electronic laboratory notebooks douglas perry, ph.d. iu school of informatics
TRANSCRIPT
Electronic Electronic Laboratory Laboratory NotebooksNotebooks
Douglas Perry, Ph.D.Douglas Perry, Ph.D.
IU School of InformaticsIU School of Informatics
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Da Vinci’s NotebookDa Vinci’s Notebook Ca. 1500Ca. 1500
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Curie’s NotebookCurie’s Notebook Ca. 1900Ca. 1900
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Prof. X’s NotebookProf. X’s Notebook
Ca. 2000Ca. 2000
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Traditional Functions of Traditional Functions of Lab NotebooksLab Notebooks
Record experimental conditionsRecord experimental conditions Store primary lab dataStore primary lab data Note experimental observationsNote experimental observations Give references to external dataGive references to external data Make interpretationsMake interpretations Draw conclusionsDraw conclusions Provide legal record for intellectual propertyProvide legal record for intellectual property
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Data vs. MetadataData vs. Metadata
DataData Raw dataRaw data Processed dataProcessed data Final resultsFinal results
MetadataMetadata Test conditionsTest conditions Methods & SOPsMethods & SOPs PersonnelPersonnel
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Paper-Based Information Paper-Based Information is Limitedis Limited
Hard to useHard to use Making entries is slow, tediousMaking entries is slow, tedious
Hard to reuseHard to reuse Protocols, repetitive information droppedProtocols, repetitive information dropped
Easily lostEasily lost Unique documents mislaid, forgottenUnique documents mislaid, forgotten
Hard to searchHard to search Poor indexing, keywords, table of contentsPoor indexing, keywords, table of contents
Hard to shareHard to share Copying difficult or not legalCopying difficult or not legal
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Paper Lab Notebooks Are Paper Lab Notebooks Are Becoming ObsoleteBecoming Obsolete
Paper notebooks have limited capacityPaper notebooks have limited capacity Raw data is massiveRaw data is massive
Data capture is archaicData capture is archaic Raw printouts can no longer be storedRaw printouts can no longer be stored
Data formats are restrictedData formats are restricted 2-D gels, photomicrographs2-D gels, photomicrographs
Record-keeping is tediousRecord-keeping is tedious Repetitive, manual entriesRepetitive, manual entries
Context of work is often lostContext of work is often lost No connection to other people, projects, labsNo connection to other people, projects, labs
Paper records no longer legally requiredPaper records no longer legally required Electronic records are legalElectronic records are legal
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““Closed” Notebooks Are Closed” Notebooks Are Often NeededOften Needed
0 10 20 30 40
Never
Yearly
Monthly
Weekly
Daily
Percent responding
Source: Collaborative Electronic Notebook Systems Association
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Time Spent on Data Time Spent on Data HousekeepingHousekeeping
Lab personnel spend >16 hr/wk Lab personnel spend >16 hr/wk managing datamanaging data
Lab managers spend up to 8 hr/wk Lab managers spend up to 8 hr/wk trying to trying to findfind data data
Proprietary information workers spend Proprietary information workers spend 8 hr/wk auditing notebooks8 hr/wk auditing notebooks
Source: Collaborative Electronic Notebook Systems Association
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Data Flow in the LaboratoryData Flow in the Laboratory
Lab Automation& Robotics
EquipmentInterfacing
LaboratoryInstruments
ChromatographyData Systems
Laboratory InformationManagement
Systems (LIMS)
DataAnalysis
DataMining
DataWarehousing
ElectronicLaboratoryNotebooks
Data Acquisition Information Processing Knowledge Management
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Scientific DataScientific DataManagement ArchitectureManagement Architecture
DBMS LIMS
Instrument Network
Local Laboratory Network
ABFSP
InstrumentData Manager
ManualData EntryGC LC
Chromatography Data System
GCSC
PC
DataWarehousing
ElectronicLaboratoryNotebook
Data Mining/Data Analysis
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ELN Is Complementary to ELN Is Complementary to LIMSLIMS
Source: Amphora Research Systems
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Functional Hierarchy in Functional Hierarchy in Laboratory InformaticsLaboratory Informatics
rules
rules
context
people
SDMS, ELN
DAQ, LAB AUTO
CDS, LIMS
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Paper vs. ElectronicPaper vs. ElectronicLaboratory NotebooksLaboratory Notebooks
PaperPaper Static, limited formatStatic, limited format Passive record keepingPassive record keeping Can meet all legal and regulatory requirementsCan meet all legal and regulatory requirements
ElectronicElectronic Dynamic, multiple formatsDynamic, multiple formats Active collaborationActive collaboration Can meet all legal and regulatory requirementsCan meet all legal and regulatory requirements
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Paper Notebooks Vs. Paper Notebooks Vs. Knowledge ManagementKnowledge Management
Knowledge is individual, not collectiveKnowledge is individual, not collective Journal paradigm fosters “private” mentalityJournal paradigm fosters “private” mentality
Limited collaboration with other labs, other locationsLimited collaboration with other labs, other locations ““Sharing” consists of old summariesSharing” consists of old summaries
Difficult to supervise scientific progress of othersDifficult to supervise scientific progress of others No easy to evaluate other’s experimentsNo easy to evaluate other’s experiments
Methods must be reinvented or reoptimizedMethods must be reinvented or reoptimized Metadata not recorded or not traceableMetadata not recorded or not traceable
Reevaluation of old data impossibleReevaluation of old data impossible Raw data of “poor” results not kept Raw data of “poor” results not kept
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Unique Benefits of ELNUnique Benefits of ELN
Integrates heterogeneous data from Integrates heterogeneous data from disparate sourcesdisparate sources
Fully searchable beyond keywords and Fully searchable beyond keywords and indicesindices
Drill-down access to raw dataDrill-down access to raw data Secure access from any computerSecure access from any computer On-the-fly analysis and feedbackOn-the-fly analysis and feedback
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New Demand for ELN:New Demand for ELN:21 CFR part 1121 CFR part 11
FDA rule initiated August 1997FDA rule initiated August 1997 Sets standards for electronic submissionSets standards for electronic submission Electronic recordsElectronic records
Thoroughly validatedThoroughly validated Automatic audit trailsAutomatic audit trails Results can be recreatedResults can be recreated
Electronic signaturesElectronic signatures Unique identityUnique identity Linked to e-recordLinked to e-record
No grandfather clauseNo grandfather clause
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eRecord DefinedeRecord Defined
““An electronic record is any combination An electronic record is any combination of text, graphics, data, audio, pictorial, of text, graphics, data, audio, pictorial, or other information represented in or other information represented in digital form that is created, modified, digital form that is created, modified, maintained, archived, retrieved, or maintained, archived, retrieved, or distributed by a computer system.”distributed by a computer system.”
--21 CFR part 11.3 (b)(6)--21 CFR part 11.3 (b)(6)
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eSignature DefinedeSignature Defined
““An electronic signature is a computer An electronic signature is a computer data compilation of any symbol or series data compilation of any symbol or series of symbols executed, adopted, or of symbols executed, adopted, or authorized by an individual to be the authorized by an individual to be the legally binding equivalent of the legally binding equivalent of the individual’s handwritten signature.”individual’s handwritten signature.”
--21 CFR part 11.3(b)(7)--21 CFR part 11.3(b)(7)
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Electronic Authoring, Electronic Authoring, Review, and ApprovalReview, and Approval
Null or current
approved version
Author Reviewer Authorizer
New approved version
ES
AUTHORINGPROCESS
REVIEW & APPROVALPROCESS
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Those Who BenefitThose Who Benefitfrom ELNfrom ELN
ScientistsScientists Data analysis, not data managementData analysis, not data management
Lab managersLab managers Data management, not notebook managementData management, not notebook management
Compliance officersCompliance officers Complete audit trails with no paper chaseComplete audit trails with no paper chase
QA/QC directorsQA/QC directors Concurrent accessibility of all dataConcurrent accessibility of all data
Corporate attorneysCorporate attorneys Complete, Complete, legallegal records for litigation support records for litigation support
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Concerns about ELNConcerns about ELN
Major change impositionMajor change imposition Restructuring of scientists’ core activitiesRestructuring of scientists’ core activities
Loss of privacyLoss of privacy Notebook is transformed from a personal journal to Notebook is transformed from a personal journal to
a community centera community center
Loss of controlLoss of control Data and metadata could be altered by othersData and metadata could be altered by others
Corporate impositionCorporate imposition Roll-out by executive fiat, not individual adoptionRoll-out by executive fiat, not individual adoption
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Cost vs. Value forCost vs. Value forLaboratory NotebooksLaboratory Notebooks
0
5
10
15
20
25
30
0 2 4 6 8 10 12
Time
Monet
ary un
its
Cost-PN Value-PN Cost-ELN Value-ELN
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ELN Impact StudyELN Impact Study
Source: Trigg J and Davis S: Transforming the Laboratory by Implementing an Electronic Laboratory Notebook, Managing the Modern Laboratory, 5:4, 2001
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Collaborative ELNCollaborative ELN
scientist
clinician
researchspecialist
nurse
dataencoder
labtechnician
labmanagerstatistician
writer
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Stratified Collaboration Stratified Collaboration Using ELNUsing ELN
dataencoder
labtechnician
labmanager
researchspecialist
clinicianscientist
Data
Information
Knowledge
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CENSACENSA
Collaborative Electronic Notebook Systems Association
ELN FunctionalityELN Functionality
Examples from KalabieExamples from Kalabie™™ and LABTrack and LABTrack ™™
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Experiment EntryExperiment Entry
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Experiment ManagementExperiment Management
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Experiment ReviewExperiment Review
3333
Making Page EntriesMaking Page Entries
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Revising Page EntriesRevising Page Entries
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Embedding GraphicsEmbedding Graphics
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Notarizing a PageNotarizing a Page
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Maintaining an Audit Maintaining an Audit TrailTrail
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Searching the NotebookSearching the Notebook
Analytical Support for R&D Programmes through ELN
Walk Up services for Analytical clients
Instrument interfacesfor direct transmissionof data to LIMS
General access from Lotus Notes
ELNELN
LIMSLIMS ReferenceData
ReferenceData
DataAcquisition
DataAcquisition
ReportsDatabaseReports
Database
ELNELNELNELN
ELNELN
Programs& ProjectsPrograms& Projects
SummaryDatabaseSummaryDatabase
LotusNotesLotusNotes
WalkUp
WalkUp
MRPMRP
Mfg Problem Solving databases
Kodak UKKodak UKKodak UKKodak UK
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A True Story…A True Story…
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The Loss…The Loss…
One month of work by postdocOne month of work by postdoc $3,000 in labor and supplies$3,000 in labor and supplies Protocol to replicate experimentsProtocol to replicate experiments
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The Consequences…The Consequences…
In effect, experiments had never been In effect, experiments had never been donedone
No preliminary data for NIH grant No preliminary data for NIH grant applicationapplication
No supporting data for related No supporting data for related publicationpublication
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The Moral…The Moral… ELN is needed as much in academia as ELN is needed as much in academia as
it is in industryit is in industry
Questions & Questions & CommentsComments