chemical safety and hazard informaon in pubchem - dchas.org · chemical safety and hazard informaon...
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ChemicalSafetyandHazardInforma5oninPubChem
JianZhang*,PaulThiessen,AstaGindulyte,LeahMcEwen,RalphStuart,EvanBolton,SteveBryant
Na5onalCenterforBiotechnologyInforma5onNa5onalLibraryofMedicineNa5onalIns5tutesofHealth
U.S.DepartmentofHealthandHumanServices
CINF80:252ndACSNa5onalMee5ng,Philadelphia,PA,August2016
BackgroundChemicalsafetyisaveryimportanttopicinchemicalindustry,academiclabs,andeveninourdailylives.Itcontainsmanyaspectsofscien5ficknowledgeandtechnicalcomponentssuchaschemicalpropertyinforma5on,toxicityandecologicaldata,exposureandriskassessmentinforma5on,andmoredetailedknowledgeregardingenvironmentandhumanhealth.Despitealotofefforts,accidentss5llhappenfrom5meto5me.Inthepastfewyears,PubChem,anopensourcechemicalinforma5on-hub,hasintegratedalotofsafetyandhazardinforma5onintoPubChem’sannota5ondatabase.Theseinforma5oncanbeaccessedthroughPubChem’swebsitesandservices.
PubChemOverview
• …publicrepositoryforchemicalinforma5on.• …threelinkeddatabases-Substance,Compound,andBioAssay
• …annota5ondatabaseforexperimentalproper5es,drugandfoodchemicaldata,safetyinforma5on,patents,literature,classifica5ons…
PubChemOverview
• …providesmanyservices:webdisplay,searchsystem,datadownload,webservices,widgets...
• ..Links,alotodlinkstootherNCBIdatabasesuchasprotein,gene,pubmed…andlinkstotheoriginaldatapages.
• …moretocome..
PubChemHomepage
Compounds: 91,671,620
Substances: 223,116,675
BioAssays: 1,218,668
TestedCompounds: 2,276,278
TestedSubstances: 3,566,030
RNAiBioAssays: 91
BioAc5vi5es: 230,635,944
ProteinTargets: 10,182
GeneTargets: 19,779
PubChemContent• Compoundsummary–uniquestructureinform5on:2dand3dimages,propertydata,drug,foodaddi5ve,chemicalsafety,agrochemical,literaturereferences,patents,andmore–PubChemmostusedinforma5on.
• Annota/ons–chemicalannota5oninforma5onfromdepositorsandopensources.
• Substancerecord–depositorprovidedsubstanceandrelatedinforma5on.
• BioAssayrecord–depositorprovidedscreeningdataandrelatedinforma5on.
PubChemCompoundContent• 2DStructure• 3DConformer• BiologicDescrip5on• NamesandIden5fiers• ChemicalandPhysical
Proper5es• RelatedRecords• ChemicalVendors• DrugandMedica5on
Informa5on• FoodAddi5vesandIngredients• AgrochemicalInforma5on• PharmacologyandBiochemistry
• UseandManufacturing• Iden5fica5on• SafetyandHazards• Toxicity• Literature• Patents• Prepara5onandReac5ons• BiomolecularInterac5onsand
Pathways• BiologicalTestResults• Classifica5on
SafetyandHazardInforma5on• 2DStructure• 3DConformer• BiologicDescrip5on• NamesandIden5fiers• ChemicalandPhysical
Proper5es• RelatedRecords• ChemicalVendors• DrugandMedica5on
Informa5on• FoodAddi5vesandIngredients• AgrochemicalInforma5on• PharmacologyandBiochemistry
• UseandManufacturing• Iden5fica5on• SafetyandHazards• Toxicity• Literature• Patents• Prepara5onandReac5ons• BiomolecularInterac5onsand
Pathways• BiologicalTestResults• Classifica5on
SafetyandHazardInforma5on
• HazardsIden5fica5on• SafetyandHazardProper5es
• FirstAidMeasures• FireFigh5ngMeasures• AccidentalReleaseMeasures
• HandlingandStorage• ExposureControlandPersonalProtec5on
• StabilityandReac5vity• TransportInforma5on• RegulatoryInforma5on• OtherSafetyInforma5on
• NamesandIden5fiers• ExperimentalProper5es• ToxicologicalInforma5on• EcologicalInforma5on
SafetyandHazardsHazardsIden5fica5onGHSClassifica5onCLPHazardClassandCategoryCodesHealthHazardFireHazardExplosionHazardHazardsSummaryFirePoten5alSkin,Eye,andRespiratoryIrrita5onsSafetyandHazardProper5esLELUELFlammabilityCri5calTemperatureCri5calPressureDangerofExplosionNFPAHazardClassifica5onNFPAFireRa5ngNFPAReac5vityRa5ngNFPAHealthRa5ngNFPAOtherPhysicalDangersChemicalDangersExplosiveLimitsandPoten5alOSHAStandardsNIOSHRecommenda5onsOtherSafetyandHazardDataFirstAidMeasuresFirstAid
FireFirstAidExplosionFirstAidExposureFirstAidInhala5onFirstAidSkinFirstAidEyeFirstAidInges5onFirstAidFireFigh5ngMeasuresFireFigh5ngExplosionFireFigh5ngOtherFireFigh5ngHazardsAccidentalReleaseMeasuresTIHGasIsola5onandEvacua5onSpillageDisposalCleanupMethodsDisposalMethodsOtherPreventa5veMeasuresHandlingandStorageNonfireSpillResponseSafeStorageStorageCondi5onsExposureControlandPersonalProtec5onRELPELPEL-TWAPEL-STELPEL-CREL-TWA
REL-STELREL-CIDLHConversionThresholdLimitValuesOtherOccupa5onalPermissibleLevelsSourcesandPoten5alExposureAssessingPersonalExposureOccupa5onalExposureLimitsInhala5onRiskEffectsofShortTermExposureEffectsofLongTermExposureRadia5onLimitsandPoten5alAcceptableDailyIntakesAllowableTolerancesPersonalProtec5onRespiratorRecommenda5onsFirePreven5onExplosionPreven5onExposurePreven5onInhala5onPreven5onSkinPreven5onEyePreven5onInges5onPreven5onProtec5veEquipmentandClothingStabilityandReac5vityAirandWaterReac5onsReac5veGroupReac5vityAlertsReac5vityProfile
Reac5vi5esandIncompa5bili5esTransportInforma5onDOTEmergencyGuidelinesShipmentMethodsandRegula5onsDOTIDandGuideDOTLabelPackagingandLabellingECClassifica5onUNClassifica5onEmergencyResponseRegulatoryInforma5onDOTEmergencyResponseGuideIsola5onNameIsola5onDistanceAtmosphericStandardsSoilStandardsFederalDrinkingWaterStandardsFederalDrinkingWaterGuidelinesStateDrinkingWaterStandardsStateDrinkingWaterGuidelinesCleanWaterActRequirementsCERCLAReportableQuan55esTSCARequirementsRCRARequirementsFIFRARequirementsFDARequirementsOtherSafetyInforma5onSafetyReferencesSafetyNotesToxicCombus5onProductsOtherHazardousReac5onsMaterialSafetyDataSheet
SafetyandHazardInforma5on
PubChemintegratedsafetyandhazardinforma5onfrom~20opensourcedomains,andprovidedsourcelinkstoallowuserstobeabletonavigatetotheoriginalinforma5onpage.
PubChemSafetyandHazardInforma5onSources
• ILO–ICSC• OSHAOccupa5onalChemicalDatabase• NIOSHPocketGuidetoChemicalHazards• CAMEOChemicalsDatabaseofHazardousMaterials• HSDB• EUREGULATION(EC)No1272/2008• SafeWorkAustralia-HazardousSubstancesInforma5onSystem(HSIS)
• JapaneseNITE-ChemicalManagementCenter(CMC)• More…
WheretofindtheInforma5on
• Getsafetyandhazardinforma5onforagivenchemical
• Getallcompoundsthathavesafetyandhazardannota5ons
• Retrievesafetyandhazardinforma5onprogramma5cally
WheretofindtheInforma5on
• Getsafetyandhazardinforma5onforagivenchemical
• Getallcompoundsthathavesafetyandhazardannota5ons
• Retrievesafetyandhazardinforma5onprogramma5cally
WheretofindthesafetyInforma5onforagivenchemicalinpubChem
• Google• PubChemhomepage• NCBIentrezPubChemcompound• Structuresearch• DirectURL• Othersearchengines:Bing,Yahoo,Baidu…
DirectURL
hbps://pubchem.ncbi.nlm.nih.gov/compound/cidhbps://pubchem.ncbi.nlm.nih.gov/compound/namehbps://pubchem.ncbi.nlm.nih.gov/compound/1140hbps://pubchem.ncbi.nlm.nih.gov/compound/toluene
WheretofindtheInforma5on
• Getsafetyandhazardinforma5onforagivenchemical
• Getallcompoundsthathavesafetyandhazardannota5ons
• Retrievesafetyandhazardinforma5onprogramma5cally
121225388121225360121215529119090965119081209119077305119075735119057962119057958119057957119057832119057828119057809119057737119057735119057734119057364119057361119057340119057336118987278118984465118984459118984398118984389118984355118984354118856763118856642118856472….
ExportedCIDs
Retrievethesubsec5oncompounds
Clickthe5060linkwillshowtheentrezcompoundpage,thenfromthe“Sendto”bubontosavethe5060CIDsasatextfile.
WheretofindtheInforma5on
• Getsafetyandhazardinforma5onforagivenchemical
• Getallcompoundsthathavesafetyandhazardannota5ons
• Retrievesafetyandhazardinforma5onprogramma5cally
Retrieveinforma5onprogramma5callyusingPubChem’sPUG_Viewservice
Datadrivenmodel:PubChem’spug_viewservicesendsthejsonblobtothefrontend,thefrontendusingscriptandcsstorenderthepage.
hbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1140/JSONhbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1140/XML
Pug_view–Par5aldataretrieval
Toretrievedataforaspecificheading,e.gExperiemtalProper5es,use:hbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1140/JSON/?response_type=display&heading=Experimental%20Proper5es
Addi5onalSafetyRelatedInforma5on
• GHSClassifica5onhbps://pubchem.ncbi.nlm.nih.gov/ghs/
• EmergencyResponseGuidebook2016hbps://pubchem.ncbi.nlm.nih.gov/erg/
Summary
• PubChemprovideschemicalsafetyandhazardinforma5onthatintegratedfromvariousopensourcesincludeNIOSH,ILO,HSDB,OSHA,NOAACameoChemicals,ECHA,andmore.
• PubChemcreatedasubsetchemicalsafetyinforma5onpage-LCSS.
• PubChemaddedGHShelppageandDOT’sEGRlookuptable.