Reviewing PubChem laboratory chemical safety summaries …Reviewing PubChem laboratory chemical...
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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
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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
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TheCurrentContextofChemicalSafetyInforma5on
• Caveatemptor:Chemistrytextbooksandlaboratorymanualsprovideaoverviewofgenericrules,followedby"seetheMSDS".
• WikipediaprovideslinkstorandomMSDSsourceswithnoevidenceofwhythatsourceisselected;somesourcesarekaput,manyaredated
• ReportsbytheNa5onalResearchCouncil,theACS,NFPAaDerspecificlaboratorysafetyincidentsfoundthisapproachtochemicalsafetyeducaFonandinformaFoninadequate.
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TheStructureofChemicalSafetyInforma5on
Increasinglywell-
defined;also
increasingvoluminous
1970's
1980's
2000's
1990's
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LessStructuredChemicalSafetyInforma5on
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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
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ProjectOverview
ObjecFveistoanalyzehowmanychemicalsinthePubChemLCSShaveGHSandNFPAdataintheWikipediaChembox
DownloadlistofChemicalsfrom
PubChemContainingLCSS
UseExceltofilterthedownloadofinformaFontoonlyPubChemCIDs
UsePubChemIdenFfierExchangetoconvertListofCIDstoInChIKeys
UseGoogleSheetstoconvertInChIKeysto
WikiNames
UseGoogleSheetstopullNFPA704datafromWikiChemboxforWiki
Names
UseGoogleSheetstopullGHSHazard
StatementsfromWikiChemboxforWikiNames
UseGoogleSheetstoanalyzedata
FutureGoalstocompareSafetyInformaFonofWikipediatoPubChem
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LCSSDatatoInChIKey
PubChemIdenFfierExchange
ConvertListofPubChemCIDstoInChIKeys
ExcelorGoogleSheets
FilterdowndatafromPubChemintoaListofPubChemCIDs
PubChemWebsite
ObtainListofChemicalswithLCSS
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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
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InChIKeytoSafetyInforma5on
GoogleSheets
AnalyzeData
GoogleSheets
ConvertWikiNametoSafetyInformaFonusingImporthtmlfuncFon
GoogleSheets
ConvertInChIKeytoWikiNameusingImportxmlfuncFon
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WikipediaChembox
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InChIKeytoWikiName
SpreadsheetsearchesWikipediaFortheInChIkeythenpullsSuggestedname.
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WikiNametoSafetyInforma5on
• GoogleSheets– ImporthtmlfuncFon– PullsSafetyInformaFonusingWikiName
• =IFError(query(IMPORTHTML(CONCATENATE("hcps://en.wikipedia.org/wiki/",C2719),"Table",1),"SELECTCol2whereCol1='GHShazardstatements'",0),"NoGHSHazardStatement")
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TheEarlySta5s5cs
• PubChemhasanLCSSviewforabout3500(2000moretocomesoon)chemicals;WikipediahasChemboxesforabout10,000chemicals
• OfthoseinthePubChemLCSScollecFon,about30%haveanentryinWikipedia
• 4%ofthePubchemcollecFonhasGHSinformaFon;12%ofthePubChemcollecFonhaveNFPAdiamondinformaFon
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FutureDirec5ons
• UnderstandtheWikipediaChemboxstructuretocollectinformaFonmoreefficiently
• DevelopaWikipedia–PubChemdatalinkthatcanprovidechemicalsafetyinformaFonwithprovencedatatotheChemBox
• ConsiderwhatchemsafetydatamakessensetoputintheWikipediaChemboxandwhatcanbelinkedtothere
The hazard portion of the acetone chembox
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LessonsLearnedaboutthisOLCCproject
• Benefits:CrosscampuscollaboraFonon"specialty"topicshelps:– Connectwithpeopledoingsimilarwork– Provideaccesstoexperts– Developrealworldproducts
• Challenges:DistanceeducaFon(learning,teachingandcollaboraFon)– Synchronizingschedules(knowingwhathashappeningontheotherend)
– Assessingunderstanding,bothorallyandwricen
– MaintainingfocusontheoverallgoalwhileaccepFngprojectdriD