pistoia alliance european conference 2015 - gerhard noelken / allotrope foundation
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©2015 Allotrope Foundation
We are a data industry: let’s act like one.
Gerhard NoelkenPfizer Allotrope Liaison
©2015 Allotrope Foundation
Today’s Environment: In the absence of standards in laboratory software
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Incomplete,
Incompatible
Software
No Standard
File Formats
Inconsistent
Metadata
Convert or transcribe
Application 1.abc
outApplication 2
input.xyz
technology A technology X
Project Test InstrumentAF 0012354 IR Fingerprinting QC Lab #33B 380 FT-IRAE0012764 Bulk & Tapped Density ASTM Standard Seive #6
AF 12989 NMR Characterization AM500 Tapped & Bulk Density Sieve XXX
AF0045674 Caractérisation RMN Nouvelle DRX600AF-0034558 IR iS10 FT-IR
.etc
.etc
.etc
.etc
.etc
.etc
.etc
.etc
.etc
.etc
.dat
.tbl.HDF
.raw .csv
.DAML.LCD
.XML
.mzML.jdx
.irf .pdid
.drdd
.asc
.cdf.frx
©2015 Allotrope Foundation
Leading to the problems that brought the collaboration together
It’s hard to find data based on intuitive
starting points [e.g. study, project, analyst,
technique]
It’s hard to integrate data from different labs
instruments, or online/offline because
the file format is different
It’s hard to mine a collection of data
because the details and the context of the
experiment is stored somewhere else
Can’t understand /interpret data later
because the context is incomplete,
inconsistent, often free text
Instrument & software interoperability is
limited…at best
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©2015 Allotrope Foundation
Allotrope Foundation
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• Subject Matter Experts
• Project FundingMember Companies
• Project Management
• Legal & Logistical Support
Secretariat
• Framework Development
• Technical Leadership
ProfessionalSoftware Firm
• Requirements & Specifications
• Contributions, PoC Applications
Partner Network
AbbVieAmgenBaxterBayerBiogen Idec
Boehringer IngelheimBristol-Myers SquibbEisai Eli LillyGenentech/Roche
GlaxoSmithKlineMerckPfizer
ACD/Labs
Agilent
Biovia
BSSN
IDBS
Mestrelab Research
Mettler Toledo
Sartorius
Shimadzu
Thermo Scientific
Waters
©2015 Allotrope Foundation
What is Allotrope Creating?
Allotrope Foundation Framework
Reusable
Software
Components
Open
Document
Standard
Open
Metadata
Repository
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Application 1 Application 2
Metadata repository
New Instrument
Instrument
.etc.etc
.etc
.etc
.etc
.etc.etc
.etc
.etc
.etc
.dat
.tbl.HDF
.raw .csv
.DAML
.LCD
.XML
.mzML
.jdx
.irf .pdid.drdd
.asc
.cdf
.frx
.adf
The set of standards used based on our requirements
Project Test InstrumentAF 0012354 IR Fingerprinting QC Lab #33B 380 FT-IRAE0012764 Bulk & Tapped Density ASTM Standard Seive #6
AF 12989 NMR Characterization AM500 Tapped & Bulk Density Sieve XXX
AF0045674 Caractérisation RMN Nouvelle DRX600AF-0034558 IR iS10 FT-IR
Project Test InstrumentAF0012354 IR Fingerprinting 380 FTIR/-SN/145453AF0012764 Bulk and Tapped Density ASTM Sieve-SN/3452AF0012989 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
With the Metadata Repository
The core of the controlled vocabulary
A toolkit that enables use of the standards & metadata in software
development
©2015 Allotrope Foundation
Small Molecule BiologicsHPLC, LC-MS, GC, GC-MS
CE, SFC, IEX, SEC RI, ICP-MS, IMS
UV-VIS, IR, NIR, Raman, FL, NMR, KF Coulometric, KF VolumetricLight Scattering, Microscope,
pH Meter, Polarimeter,Potentiostat, Coulometer
XRD, SEM, Viscometer, Water ActivityBalance, DSC, TGA, DissolutionSterility, Reconstitution Time
Osmolality, TOC
PCR, qPCR, cIEF, iCEELISA, EIA
Flow Cytometry,O2 sensor, SDS-PAGE
EndotoxinConductivity
Far/Near UV CDPeptide DigestionPlasmid Retention
Genotypic Verification
DisintegrationCalorimetry,Flowability
Surface AreaHardness
Optical RotationWet Chemistry
TLC
The Analytical “Laboratory” Data Landscape
Delivering a Solution Across Technologies and Modalities will Enhance Value and Adoption
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©2015 Allotrope Foundation
The basic analytical workflow and data flow standardized
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Plan Analysis
Prepare Samples
Submit Samples
Control Inst. Acquire
Data
Process Data
Analyze Data
Reports Results
Store, Archive
Data
Request ReportSearch
& Reuse Data
Sample Prep Data
Instrument Instructions
Instrument Data
Processed Data
Analyzed Data
Reported Results Stored DataAnalytical
Method
Data & Metadata
ProcessStep
Legend
Ultimately the collective meta data is EVIDENCE that supports a DECISION about your MANUFACTURING PROCESS or MATERIAL
©2015 Allotrope Foundation
The basic analytical workflow and data flow standardized
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Plan Analysis
Prepare Samples
Submit Samples
Control Inst. Acquire
Data
Process Data
Analyze Data
Reports Results
Store, Archive
Data
Request Report & Share
Search & Reuse
Data
Sample Prep Data
Instrument Instructions
Instrument Data
Processed Data
Analyzed Data
Reported Results Stored DataAnalytical
Method
Data & Metadata
ProcessStep
Legend
Standard data file format & metadata
Control Inst. Acquire
Data
Process Data
Analyze Data
InteroperabilityMore automated reporting,
Powerful searching
©2015 Allotrope Foundation
ADF Key Requirements
• Large data volume, small file size, fast
• Arbitrary techniques; extensible
• Platform independent
Technical capabilities
• Who, what, when, where, why and how
• Scientist, sample, time stamp/audit trail, instrument, purpose, method
Comprehensive Metadata
• Documented file format
• Vendor neutral format
• Adaptable and extensible
Long term data access
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©2015 Allotrope Foundation
Allotrope Data Format
Data stored in public formats, incl. images, pdf, video
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Platform Independent File Format
HDF5
Data DescriptionResource Description Framework
(RDF) Model
Data Cubes Universal data container
Data Package Virtual file system
Contains semantic descriptions of:• Method, instrument, sample, process, result, etc.• Data cube metadata• Binary file metadata
Binary representation analytical data in one- or multidimensional arrays
©2015 Allotrope Foundation
ADF Class Library
Platform independent file format(HDF 5)
Data Package API Data Cube API
Data Description API (Jena, dotNetRDF)
Analytical Data API
Taxo
no
mie
s
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Triple Store API
April2015
April2015
Feb 2015
©2015 Allotrope Foundation
A lot of good ideas that can be used:More than 100 relevant public standards & ontologies, highly connected
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International Standards Organization
Open Geospatial Consortium
World Wide Web Consortium
…
SensorML
AnIML
S88/BatchML
mzML
…
Analytical Data
Standards
Metadata
Standards
Allotrope
Framework
©2015 Allotrope Foundation
Allotrope Taxonomy Concept• Create library of extensible taxonomies
– Easy to understand and maintain by SMEs and Vendors
– Hosted in the public Allotrope Metadata Repository
– Collaborative development across membership & APN
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©2015 Allotrope Foundation
Why we’re not yet another …• We share the same pain points – so we’re sharing a significant
upfront investment in fixing the root causes of the problem (not a “band aid”)
• We’re collaborating across industries to provide the vendor community a set of coherent, community-wide requirements
• Doing the work on real problems, with code, and in the lab to test assumptions is a great way to make progress
• It takes money, commitment and time from scientists, lab managers, and senior managers; leveraging vast team of SMEs across 13 companies
• We’ve engaged professionals – software engineers, architects, laboratory automation, attorneys, scientists, process/domain experts, project managers
• We are making tangible progress, hitting milestones, and will deploy the first production Framework in 2016
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©2015 Allotrope Foundation
Examples of 2015 Integration Projects
• Converters are a temporary, expedient solution to transform data into the Allotrope Data Format
Converters
• Leverage contextual metadata for natural language search
• “find all lots with impurity at retention time 10.2 s greater than 0.01 area percent”
• Lightweight universal viewer for any technique
Data Storage & Access
• Standard platform for the planning, execution, analysis & reporting of analytical chemistry leveraging the Allotrope Framework
• Includes IoT instrument integration; metadata repository/method management; workflow execution
Automation of Analytical Chemistry
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©2015 Allotrope Foundation
Collaboration with the Vendor community
Launched in March 2014
• Designed to provide equal opportunities for all partners
• Contains elements for the Development, QA/Support, Marketing and Sales teams of Allotrope Partners
http://partners.allotrope.org
• Portal for any vendor to collaborate with Allotrope Foundation and contribute to the Framework
Expanded opportunities for participation in 2015
• Integration projects & PoCs
• Focused engagement with thought leaders & SMEs
• Well defined roadmap and governance
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©2015 Allotrope Foundation
Project Trajectory
2013
2014
20152016
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Allotrope Foundation
Initiated software development and evaluations
Established feasibility through PoCs; ADF design & due diligence
Framework DevelopmentIntegration at Members
Framework used in production
First Public release
©2015 Allotrope Foundation
Questions?Network with Peers: upcoming workshops• Allotrope Cross-Industry Workshops
– April 24, 2015 (Cambridge, MA)– June 9, 2015 (Leverkusen, Germany)– September 16, 2015 (Chicago, IL)
• Allotrope Partner Network Workshops– September 15, 2015 (Chicago, IL)
Presentations
• BioIT World, April 23 (Cambridge, MA)
• COSMOS Aug 17-19 (San Diego, CA)
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To join or get additional information, contact:
James Vergis, Ph.D.
Science Advisor | Drinker Biddle & Reath LLP
1-202-230-5439
James.Vergis@dbr.com
more.info@allotrope.org www.allotrope.org
©2015 Allotrope Foundation 19
©2015 Allotrope Foundation 20
Federated standards we use everyday…
http://
TCP/IP
KashmirLed Zeppelin
SMTPMIME
ASCIISSL
©2015 Allotrope Foundation
MP3 Attributes
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• Platform Independent
• Standardized metadata
• Efficient Storage
• Share songs (data)
• Open standards
Music is recorded and stored in standard formats with the contextual metadata needed to find, share and enjoy it years later.
©2015 Allotrope Foundation
Allotrope Data Format (ADF) Scope
• Measurement process offline, online, PAT
• Research through Manufacturing process chemistry, formulation, bioprocessing
• Records management record retention, regulatory submissions, reporting
Holistic solution for industry
• Regulators, bench scientist, data analysts, modelers, manufacturing, archivists, IT
Requirements from range of perspectives & roles
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©2015 Allotrope Foundation
The basic analytical workflow and data flow standardized
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Plan Analysis
Prepare Samples
Submit Samples
Control Inst. Acquire
Data
Process Data
Analyze Data
Reports Results
Store, Archive
Data
Request ReportSearch
& Reuse Data
Sample Prep Data
Instrument Instructions
Instrument Data
Processed Data
Analyzed Data
Reported Results Stored DataAnalytical
Method
Data & Metadata
ProcessStep
Legend
Standard data file format & metadata
©2015 Allotrope Foundation
Jan Feb Mar Apr May Jun Jul Aug Sep Oct
Allotrope Framework High Level Project Plan
Draft Data Description
API
DraftAnalytical Data API
Release Version 1.0
2015
Draft ADF Format & APIData Description API
ADF Format & API Version 1.0
Draft Taxonomies Taxonomies Version 1.0Equipment Process
Material Result
Data Cube API
Data Package API
Data Description API Version 1.0
Data Cube API Version 1.0
Data Package API Version 1.0
Draft Analytical Data API Analytical Data API Version 1.0
Alpha release to
APN
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Analytical Techniques
Taxonomies Version 1.0
©2015 Allotrope Foundation
Allotrope Taxonomies• Create library of extensible taxonomies
– Using WC3 standard SKOS
– Easy to understand and maintain by SMEs and Vendors
– Hosted in the public Allotrope Metadata Repository
– Collaborative development across membership & APN
• Start by harvesting existing available concepts– PSI-MS; IUPAC; RSC Chemical Methods Ontology; Dictionary of
weighing terms; AnIML
• Create data description models using ontologies and data shapes (Shapes Constraints Language; WC3)– Link to taxonomies to add meaning
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©2015 Allotrope Foundation 30
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