allotrope framework drives innovation in labinformatics” · pdf file“allotrope...

©2016 Allotrope Foundation

“Allotrope Framework drives Innovation in LabInformatics”

Dr. Gerhard Noelken

Pfizer Technology and Innovation Group Paperless, April 19, 2016


Agenda

• Innovation in LabInformatics

• Introduction to Allotrope Framework

• Two examples of progress in key areas

– Data integrity and taxonomies

– Real world testing in Integration projects

• How could your company benefit?

2


Innovation in LabInformatics• As I walk through the labs …

– Scientists talk about software systems as an additional burden• I cannot get to my data• Cannot easily align my data with data from other sources

– The Lab of the Future (Google glasses, IoT) has not happened yet

• Why is this?– Change is slow, humans are change averse– Current systems are just “good enough” in many areas

• To implement change you need to have– a fundamental reason and– support from scientist and management alike

3

Semantic technologyComputers will become capable of evaluating relationshipsin our data for us

Data integrityThe extent to which all data are complete, consistent and accurate throughout the data lifecycle. (MHRA 2015)


Agenda







4


Allotrope Foundation: Driving the Change

5

• 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

AbbVieAmgenBaxterBayer

BiogenBoehringer IngelheimBristol-Myers SquibbEli Lilly

Genentech/RocheGlaxoSmithKlineMerck & Co.Pfizer

ACD/Labs

Agilent

Biovia

Bruker

BSSN

IDBS

LabAnswer

LabVantage

LEAP Technologies

Mestrelab Research

Mettler Toledo

PerkinElmer

Persistent Systems

Riffyn

Sartorius

Shimadzu

Tetra Science

Thermo Scientific

Waters

Zifo RnD Solutions

Frauenhofer IPA

Erasmus Univ. Med Center

J. Paul Getty Trust

(UK) Science and Technology Facilities Council

University of Southampton

University of Strathclyde


What is Allotrope Creating?

Allotrope Foundation Framework

Reusable

Software

Components

Open

Document

Standard

Open

Metadata

Repository

6

.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

Application 1 Application 2

Metadata repository

New Instrument

Instrument A toolkit that enables the consistent use of

standards & metadata in software development


Allotrope Data Format (ADF)

* Use is optional

7

RDF Model

Universal data container

Virtual file system *

Contains:

• Method, instrument, sample,

process, result, etc.

• Data cube metadata

• Data package metadata

• …

Analytical data represented by

one- or multidimensional arrays.

HDF5

Platform Independent File Format

Analytical data represented by

arbitrary formats, incl. native

instrument formats, images, pdf,

video, etc.

Specifically designed to store and

organize large amounts of numerical

data.


Agenda







8


High Variety of Result Data

chromatographypH thermogravimetry

HPLC-MS-MSmass spectroscopy HPLC-MS

cell counterNMR9


Allotrope Foundation Taxonomies


Utilizing the Semantic Spectrum (Moving Beyond Taxonomies)

11

Code (Lists) Terms (Soil, Plant, etc.)

Controlled Vocabulary

(Agreed Upon Terms)

Taxonomy

(Hierarchy)

Thesaurus

(Preferred Labels, Synonyms, etc.)RDF Models

(Triples as Graphs)


The basic analytical workflow and data flow standardized

12

Plan Analysis

Prepare Samples

Submit Samples

Control Inst. Acquire

Data

Process Data

Analyze Data

Reports Results

Store, Archive

Data

Request ReportSearch

& Reuse Data


The ADF enables a self-contained documentation of the data & metadata

Plan Analysis

Prepare Samples

Submit Samples

Control Inst. Acquire Data

Process Data

Analyze Data

Reports Results

Store, Archive

Data

Request

Data & Metadata

ProcessStep

Legend

Standard data file format for data & metadataOutput from one system becomes the input to the nextThe APIs enable the use of one vendor agnostic file format

Control Inst. Acquire Data

Process Data

Analyze Data

Interoperability(Plug & Play)

Report & Share

Search & Reuse Data

More automated reporting,Powerful searching

Analytical Method

Sample Prep Data

Instrument Instruction

Instrument Data

Processed Data

Analyzed Data

Reported Results Stored Data

13


Allotrope Data FormatData Description

Data Cubes

Data Package(s) (optional)

14

Request Sample prep Method Data acquisitionInstrument instruct.

Chromatogram 2D HDF Chromatogram 2D HDF

Chromatogram: 3D HDFChromatogram: 2D HDF


Agenda







15


Reducing it to practice

Integration projects:

• Early adoption and acceleration of AF Framework

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-world

requirements and implementation.

16

DevelopmentResearch Commercial

Member non-GMP GMPInstrument

Member 6

Member 3

Member 2

Member 9

Member 1

Member 5

Member 8 Drug Substance Release & Stability

Structure ID, Purification,

In vitro bioanalysis

Method ScreeningHPLC-UV/MS

HPLC-UV

Balance

HPLC-UV/MS

Structure IDHPLC-MS

Fermentation

Process ControlBioanalyzer

Small and Large Molecule CMCMultiple

types

Member 7

Elemental ImpuritiesICP-MS

Assay, PurityHPLC-UV

pH, Weighing, GC, Karl Fischer, TGA,

NMR , Cell Density/Viability, Blood

Gas Analyzer , Cell Culture Analyzer,

Capillary Electrophoresis

…

Member 4 CRO IntegrationHPLC-UV

Member 10 LC Data to ADF Converter/AdapterHPLC-UV

Allotrope Integration Projects: sharing cost and value

Plan Analysis

Data Converter

ICP-MS MassHunter

LC-UV-MS

MassLynx

ChemStation

Allotrope Integration Projects - January 2016

18

Prepare Samples

Submit Samples

Acquire Data

Process Data

Analyze Data

Reports Results

Store, Archive Data

Manage Instrument

Internet of Things Device Registry

HPLC Agilent

Instrument Interface

HPLCBioanalyser

LabSolutions

Empower

BioBook

Dispatch-Receipt Service

Chain-of-Custody

{any}

Queue Service

Samples

Data Retention

HadoopECMNG8

GSK

Methods Repository

LC-UV-MS

ADF

GSK

BMSBMS

Baxter

Amgen

Bayer

Lilly

Merck

Bayer

BMS

Pfizer

Roche

Taxonomies, Ontologies, Data Shapes, Blueprints

Merck

{any}

{any}

Agilent

Waters

idbs

Shimadzu

Waters

Taxonomy Management

ELN Integration

{any} OneLab

Amgen BIOVIA

Report Generator

ADFLC-UV-MS

Merck

Agilent

Waters

Analytics

Agenda







19


The Framework will provide direct benefitLess Manual Document

Preparation• Find data quickly/logically

• Eliminate Copy/paste

• No more Transcription/conversion

• Source agnostic

Improved Data Integrity

• Eliminate error due to manual text entry or transcription

• Complete, consistent, accurate metadata

Seamless data exchange & with partners & CROs

• One data file format

• One consistent vocabulary

• Reduced cost & complexity to CROs, CMOs, partnerships

Lower Data Management Costs

• Interoperability

• Future-proof against future data migrations

• Reduced technical debt: no more maintenance of legacy systems

• Improved archiving

Facilitate Regulatory Compliance

• Improved instrument & software validation tracking

• Reduced complexity in system documentation

• Simpler to support questions/investigations

Extracting Knowledge & Value from Data

• Greatly enhance speed to answer/decision

• Remove data silos

• Create an ecosystem for innovation

• Facilitates data mining & analytics

20What are your priorities?

Pfizer Integration project

Q4 2015 Limited scope Integration Project

Sample ID entry in Biovia ELN

Empower 3Cloud Data

storageADF HPLC data with sample ID

AF HPLC Taxonomy

DevelopmentResearch Commercial

Member non-GMP GMPInstrument

Member 6

Member 9

Member 8 Drug Substance Release & Stability

Structure ID, Purification,

In vitro bioanalysis

Method ScreeningHPLC-UV/MS

HPLC-UV

Balance

HPLC-UV/MS

Member 10 LC Data to ADF Converter/AdapterHPLC-UV

example

Member 1 Small and Large Molecule CMCMultiple

typespH, Weighing, GC, Karl Fischer, TGA,

NMR , Cell Density/Viability, Blood

Gas Analyzer , Cell Culture Analyzer,

Capillary Electrophoresis

…

taxonomies

methods

repository

data repository

adapter

instrument adapter

Summary

• The Allotrope Framework supports your progress in Data integrity and Semantic technology

• Current Allotrope members test-drive the Framework in current Integration projects to make sure it is mature for your use-case

• The Allotrope Framework will be publicly released by the end of 2016

allotrope framework drives innovation in labinformatics” · pdf file“allotrope...

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