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Chemical Safety and Hazard Information in Pubchem

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Chemical Safety and Hazard Information in Pubchem CINF80: 252nd ACS Naonal Mee5ng, Philadelphia, PA, August 2016 Chemical Safety and Hazard Informaon in PubChem Jian Zhang*, Paul Thiessen, Asta Gindulyte, Leah McEwen, Ralph Stuart, Evan Bolton, Steve Bryant Naonal Center for Biotechnology Informaon Naonal Library of Medicine Naonal Ins5tutes of Health U.S. Department of Health and Human Services Background Chemical safety is a very important topic in chemical industry, academic labs, and even in our daily lives. It contains many aspects of scien5fic knowledge and technical components such as chemical property informaon, toXicity and ecological data, eXposure and risk assessment informaon, and more detailed knowledge regarding environment and human health. Despite a lot of efforts, accidents s5ll happen from 5me to 5me. In the past few years, PubChem, an open source chemical informaon-hub, has integrated a lot of safety and hazard informaon into PubChem’s annotaon database. These informaon can be accessed through PubChem’s web sites and services. Lab Accidents 2012 U Florida NaN3 EXplosion Chemical Safety Informaon Chemical Safety Informaon Online PubChem Integrated Safety and Hazard Informaon from 20+ Sources PubChem Overview • … public repository for chemical informaon. • … three linked databases - Substance, Compound, and BioAssay • … annotaon database for eXperimental proper5es, drug and food chemical data, safety informaon, patents, literature, classificaons… PubChem Overview • … provides many services: web display, search system, data download, web services, widgets... • .. Links, a lot od links to other NCBI database such as protein, gene, pubmed… and links to the original data pages. • … more to come .. PubChem - where • Google “pubchem” • hps://pubchem.ncbi.nlm.nih.gov/ • PubChem Homepage Compounds: 91,671,620 Substances: 223,116,675 BioAssays: 1,218,668 Tested Compounds: 2,276,278 Tested Substances: 3,566,030 RNAi BioAssays: 91 BioAcvies: 230,635,944 Protein Targets: 10,182 Gene Targets: 19,779 PubChem Content • Compound summary – unique structure inform5on: 2d and 3d images, property data, drug, food addi5ve, chemical safety, agrochemical, literature references, patents, and more – PubChem most used informaon. • Annota/ons – chemical annotaon informaon from depositors and open sources. • Substance record – depositor provided substance and related informaon. • BioAssay record – depositor provided screening data and related informaon. PubChem Compound Content • 2D Structure • Use and Manufacturing • 3D Conformer • Iden5ficaon • Biologic Descripon • Safety and Hazards • Names and Iden5fiers • ToXicity • Chemical and Physical • Literature Properes • Patents • Related Records • Preparaon and Reac5ons • Chemical Vendors • Biomolecular Interac5ons and • Drug and Medicaon Pathways Informaon • Biological Test Results • Food Addi5ves and Ingredients • Classificaon • Agrochemical Informaon • Pharmacology and Biochemistry Safety and Hazard Informaon • 2D Structure • Use and Manufacturing • 3D Conformer • Iden5ficaon • Biologic Descripon • Safety and Hazards • Names and Iden5fiers • ToXicity • Chemical and Physical • Literature Properes • Patents • Related Records • Preparaon and Reac5ons • Chemical Vendors • Biomolecular Interac5ons and • Drug and Medicaon Pathways Informaon • Biological Test Results • Food Addi5ves and Ingredients • Classificaon • Agrochemical Informaon • Pharmacology and Biochemistry Safety and Hazard Informaon Safety and Hazards Fire First Aid REL-STEL Reac5vi5es and Incompabili5es Hazards Iden5ficaon EXplosion First Aid REL-C Transport Informaon GHS Classificaon EXposure First Aid IDLH DOT Emergency Guidelines CLP Hazard Class and Category Codes Inhalaon First Aid Conversion Shipment Methods and Regulaons Health Hazard • Hazards Iden5ficaon Skin First Aid • Threshold Limit Values Stability and Reac5vity DOT ID and Guide Fire Hazard Eye First Aid Other Occupaonal Permissible Levels DOT Label EXplosion Hazard • Inges5on First Aid • Sources and Poten5al EXposure Packaging and Labelling Hazards Summary Safety and Hazard Fire Figh5ng Measures Assessing Personal EXposure Transport Informaon EC Classificaon Fire Poten5al Properes Fire Fighng Occupaonal EXposure Limits UN Classificaon Skin, Eye, and Respiratory Irritaons Explosion Fire Fighng Inhalaon Risk • Regulatory Informaon Emergency Response Safety and Hazard Proper5es Other Fire Figh5ng Hazards Effects of Short Term EXposure Regulatory Informaon LEL • First Aid Measures Accidental Release Measures • Effects of Long Term EXposure Other Safety Informaon DOT Emergency Response Guide UEL TIHGas Radiaon Limits and Poten5al Isolaon Name Flammability • Fire Figh5ng Measures Isolaon and Evacuaon Acceptable Daily Intakes Isolaon Distance Cri5cal Temperature Spillage Disposal Allowable Tolerances Atmospheric Standards Cri5cal Pressure • Cleanup Methods Personal Protec5on Soil Standards Danger of EXplosion Accidental Release Disposal Methods • Respirator Recommendaons Names and Iden5fiers Federal Drinking Water Standards NFPA Hazard Classificaon Measures Other Preventave Measures Fire Prevenon Federal Drinking Water Guidelines NFPA Fire Rang Handling and Storage • Explosion Prevenon EXperimental Proper5es State Drinking Water Standards NFPA Reac5vity Rang Nonfire Spill Response Exposure Prevenon State Drinking Water Guidelines NFPA Health Rang • Handling and Storage Safe Storage Inhalaon Preven5on Clean Water Act Requirements NFPA Other Storage Condi5ons Skin Prevenon • ToXicological Informaon CERCLA Reportable Quan55es Physical Dangers • EXposure Control and EXposure Control and Personal Eye Prevenon TSCA Requirements Chemical Dangers Protec5on • Inges5on Preven5on Ecological Informaon RCRA Requirements EXplosive Limits and Poten5al Personal Protec5on REL Protec5ve Equipment and Clothing FIFRA Requirements OSHA Standards PEL Stability and Reac5vity FDA Requirements NIOSH Recommendaons PEL-TWA Air and Water Reac5ons Other Safety Informaon Other Safety and Hazard Data PEL-STEL Reac5ve Group Safety References First Aid Measures PEL-C Reac5vity Alerts Safety Notes First Aid REL-TWA Reac5vity Profile ToXic Combus5on Products Other Hazardous Reac5ons Material Safety Data Sheet Safety and Hazard Informaon PubChem integrated safety and hazard informaon from ~20 open source domains, and provided source links to allow users to be able to navigate to the original informaon page. PubChem Safety and Hazard Informaon Sources PubChem Safety and Hazard Informaon Sources • ILO – ICSC • OSHA Occupaonal Chemical Database • NIOSH Pocket Guide to Chemical Hazards • CAMEO Chemicals Database of Hazardous Materials • HSDB • EU REGULATION (EC) No 1272/2008 • Safe Work Australia - Hazardous Substances Informaon System (HSIS) • Japanese NITE - Chemical Management Center (CMC) • More … Where to find the Informaon • Get safety and hazard informaon for a given chemical • Get all compounds that have safety and hazard annotaons • Retrieve safety and hazard informaon programmacally Where to find the Informaon • Get safety and hazard informaon for a given chemical • Get all compounds that have safety and hazard annotaons • Retrieve safety and hazard informaon programmacally Where to find the safety Informaon for a given chemical in pubChem • Google • PubChem homepage • NCBI entrez PubChem compound • Structure search • Direct URL • Other search engines: Bing, Yahoo, Baidu… Case study: toluene: from Google Case study: toluene: from PubChem/Entrez Direct URL hps://pubchem.ncbi.nlm.nih.gov/compound/cid hps://pubchem.ncbi.nlm.nih.gov/compound/name hps://pubchem.ncbi.nlm.nih.gov/compound/1140 hbps://pubchem.ncbi.nlm.nih.gov/compound/toluene Save or download the informaon on browser hbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/ data/compound/1140/JSON/?response_type=display Where to find the Informaon • Get safety and hazard informaon for a given chemical • Get all compounds that have safety and hazard annotaons • Retrieve safety and hazard informaon programmacally Get all compounds that have safety and hazard annotaons 121225388 121225360 121215529 119090965 119081209 119077305 119075735 119057962 119057958 119057957 119057832 119057828 119057809 119057737 119057735 119057734 119057364 EXported CIDs 119057361 119057340 119057336 118987278 118984465 118984459 118984398 118984389 118984355 118984354 118856763 118856642 118856472 …. Retrieve the subsec5on compounds Click the 5060 link will show the entrez compound page, then from the “Send to” bubon to save the 5060 CIDs as a teXt file. Where to find the Informaon • Get safety and hazard informaon for a given chemical • Get all compounds that have safety and hazard annotaons • Retrieve safety and hazard informaon programmacally Retrieve informaon programmacally using PubChem’s PUG_View service Data driven model: PubChem’s pug_view service sends the json blob to the front end, the front end using script and css to render the page. hbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/1140/JSON hbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/1140/XML Pug_view – Par5al data retrieval To retrieve data for a specific heading, e.g EXperiemtal Properes, use: hbps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/1140/JSON/? response_type=display&heading=EXperimental%20Proper5es PubChem LCSS – A subset PubChem LCSS – A subset PubChem LCSS – where PubChem LCSS - URL hbps://pubchem.ncbi.nlm.nih.gov/compound/toluene#datasheet=lcss #datasheet=lcss Addi5onal Safety Related Informaon • GHS Classificaon hps://pubchem.ncbi.nlm.nih.gov/ghs/ • Emergency Response Guidebook 2016 hps://pubchem.ncbi.nlm.nih.gov/erg/ Summary • PubChem provides chemical safety and hazard informaon that integrated from various open sources include NIOSH, ILO, HSDB, OSHA, NOAA Cameo Chemicals, ECHA, and more. • PubChem created a subset chemical safety informaon page - LCSS. • PubChem added GHS help page and DOT’s EGR look up table. Acknowledgements PubChem Crew Renata Geer Jane He Gang Fu Sunghwan Kim Bo Yu Ben Shoemaker Siqian He Jiyao Wang Jie Chen Yanli Wang Tiejun Cheng .
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