Pistoia Alliance European Conference 2015 - Gerhard Noelken / Allotrope Foundation
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Slides from a presentation given at the Pistoia Alliance European Conference 2015, in Zurich, Switzerland.
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Pistoia Alliance European Conference 2015 - Gerhard Noelken / Allotrope Foundation
- 1. ©2015 Allotrope Foundation We are a data industry: let’s act like one. Gerhard Noelken Pfizer Allotrope Liaison
- 2. ©2015 Allotrope Foundation Today’s Environment: In the absence of standards in laboratory software 2 Incomplete, Incompatible Software No Standard File Formats Inconsistent Metadata Convert or transcribe Application 1 .abc out Application 2 input .xyz technology A technology X Project Test Instrument AF 0012354 IR Fingerprinting QC Lab #33B 380 FT-IR AE0012764 Bulk & Tapped Density ASTM Standard Seive #6 AF 12989 NMR Characterization AM500 Tapped & Bulk Density Sieve XXX AF0045674 Caractérisation RMN Nouvelle DRX600 AF-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
- 3. ©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 3
- 4. ©2015 Allotrope Foundation Allotrope Foundation 4 • Subject Matter Experts • Project Funding Member Companies • Project Management • Legal & Logistical Support Secretariat • Framework Development • Technical Leadership Professional Software Firm • Requirements & Specifications • Contributions, PoC Applications Partner Network AbbVie Amgen Baxter Bayer Biogen Idec Boehringer Ingelheim Bristol-Myers Squibb Eisai Eli Lilly Genentech/Roche GlaxoSmithKline Merck Pfizer ACD/Labs Agilent Biovia BSSN IDBS Mestrelab Research Mettler Toledo Sartorius Shimadzu Thermo Scientific Waters
- 5. ©2015 Allotrope Foundation 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 .mz ML .jdx .irf .pdid .drdd .asc .cdf .frx .adf The set of standards used based on our requirements Project Test Instrument AF 0012354 IR Fingerprinting QC Lab #33B 380 FT-IR AE0012764 Bulk & Tapped Density ASTM Standard Seive #6 AF 12989 NMR Characterization AM500 Tapped & Bulk Density Sieve XXX AF0045674 Caractérisation RMN Nouvelle DRX600 AF-0034558 IR iS10 FT-IR Project Test Instrument AF0012354 IR Fingerprinting 380 FTIR/-SN/145453 AF0012764 Bulk and Tapped Density ASTM Sieve-SN/3452 AF0012989 NMR Characterization AM500-SN/0034578 AF0013142 Bulk and Tapped Density ASTM Sieve-SN/09783 AF0045674 NMR Characterization DRX600-SN/10234567 AF0034558 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
- 6. ©2015 Allotrope Foundation Small Molecule Biologics HPLC, LC-MS, GC, GC-MS CE, SFC, IEX, SEC RI, ICP-MS, IMS UV-VIS, IR, NIR, Raman, FL, NMR, KF Coulometric, KF Volumetric Light Scattering, Microscope, pH Meter, Polarimeter, Potentiostat, Coulometer XRD, SEM, Viscometer, Water Activity Balance, DSC, TGA, Dissolution Sterility, Reconstitution Time Osmolality, TOC PCR, qPCR, cIEF, iCE ELISA, EIA Flow Cytometry, O2 sensor, SDS-PAGE Endotoxin Conductivity Far/Near UV CD Peptide Digestion Plasmid Retention Genotypic Verification Disintegration Calorimetry, Flowability Surface Area Hardness Optical Rotation Wet Chemistry TLC The Analytical “Laboratory” Data Landscape Delivering a Solution Across Technologies and Modalities will Enhance Value and Adoption 6
- 7. ©2015 Allotrope Foundation The basic analytical workflow and data flow standardized 7 Plan Analysis Prepare Samples Submit Samples Control Inst. Acquire Data Process Data Analyze Data Reports Results Store, Archive Data Request Report Search & Reuse Data Sample Prep Data Instrument Instructions Instrument Data Processed Data Analyzed Data Reported Results Stored DataAnalytical Method Data & Metadata Process Step Legend Ultimately the collective meta data is EVIDENCE that supports a DECISION about your MANUFACTURING PROCESS or MATERIAL
- 8. ©2015 Allotrope Foundation The basic analytical workflow and data flow standardized 8 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 Process Step Legend Standard data file format & metadata Control Inst. Acquire Data Process Data Analyze Data Interoperability More automated reporting, Powerful searching
- 9. ©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 9
- 10. ©2015 Allotrope Foundation Allotrope Data Format Data stored in public formats, incl. images, pdf, video 10 Platform Independent File Format HDF5 Data Description Resource 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
- 11. ©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 Taxonomies 11 Triple Store API April 2015 April 2015 Feb 2015
- 12. ©2015 Allotrope Foundation A lot of good ideas that can be used: More than 100 relevant public standards & ontologies, highly connected 12 International Standards Organization Open Geospatial Consortium World Wide Web Consortium … SensorML AnIML S88/BatchML mzML … Analytical Data Standards Metadata Standards Allotrope Framework
- 13. ©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 13
- 14. ©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 14
- 15. ©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 15
- 16. ©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 16
- 17. ©2015 Allotrope Foundation Project Trajectory 2013 2014 2015 2016 17 Allotrope Foundation Initiated software development and evaluations Established feasibility through PoCs; ADF design & due diligence Framework Development Integration at Members Framework used in production First Public release
- 18. ©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) 18 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
- 19. ©2015 Allotrope Foundation 19
- 20. ©2015 Allotrope Foundation 20 Federated standards we use everyday… http:// TCP/IP Kashmir Led Zeppelin SMTP MIME ASCII SSL
- 21. ©2015 Allotrope Foundation MP3 Attributes 21 • 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.
- 22. ©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 22
- 23. ©2015 Allotrope Foundation The basic analytical workflow and data flow standardized 23 Plan Analysis Prepare Samples Submit Samples Control Inst. Acquire Data Process Data Analyze Data Reports Results Store, Archive Data Request Report Search & Reuse Data Sample Prep Data Instrument Instructions Instrument Data Processed Data Analyzed Data Reported Results Stored DataAnalytical Method Data & Metadata Process Step Legend Standard data file format & metadata
- 24. ©2015 Allotrope Foundation Jan Feb Mar Apr May Jun Jul Aug Sep Oct Allotrope Framework High Level Project Plan Draft Data Description API Draft Analytical Data API Release Version 1.0 2015 Draft ADF Format & API Data Description API ADF Format & API Version 1.0 Draft Taxonomies Taxonomies Version 1.0 Equipment 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 24 Analytical Techniques Taxonomies Version 1.0
- 25. ©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 25
- 26. ©2015 Allotrope Foundation 26
- 27. ©2015 Allotrope Foundation 27
- 28. ©2015 Allotrope Foundation 28
- 29. ©2015 Allotrope Foundation 29
- 30. ©2015 Allotrope Foundation 30
Editor's Notes
- The root of the problem is the absence of standards in the current laboratory software environment. Substantial funds are invested into treating the symptoms of our data management problems We patch local gaps in the software, fix specific problems, and investment in large integration efforts, But are left with the fundamental, underlying root problems Lack of standard data format: Each instrument may have its own format created. Conversion is needed in order to read the data. Lack of standards for metadata: The contextual metadata describing analytical methods, instruments, processes, and even the reasons for doing an experiment are inconsistent, incomplete, and often spread over multiple applications in the analytical workflow Lack of standard interface between software applications: Finally, because the software we use across the analytical workflow is often from different sources, they are written using different technologies, and read and write different formats, so don’t often talk to one another without a custom integration effort
- Transition to next slide: These are a few examples of issues that affect our entire analytical data lifecycle
- While the Pharmaceutical Company member reps make fund the work, and provide subject matter experts, the Foundation and Project benefit from excellent pofessional partnership and support of DBR for the Project and Consortium management, as well as legal, logistical and scientific advise. They are not only professionals at running an organization like this, (so do a better job than if it were left up to the scientists), it allows the members to focus on the technical and strategic issues. Osthus is the professional data and systems integrator we have partnered with to engineer and build the framework. As we will discuss more later- we created a partner program to enable the collaboration with instrument and software vendors
- Data standards are necessary but NOT sufficient to solve the problems- the solution requires a holistic approach to build standards into the software used throughout the data lifecycle. Without adoption, a data standard alone is an abstract that cannot alone create change, the standard needs to be adopted, which ultimately means it has to be integrated into the software used to generate and manage data. The Allotrope Framework embodies a three pronged approach to driving adoption: Document standard Store data and metadata in a vendor agnostic, common, non-proprietary file format Ready for Archiving Easy data sharing & retrieval Taxonomies- Metadata repository Ensures accurate, complete, & consistent experiment context is stored along with data Reusable software components Provide access to data, metadata, and business objects Available for integration with vendor or in-house software
- No single public standard that covers them all 2 imporetant concepts in the ADF design- first is the landscape of technicques
- Over the course of that workflow, important context, or metadata is created- starting with things like the purpose, project, whether or not it’s a GxP process, etc In the planning stage experimental and instrument parameters are established, details of the analysis and any fitting algorithm contextualize results. All of this is context we would like to have to be to find and analyze the data later, but it’s often incompletely captured, captured as free text, or spread over multiple software applications Ultimately the collective meta data is EVIDENCE that supports a DECISION about your MANUFACTURING PROCESS or MATERIAL…
- That standardization of the interface between software applications also creates a more plug-and-play environment, making it much easier to substitute one brand of instrument for another, use a different analysis application to access and alternative processing algorithm, or simply avoid having to rebuild custom interfaces when one of your pieces of software requires an upgrade. Finally, reporting is more powerful because it’s based on meaningful criteria, and uses an index based on standardized terminology, and an index which has been built using the complete and consistent captured context of everything that happened along the workflow
- HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of data types, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible
- Only the start! ADF design & practices being developed facilitate rapid taxonomy development with SMES, and thus extension to additional techniques
- Standards Evaluated > 100 public standards against scientific and business requirements across the full data lifecycle, from creation to archiving Developed reference architecture for data archiving based on public standards Federated select standards and ontologies for use by the Framework Development Created first version of Framework (pre-release), with class libraries for ADF, metadata repository and data archive Created proof-of-concept software and delivered to all members Benchmarked ADF performance using MS data Launched the Allotrope Partner Network to partner with instrument and software vendors to facilitate adoption Initiated interactions with FDA
- Second important concept in ADF design is the dimension of the process in which analytical measurements are used Drivers of adoption
- Adoption of the standards by way of the Allotrope Framework standardize the data format, the contextual metadata (the orange box) and the inputs and outputs between software applications (the orange arrows). The metadata will be stored with the data. This additionally opens up significantly more opportunity for automating the workflow- for example when the instrument parameters can be automatically sent to the instrument from the LIMS or ELN where they are first selected, removing the need for a human to read a document created in one system, and reenter the parameters in another.