Download - Chemical Safety and Hazard Informaon in PubChem - dchas.org · Chemical Safety and Hazard Informaon in PubChem Jian Zhang*, Paul Thiessen, Asta Gindulyte, Leah McEwen, Ralph Stuart,

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

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

Getallcompoundsthathavesafetyandhazardannota5ons

121225388121225360121215529119090965119081209119077305119075735119057962119057958119057957119057832119057828119057809119057737119057735119057734119057364119057361119057340119057336118987278118984465118984459118984398118984389118984355118984354118856763118856642118856472….

ExportedCIDs

Retrievethesubsec5oncompounds

Clickthe5060linkwillshowtheentrezcompoundpage,thenfromthe“Sendto”bubontosavethe5060CIDsasatextfile.

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–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

Download - Chemical Safety and Hazard Informaon in PubChem - dchas.org · Chemical Safety and Hazard Informaon in PubChem Jian Zhang*, Paul Thiessen, Asta Gindulyte, Leah McEwen, Ralph Stuart,

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