CINF80: 252nd ACS Naonal Meeng, 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 Instutes 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 scienfic 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 sll happen from me to me.

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 properes, 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 informon: 2d and 3d images, property data, drug, food addive, chemical safety, agrochemical, literature references, patents, and more – PubChem most used informaon. • Annotaons – 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 • Idenficaon • Biologic Descripon • Safety and Hazards • Names and Idenfiers • Toxicity • Chemical and Physical • Literature Properes • Patents • Related Records • Preparaon and Reacons • Chemical Vendors • Biomolecular Interacons and • Drug and Medicaon Pathways Informaon • Biological Test Results • Food Addives and Ingredients • Classificaon • Agrochemical Informaon • Pharmacology and Biochemistry Safety and Hazard Informaon

• 2D Structure • Use and Manufacturing • 3D Conformer • Idenficaon • Biologic Descripon • Safety and Hazards • Names and Idenfiers • Toxicity • Chemical and Physical • Literature Properes • Patents • Related Records • Preparaon and Reacons • Chemical Vendors • Biomolecular Interacons and • Drug and Medicaon Pathways Informaon • Biological Test Results • Food Addives and Ingredients • Classificaon • Agrochemical Informaon • Pharmacology and Biochemistry Safety and Hazard Informaon Safety and Hazards Fire First Aid REL-STEL Reacvies and Incompabilies Hazards Idenficaon 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 Idenficaon Skin First Aid • Threshold Limit Values Stability and Reacvity DOT ID and Guide Fire Hazard Eye First Aid Other Occupaonal Permissible Levels DOT Label Explosion Hazard • Ingeson First Aid • Sources and Potenal Exposure Packaging and Labelling Hazards Summary Safety and Hazard Fire Fighng Measures Assessing Personal Exposure Transport Informaon EC Classificaon Fire Potenal 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 Properes Other Fire Fighng 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 Potenal Isolaon Name Flammability • Fire Fighng Measures Isolaon and Evacuaon Acceptable Daily Intakes Isolaon Distance Crical Temperature Spillage Disposal Allowable Tolerances Atmospheric Standards Crical Pressure • Cleanup Methods Personal Protecon Soil Standards Danger of Explosion Accidental Release Disposal Methods • Respirator Recommendaons Names and Idenfiers 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 Properes State Drinking Water Standards NFPA Reacvity Rang Nonfire Spill Response Exposure Prevenon State Drinking Water Guidelines NFPA Health Rang • Handling and Storage Safe Storage Inhalaon Prevenon Clean Water Act Requirements NFPA Other Storage Condions Skin Prevenon • Toxicological Informaon CERCLA Reportable Quanes Physical Dangers • Exposure Control and Exposure Control and Personal Eye Prevenon TSCA Requirements Chemical Dangers Protecon • Ingeson Prevenon Ecological Informaon RCRA Requirements Explosive Limits and Potenal Personal Protecon REL Protecve Equipment and Clothing FIFRA Requirements OSHA Standards PEL Stability and Reacvity FDA Requirements NIOSH Recommendaons PEL-TWA Air and Water Reacons Other Safety Informaon Other Safety and Hazard Data PEL-STEL Reacve Group Safety References First Aid Measures PEL-C Reacvity Alerts Safety Notes First Aid REL-TWA Reacvity Profile Toxic Combuson Products Other Hazardous Reacons 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 hps://pubchem.ncbi.nlm.nih.gov/compound/toluene

Save or download the informaon on browser hps://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 subsecon compounds

Click the 5060 link will show the entrez compound page, then from the “Send to” buon 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. hps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/1140/JSON hps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/1140/XML

Pug_view – Paral data retrieval

To retrieve data for a specific heading, e.g Experiemtal Properes, use: hps://pubchem.ncbi.nlm.nih.gov/rest/pug_view/data/ compound/1140/JSON/? response_type=display&heading=Experimental%20Properes PubChem LCSS – A subset PubChem LCSS – A subset PubChem LCSS – where PubChem LCSS - URL

hps://pubchem.ncbi.nlm.nih.gov/compound/toluene#datasheet=lcss

#datasheet=lcss Addional 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