Chemical Safety and Hazard Informa5on in PubChem Jian Zhang*, Paul Thiessen, Asta Gindulyte, Leah McEwen, Ralph Stuart, Evan Bolton, Steve Bryant Na5onal Center for Biotechnology Informa5on Na5onal Library of Medicine Na5onal Ins5tutes of Health U.S. Department of Health and Human Services CINF80: 252nd ACS Na5onal Mee5ng, Philadelphia, PA, August 2016
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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.
LabAccidents
2012UFloridaNaN3Explosion
ChemicalSafetyInforma5on
ChemicalSafetyInforma5onOnline
PubChemIntegratedSafetyandHazardInforma5onfrom20+Sources
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..
PubChem-where
• Google“pubchem”• hbps://pubchem.ncbi.nlm.nih.gov/•
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
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…
Casestudy:toluene:fromGoogle
Casestudy:toluene:fromPubChem/Entrez
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
Saveordownloadtheinforma5ononbrowser
hbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/compound/1140/JSON/?response_type=display
WheretofindtheInforma5on
• Getsafetyandhazardinforma5onforagivenchemical
• Getallcompoundsthathavesafetyandhazardannota5ons
• Retrievesafetyandhazardinforma5onprogramma5cally
Getallcompoundsthathavesafetyandhazardannota5ons
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
PubChemLCSS–Asubset
PubChemLCSS–Asubset
PubChemLCSS–where
PubChemLCSS-URL
hbps://pubchem.ncbi.nlm.nih.gov/compound/toluene#datasheet=lcss
#datasheet=lcss
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.
Acknowledgements
PubChemCrewGangFuBoYuSiqianHeJieChenTiejunCheng
RenataGeerJaneHeSunghwanKimBenShoemakerJiyaoWangYanliWang
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