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Allotrope Framework implementationin the Bioanalytical Lab
Dr. Gerhard NoelkenAll t B D b Pfi All t Li iAllotrope BoD member, Pfizer Allotrope Liaison
EBF 8th Open Meeting
©2015 Allotrope Foundation
EBF 8th Open Meeting19 November 2015
Allotrope Foundation• Subject Matter Experts
Member CompaniesAbbVieAmgen
BiogenBoehringer Ingelheim
Genentech/RocheGlaxoSmithKline
• Project FundingMember Companies Baxter
BayerBristol‐Myers SquibbEli Lilly
Merck & Co.Pfizer
• Project Management• Legal & Logistical Support
Secretariat
• Legal & Logistical Support
F k D l tProfessional • Framework Development• Technical Leadership
ProfessionalSoftware Firm
• Requirements & SpecificationsPartner Network
ACD/LabsAgilent Biovia
Mettler ToledoPersistentRiffyn
Waters
Erasmus Univ.
• Contributions, PoC ApplicationsBioviaBSSNIDBS
RiffynSartoriusShimadzu
Med CenterUniversity of Southampton
©2015 Allotrope Foundation 2
Mestrelab Research Thermo Scientific
What is Allotrope Creating?p g
Application 1 Application 2
Instrument A toolkit that enables use of the standards &Application 1 Application 2
Metadata
New Instrument
use of the standards & metadata in software
development
Allotrope Foundation FrameworkAllotrope Foundation FrameworkReusable
Metadata repository
Software Components
St d d Open l f f d d b lStandard
File Format
pMetadata
Repository
dat
File format for any technique or instrument
Project Test InstrumentAF 0012354 IR Fingerprinting QC Lab #33B 380 FT‐IR
Standard vocabulary & structure for metadata
.etc
.etc
.etcetc
.etc
.etc
.dat
.tbl.HDF
.raw .csv
.DAML
.LCD
.XMLjd f
AF 0012354 IR Fingerprinting QC Lab #33B 380 FT IRAE0012764 Bulk & Tapped Density ASTM Standard Seive #6AF 12989 NMR Characterization AM500
Tapped & Bulk Density Sieve XXXAF0045674 Caractérisation RMN Nouvelle DRX600AF‐0034558 IR iS10 FT‐IR
.etc.etc
.etc
.etc
.etc
.mzML
.jdx
.irf .pdid.drdd
.asc
.cdf
.frx
.adf AF 0034558 IR iS10 FT IR
Project Test InstrumentAF0012354 IR Fingerprinting 380 FTIR/‐SN/145453AF0012764 Bulk and Tapped Density ASTM Sieve‐SN/3452
With the Metadata Repository
©2015 Allotrope Foundation 3
pp y /AF0012989 NMR Characterization AM500‐SN/0034578 AF0013142 Bulk and Tapped Density ASTM Sieve‐SN/09783AF0045674 NMR Characterization DRX600‐SN/10234567AF0034558 IR Fingerprinting iS10 FTIR/‐SN/341980
Allotrope Data Format (ADF)
Contains:Contains:• Method, instrument, sample,
process, result, etc.• Data cube metadata
Allotrope Data Format
Data DescriptionData DescriptionRDF ModelRDF Model
• Data package metadata• …
Data Cubes Data Cubes Universal data containerUniversal data container
Analytical data represented by one- or multidimensional arrays.
Universal data containerUniversal data container
Data Package Data Package
Analytical data represented by arbitrary formats, incl. native i t t f t i df Data Package Data Package
Virtual file system *Virtual file system *instrument formats, images, pdf, video, etc.
Specificall designed to store and HDF5Platform Independent File Format
Specifically designed to store and organize large amounts of numerical data.
©2015 Allotrope Foundation * Use is optional
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Example: 36‐Month Stability ProtocolMethod, Impurities, Peaks, Decisions, Stability Time Point, Packaging Configuration, Storage
Allotrope Data Format Conditions, Sample Preparation Events, Weights, Concentrations, Specifications, Integration Events, Scientist, Time Stamps,
di il S l iAllAll Metadata & ResultsMetadata & Results Audit Trail, Measurement System, Real‐Time SOP & Compliance Checks
ChromatogramsChromatogramsPressure TracesPressure Traces
Vendor File FormatsVendor File Formats
Enterprise AnalyticsLong‐Term PreservationStability Reports
HDF5
Vendor File FormatsVendor File Formats Regulatory SubmissionsInspections, AuditsData ExchangeHDF5
Platform Independent File Format
Data ExchangeConfidence in Data
©2015 Allotrope Foundation 5
Allotrope Taxonomies: An Extensible Metadata ModelMetadata Model
• A library of extensible • Initial versions of 12A library of extensible taxonomies– Uses W3C standards
• Initial versions of 12 analytical techniques already implemented:
– Easy to understand and maintain by SMEs and Vendors
St t b h ti i ti
implemented:– gas chromatography– Karl Fischer
• Start by harvesting existing available concepts– PSI‐MS; IUPAC; RSC Chemical
– liquid chromatography– mass spectrometry
nuclear magnetic resonancePSI MS; IUPAC; RSC Chemical Methods Ontology; Dictionary of weighing terms; AnIML, etc
R d ibl & ffi i
– nuclear magnetic resonance spectroscopy
– thermogravimetric analysis• Reproducible & efficient
collaboration modelLeverages knowledge engineers
– ultra violet spectrometry– cell counter
cell culture analyzer– Leverages knowledge engineers & member company scientists
– 2‐3 weeks to develop initial
– cell culture analyzer– blood gas analysis– balance
©2015 Allotrope Foundation
version of a new taxonomy – pH6
More Taxonomies Available in 1Q 2016• Instrument Taxonomies
P t i Ch t i ti• Other Taxonomies
IDMP Id tifi ti f M di i l– Protein Characterization– Microplate Reader– Flow Cytometer
– IDMP‐Identification of Medicinal Products
– Extend Process (S88)Flow Cytometer– Protein Purification– Millipore Filtration System
( )– Extend Materials– Extend Equipment
– Differential Scanning Calorimetry (DSC)X R P Diff ti (XRPD)
– Investigation/Study/Analysis– Phase of Development
R t f Ad i i t ti– X‐Ray Power Diffraction (XRPD)– Particle Sizer– Roller Press
– Route of Administration– Product Quality Attributes– Container CategoriesRoller Press
– Tablet Pressing– Tablet Coating
Container Categories– Chemical Reactions
– Dynamic Vapor Sorption (DVS)– solid‐state NMR (ssNMR) Funded by Individual Allotrope
Member
©2015 Allotrope Foundation
– Infrared Spectroscopy (IR)7Shared with Allotrope Foundation
Allotrope Foundation Taxonomies
©2015 Allotrope Foundation
The ADF enables a self‐contained documentation of the data & metadata
ProcessStep
Legend
Data & Metadata Interoperability
(Plug & Play)More automated reporting,
Powerful searching
Request Control Inst. Acquire Data
Process Data
Analyze Data
Report & Share
Search & Reuse Data
Plan A l i
Prepare S l
Submit S l
Control Inst. A i D
Process D
Analyze D
Reports R l
Store, ArchiveAnalysis Samples Samples Acquire Data Data Data Results Archive Data
Analytical Sample Prep Instrument Instrument Processed Analyzed Reported St d D tAnalytical Method
Sample Prep Data
Instrument Instruction
Instrument Data
Processed Data
Analyzed Data
Reported Results Stored Data
Standard data file format for data & metadataOutput from one system becomes the input to the next
©2015 Allotrope Foundation
The APIs enable the use of one vendor agnostic file format
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Integration Projects Reduce it to Practice
• Divide and conquer: members share the costs and benefits
• Early adoption and acceleration of AF Framework development through delivery of Framework components.development through delivery of Framework components.
• Accelerate vendor adoption via collaboration on delivering specific capabilities through the integration projects
• Ensure the validity of the Framework through real‐worldEnsure the validity of the Framework through real world requirements and implementation.
• Benefit the sponsoring companies in terms of shared development of new functionality & shared experience
• Drive integration of the Framework into the IT/IS Roadmap
©2015 Allotrope Foundation 10
Integration ProjectsDevelopmentResearch CommercialM lti l
B
A Small and Large Molecule CMCMultiple types
Elemental ImpuritiesICP‐MS
pH, Weighing, GC, Karl Fischer, TGA, NMR , Cell Density/Viability, Blood Gas Analyzer , Cell Culture Analyzer, Capillary Electrophoresis
C FermentationProcess ControlBioanalyzer
…
D CRO IntegrationHPLC‐UV
E
St t ID P ifi ti
Structure IDHPLC‐MS
D CRO IntegrationHPLC UV
F Structure ID, Purification,In vitro BioanalysisHPLC‐UV/MS
G Assay, PurityHPLC‐UV
I
H Drug Substance Release & Stability
Method ScreeningHPLC‐UV/MS
HPLC‐UVBalance
I Method ScreeningHPLC UV/MS
J LC Data to ADF Converter/AdapterHPLC‐UV
©2015 Allotrope Foundation 11
Member non‐GMP GMPInstrument
APN Member PoCs
ADF multipleAPN M b APNM bAF TaxonomiesADF multiple techniques(results only)
APN Member “ELN”
APN Member “SDMS”
Integration Project AGMP Development
AF TaxonomiespHWeighing
TGANMR
LES
WeighingHPLCUVMSGC
NMR Cell Density/ViabilityBlood Gas Analyzer Cell Culture AnalyzerCapillary Electrophoresis
ADF multiple
GCKarl Fischer
Capillary Electrophoresis…
Instruments Data Lake(Hadoop)
ADF multiple techniques(results only)
©2015 Allotrope Foundation 12
SSummary
20162015
2016• Framework Development
• Framework used in production• First Public release
2014• Established feasibility through PoCs
Framework Development• Integration at Members
2013
y g• ADF design & due diligence
2013• Initiated software development
and evaluations
2012 Allotrope Foundation
©2015 Allotrope Foundation 13
Allotrope Foundation
The Framework will provide Business benefitLess Manual Document Preparation
Improved Data Integrity
Seamless data exchange & with partners & CROsPreparation
• Find data quickly/logically• Eliminate Copy/paste• No more
• Eliminate error due to manual text entry or transcription
partners & CROs• One data file format• One consistent vocabulary• Reduced cost & complexity• No more
Transcription/conversion• Source agnostic
transcription• Complete, consistent, accurate metadata
• Reduced cost & complexity to CROs, CMOs, partnerships
Lower Data Facilitate Regulatory Extracting Knowledge Management Costs
• Interoperability
g yCompliance
• Improved instrument &
g g& Value from Data
• Greatly enhance speed to • Future‐proof against future data migrations
• Reduced technical debt: no
software validation tracking
• Reduced complexity in d i
answer/decision• Remove data silos• Create an ecosystem for
more maintenance of legacy systems
• Improved archiving
system documentation• Simpler to support questions/investigations
innovation• Facilitates data mining & analytics
©2015 Allotrope Foundation 14What are your priorities?
Thank you!
To join or get additional information, contact:
James Vergis, Ph.D.
To join or get additional information, contact:
James Vergis, Ph.D.James Vergis, Ph.D. Science Advisor | Drinker Biddle & Reath LLP1‐202‐230‐5439
James Vergis, Ph.D. Science Advisor | Drinker Biddle & Reath LLP1‐202‐230‐5439James.Vergis@dbr.commore.info@allotrope.org www.allotrope.orgJames.Vergis@dbr.commore.info@allotrope.org www.allotrope.org
©2015 Allotrope Foundation 15