical-based spreadsheet format with columns representing multiple values
Investigation File
Ontology References
Investigation Description
Investigation Contacts
Investigation Publications
Investigation File (cont.)Study Description
Study Design
Study Contacts
Investigation File (cont.)Study Publications
Study Assays
Study Factors
Study Protocols
nano-TAB structure1. Describe the Investigation and Studies2. Identify Study Samples3. Record Assay Conditions and Measurementsi_xxx.txtm_xxx.txts_xxx.txta_xxx.txtInvestigation FileStudy File(s)Material File(s)Assay File(s)ISA-TAB-Nano Study FileProvides mapping between the study samples, materials, and processing events Samples can be:Biological materialsNanomaterialsSmall moleculesFor physical-chemical characterizations of nanomaterials, the sample is the nanomaterialFor in vitro and in vivo characterizations, the sample is the biological specimen (cell line, animal, etc.)Horizontal spreadsheet describing the biological materials and association with the nanomaterials described in the Material file
Study File
Biological Sample Identifier Biological Sample Characteristics ProtocolBiological Sample Study FactorsISA-TAB-Nano Material FilePrimary file for describing:Nanomaterial composition and formulationPhysical propertiesStructureAllows for:Comparison of nanomaterials across nanotechnology resources Association with optional files; e.g., a Structure file for representing the 3D structure of the nanomaterialHorizontal spreadsheet describing the nanomaterial sample, associated components, material characteristics, and material linkagesMaterial File
Material Identifiers Material Description Intended Application Material Type Chemical Name CharacteristicsMaterial File (cont.)
Material Linkage Material File
Characteristics Structure FileNCL Dendrimer-Based MRI Contrast Agents
AtomHeadernano-TAB structure1. Describe the Investigation and Studies2. Identify Study Samples3. Record Assay Conditions and Measurementsi_xxx.txtm_xxx.txts_xxx.txta_xxx.txtInvestigation FileStudy File(s)Material File(s)Assay File(s)ISA-TAB-Nano Assay FileDescribes the protocol parameters and factors, including:TemperatureMedia/solventConcentrationProvides references or links to assay results, including:MeasurementsInstrumentationDerived data filesTemplates available for the top Nano WG assaysSize by DLS (Physico-Chemical)Zeta Potential (Physico-Chemical)Hemolysis (In Vitro)Hepatocarcinoma Cytoxicity (MTT and LDH) (In Vitro)Caspase 3 Apoptosis (In Vitro)Toxicity (ADME, Single/Repeat Dose) (In Vivo)Your assay here!
nano-TAB Assay FileHorizontal-based spreadsheet format with the following sections:SAMPLE NAMESPROTOCOL PARAMETERSASSAY FACTORSASSAY MEASUREMENTSASSAY FILESAssay File Size by DLS
Sample Names Protocol Parameters Assay Factors Assay Measurements Assay Filesnano-TAB futureASTM ballotUser guideBasic descriptions of elements, glossaryOrganized collection of examplesTutorialsEasier NPO annotation and integrationList of most relevant termsList of missing termsReal world applicationsClient engagementFriendly user support
http://cananolab.nci.nih.gov/caNanoLab/welcome.do
http://nbi.oregonstate.edu/knowledgebaseAdditional nano-TAB reading and project teamnano-TAB Project Site: http://goo.gl/yKFewASTM nano-TAB Work Item WK28974: http://goo.gl/OjSOX ISA-TAB: http://isatab.sourceforge.net caBIG ICR Nano WG Data Standards Document: http://goo.gl/sDEvpNanoParticle Ontology (NPO): http://www.nano-ontology.org
Nano-TAB project team
Nathan Baker, PNNLAmy Bednar, ERDCElaine Freund, 3rd MillenniumMarty Fritts, NCLSharon Gaheen, SAICLiz Hahn-Dantona, Lockheed MartinStacey Harper, Oregon State UniversityMark Hoover, NIOSHFred Klaessig, Pennsylvania Bio Nano SystemsJuli Klemm, NCI CBIITDavid Paik, Stanford UniversitySue Pan, SAICGrace Stafford, T
