Reviewing PubChem laboratory chemical safety summaries …Reviewing PubChem laboratory chemical...

Reviewing PubChem laboratory chemical safety summaries

for different user types

Brian Murphy University of Arkansas, Little Rock

Ralph Stuart

Chemical Hygiene Officer, Keene State College

R.E. Belford University of Arkansas, Little Rock

Leah McEwen

Chemistry Librarian, Cornell University March, 2016

My Experience with On-Line Distance Education

•  Developed Lab-XL project with EPA Region 1 and DC from 1996-2000

•  Taught HAZWOPER (chemical safety for field students) with an on-line component from 2000 to 2011

•  Participated in the 2004 OLCC On Lab Safety •  Used Mediawiki platform for student assignments

and reports

TheCurrentContextofChemicalSafetyInforma5on

•  Caveatemptor:Chemistrytextbooksandlaboratorymanualsprovideaoverviewofgenericrules,followedby"seetheMSDS".

•  WikipediaprovideslinkstorandomMSDSsourceswithnoevidenceofwhythatsourceisselected;somesourcesarekaput,manyaredated

•  ReportsbytheNa5onalResearchCouncil,theACS,NFPAaDerspecificlaboratorysafetyincidentsfoundthisapproachtochemicalsafetyeducaFonandinformaFoninadequate.

TheStructureofChemicalSafetyInforma5on

Increasinglywell-

defined;also

increasingvoluminous

1970's

1980's

2000's

1990's

LessStructuredChemicalSafetyInforma5on

LookingforStructureintheElectronicData

•  How large is the PubChem chem safety information universe?

•  How high quality is it (including consistency & provenance information)?

•  How large is the Wikipedia chem safety information universe?

•  How high quality is it?

How much overlap is there between the two?

Key safety information fields: -  GHS class designation(s) and

signal word -  NFPA diamond information

10,000 Chemboxes

Millions of chemicals; 3500 with GHS info

ProjectOverview

ObjecFveistoanalyzehowmanychemicalsinthePubChemLCSShaveGHSandNFPAdataintheWikipediaChembox

DownloadlistofChemicalsfrom

PubChemContainingLCSS

UseExceltofilterthedownloadofinformaFontoonlyPubChemCIDs

UsePubChemIdenFfierExchangetoconvertListofCIDstoInChIKeys

UseGoogleSheetstoconvertInChIKeysto

WikiNames

UseGoogleSheetstopullNFPA704datafromWikiChemboxforWiki

Names

UseGoogleSheetstopullGHSHazard

StatementsfromWikiChemboxforWikiNames

UseGoogleSheetstoanalyzedata

FutureGoalstocompareSafetyInformaFonofWikipediatoPubChem

LCSSDatatoInChIKey

PubChemIdenFfierExchange

ConvertListofPubChemCIDstoInChIKeys

ExcelorGoogleSheets

FilterdowndatafromPubChemintoaListofPubChemCIDs

PubChemWebsite

ObtainListofChemicalswithLCSS

8

ObtainingLCSSListofChemicals

ClickHeretoViewListofCompoundswithanLCSS

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FilterPubChemInforma5onintoCIDs

First=MID(Sheet0!A5,FIND("CID: ",Sheet0!A5)+5,LEN(Sheet0!A5))Then Filter off cells with errors

This will yield list of PubChem CIDs

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Conver5ngCIDtoInChIKey

PubChemIdenFfierExchangewillconvertPubChemCIDtoInChIKey

11

InChIKeytoSafetyInforma5on

GoogleSheets

AnalyzeData

GoogleSheets

ConvertWikiNametoSafetyInformaFonusingImporthtmlfuncFon

GoogleSheets

ConvertInChIKeytoWikiNameusingImportxmlfuncFon

12

WikipediaChembox

13

InChIKeytoWikiName

SpreadsheetsearchesWikipediaFortheInChIkeythenpullsSuggestedname.

14

WikiNametoSafetyInforma5on

•  GoogleSheets–  ImporthtmlfuncFon– PullsSafetyInformaFonusingWikiName

•  =IFError(query(IMPORTHTML(CONCATENATE("hcps://en.wikipedia.org/wiki/",C2719),"Table",1),"SELECTCol2whereCol1='GHShazardstatements'",0),"NoGHSHazardStatement")

15

TheEarlySta5s5cs

•  PubChemhasanLCSSviewforabout3500(2000moretocomesoon)chemicals;WikipediahasChemboxesforabout10,000chemicals

•  OfthoseinthePubChemLCSScollecFon,about30%haveanentryinWikipedia

•  4%ofthePubchemcollecFonhasGHSinformaFon;12%ofthePubChemcollecFonhaveNFPAdiamondinformaFon

FutureDirec5ons

•  UnderstandtheWikipediaChemboxstructuretocollectinformaFonmoreefficiently

•  DevelopaWikipedia–PubChemdatalinkthatcanprovidechemicalsafetyinformaFonwithprovencedatatotheChemBox

•  ConsiderwhatchemsafetydatamakessensetoputintheWikipediaChemboxandwhatcanbelinkedtothere

The hazard portion of the acetone chembox

LessonsLearnedaboutthisOLCCproject

•  Benefits:CrosscampuscollaboraFonon"specialty"topicshelps:–  Connectwithpeopledoingsimilarwork–  Provideaccesstoexperts–  Developrealworldproducts

•  Challenges:DistanceeducaFon(learning,teachingandcollaboraFon)–  Synchronizingschedules(knowingwhathashappeningontheotherend)

–  Assessingunderstanding,bothorallyandwricen

– MaintainingfocusontheoverallgoalwhileaccepFngprojectdriD