pistoia alliance european conference 2015 - gerhard noelken / allotrope foundation

©2015 Allotrope Foundation

We are a data industry: let’s act like one.

Gerhard NoelkenPfizer Allotrope Liaison


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


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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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


What is Allotrope Creating?

Allotrope Foundation Framework

Reusable

Software

Components

Open

Document

Standard

Open

Metadata

Repository

5

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


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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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



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Plan Analysis

Prepare Samples

Submit Samples


Data

Process Data

Analyze Data

Reports Results

Store, Archive

Data

Request Report & Share

Search & Reuse

Data

Sample Prep Data


Instrument Data

Processed Data

Analyzed Data


Method

Data & Metadata

ProcessStep

Legend

Standard data file format & metadata


Data

Process Data

Analyze Data

InteroperabilityMore automated reporting,

Powerful searching


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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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


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


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


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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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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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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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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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


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

[email protected]

[email protected] www.allotrope.org

mailto:[email protected]

mailto:[email protected]

http://www.allotrope.org/


Federated standards we use everyday…

http://

TCP/IP

KashmirLed Zeppelin

SMTPMIME

ASCIISSL


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.


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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Plan Analysis

Prepare Samples

Submit Samples


Data

Process Data

Analyze Data

Reports Results

Store, Archive

Data

Request ReportSearch

& Reuse Data

Sample Prep Data


Instrument Data

Processed Data

Analyzed Data


Method

Data & Metadata

ProcessStep

Legend

Standard data file format & metadata


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


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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pistoia alliance european conference 2015 - gerhard noelken / allotrope foundation

Science

software applications

software vendors4what

professional data

data industry

lack of standards

contextual metadata

analytical methods

absence of standards