high-quality integration using semantics · sample management erp web pages, wikis instrument...

High-quality integration using Semantics

Lab of the Future, 2019 Wellcome Genome Campus, Cambridge, UK

Etzard Stolte, PhD – Global Hd Knowledge Management PTD F. Hoffmann-La Roche

Die Zeit, 2019

© Copyright 2018 FA Hoffmann La Roche – [email protected] - The information contained herein is subject to change without notice.

Genentech, R&D andcommercial operations US

R&D sites in Pharmaand Diagnostics

CHF 57 billion sales

R&D sites in pharma and diagnostics worldwide30

Roche Group Headquarters in Basel, Switzerland

employees worldwide94 442

Chugai, R&D and commercialoperations Japan

Roche - a global pioneer in pharmaceuticals and diagnostics

2

Among top 10 R&D investors worldwide across industries (for 2018)

CHF 11 billion invested into R&D


Pharma Technical DevelopmentProcess development, formulation design, clinical manufacturing, device development

Research GenentechgRED

Pharma Technical Development

Research BaselpRED

DevelopmentPD

ManufacturingPT

3

• About 2500 FTE• 800 applications in use, 330 GxP• 130 applications used daily• Most applications are owned by other

functions (e.g. Research & Development)


Integration Challenge

4

Complex Information Landscape across 800 systems, 127 used daily

Regulatory, Safety

• Enabling Computer System Validation (CSV), GxP and quality management systems and processes

• e.g. TrackWise, IDM, SpecA

Strategy, PM, MDM

• Tools, processes, governance, that consistently define and manage the critical data of an organization

• e.g. MDMS, Roformis, SAP

Lab & Manufacturing

• Platforms to control, manage and document all activities in the laboratory and manufacturing

• e.g. B/Pali, Damaz, PMX, cELN

Knowledge Mngt

• Tools, processes & governance to build a culture that values, shares, and re-uses our information and knowledge

• e.g. SysWiki, TP, Discourse,

Data/Inf Mngt

• Tools, policies, and best practices to ensure that data are understandable, trusted, accessible, and interoperability

• e.g. MIA, ECM, BaseCamp, CTMS


Knowledge Management

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Integration Roadmap

• Discovering, accessing and re-using internal & external data, information and knowledge sources more effectively• Complex information landscape, but one

integration platform• Integrate, not replace existing processes

& systems• Targeting the use of semantics where

e.g. master data or curation are missing• Focusing on quality, to increase our

opportunities for innovation• Culture / Mind change is a key goal for

each phasestructuredun-structured

text

ual

num

eric

al

Documents on e.g. fileshares

Document Management

Systems

LIMS

ELN

Files on e.g. FileShares

Sample Management

ERPWeb pages, Wikis

Instrument database

1. Semantic Integration Platform

2. Single Document Management

Process

4. Information LifeCycle

Management

3. Numerical Integration

2015 -2018

2017 -2020


Hype Cycle for AI

6

Gartner, 2019

Quality!


Example – NLP - Taxonomies

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The foundation for any semantic understanding

• 86 taxonomies, internal & external, commercial & open-source & home-grown

• majority internally hosted

• no alignment / merging

• -> high ETL costs, but no run-time impact

• -> no consistent semantic context

• -> highly relevant & specific concepts


Example – NLP – Concept Extraction & Matching

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2018 Roche-wide announcement


Example – NLP – Named Entity Recognition (NER)

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Direct Data Access - show me the data behind this reference…

everywhere we encounter cryptic identifiers

Semantic Web detect identifiers and adds web links to source, e.g. to a LIMS, ELN, IDM, etc.

for example, a new link would open the analysis behind the ID

in a LIMS system, or an ELN record -> parsing is hard


Examples – Model based integration

• A complete data catalogue across all data/information/knowledge systems

• Uses Minimal Attribute Set (8 attributes chosen to find all data)

• Data Models behind each attribute for higher accuracy

• Around 60 systems (LIMS, ELN, etc.) target out of 127 total

• Will offer Search front-end and URI (Unified Resource Identifiers)

• Incomplete models are key challenge

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“Smart” Data Catalogue - Find all relevant experimental data

Find data at scale

Classify Visibility


Examples – NLP - Natural Language Processing

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AI / ML Examples

NN - Automated Translation• On the fly translation in good

quality• Challenge: documents contain

many, many data types; complex access controls across sytems

NLP – Expert Finder• Match colleagues to concepts• Challenge: meta data quality

NLP – Fact extraction• Return relevant details, e.g. table

rows / columns; text snippets; database entries

• Challenge: text understanding w/ brief context


Integration methods have evolved

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Moving to loosely coupled, semantic approaches

monolithicone system

1980

client/servercommon codebase

1990

components / APIscommon frameworks

2000

SOA / iPaaScommon protocols

2010

fabricscommon semantics

2020

Syntax

Structure

Semantic

Interfaces & Implicit Semantics

Artificial Intelligence & Explicit Semantics


KM Integration Platform

Agility, Costs, IP control• Open source, in-house• Scalable to large user & data numbers

• Enable by semantic & machine learning services• Processing pipelines to segment, enrich & index

data / information / knowledge

• Runs on internal High Performance Computer cluster

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Buy if you can, build if you must

Semantics, Enrichment, Translation, Machine Learning, Analytics2016

Semantic & Numerical Integration

Experiment / Pilot

FAIR (Findable, Accessible, Integrable, Re-usable)2017Capture & Collaboration

Pilot / Service

Document Systems(across Pharma)

Numerical Databases(100 identified)

Websites(internal & external)

KM Integration Platform (KIP)Semantic & Numerical Integration

2016

Master Data & Registration systems

Taxonomies &Ontologies other…

Service

Models


Knowledge Management

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Our platform will be worth your while

adapted from PT KM Grab&Go Deck 2015

Company Benefits from KM program

Merck 81% increase in employee engagement

Chevron $2 Billion reduction in annual operating costs within 7 years

Dow Chemical $4 Million savings in first year, $100 million total

Schlumberger 300% increase in daily output productivity

Hewlett-Packard 50% reduction in customer support operating costs in 2 years

A mature KM approach will deliver > 2 x return on investmentAmerican Productivity & Quality Center (APQC) Benchmark Study

5 x in PTD


Next Generation Knowledge Management @ PTD

• “KM is such a hot topic right now”• “Super. Search is ‘the’ most important capability in Roche”• “.. I am really exited to see what you guys created”• “I wanted to let you and team know that I love this tool..”• “This is really nice!” “AWESOME!”• “Whoa!!! That's incredible!!!!!” • “I like it. Thanks a bunch!”• “.. this search is really great!”• "This is a great achievement! “• “Thanks to you .. this work is amazing!”

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Our focus on quality has been well received

• “Well done! Thank you for your leadership.”

• It's an amazing tool! I am really impressed by the convenience and speed! Thank you so much!”

• “Supercool ….. really great!”• “I cannot remember another IT project that

went so well”• “Outstanding outcome ... in a short time…“• “Super, what you guys are delivering”


Thank You!Next Generation Knowledge Management @ PTD

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Long-term vision

Data Dictionary Data Commons Insight Pipeline

Personal Cloud Semantic Integration Automated Quality Controls

Standardization& Efficiency

Quality & Compliance

Semantic Integration & Text Unterstanding

Numerical Integration & Analysis

Collaboration& Insights

FAIR Data & Information

Security & Privacy Integrated Laboratory

Expectationsleading tonew trends

Industry &Technology-trends driving

Meaning Based Computing

Project portfolio, strategic goals


Doing now what patients need next