Analytical data, the web, and standards for unified laboratory informatics databases

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1 Analytical data, the web, and standards for unified laboratory informatics databases Presented By Patrick D. Wheeler & Graham A. McGibbon ACS San Diego 16 March, 2016

2 Sources Process, Analyze Interfaces, Visualize Analysis Workflow Design Do Present 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 3

Case for Live Data Enablement Vendor % FAIL QC Vendor A: 23% Vendor B: 9% Vendor C: 12% Vendor D: 18% Vendor D : 32% Vendor E: 10% Vendor D : 33% Vendor F: 19% Vendor G: 9% Vendor H: 6% Vendor X: 0%

3 Case for Live Data Enablement Vendor % FAIL QC Vendor A: 23% Vendor B: 9% Vendor C: 12% Vendor D: 18% Vendor D : 32% Vendor E: 10% Vendor D : 33% Vendor F: 19% Vendor G: 9% Vendor H: 6% Vendor X: 0% multiple vendors: ( 10 fragments/vendor) 8% TOTAL: 16% Percentage of NMR QC failure rates for a random set of commercially available fragment compounds.

4 Accessibility Rules around software use have been re-written, rationalized, and simplified. Users expectations are legitimately higher. 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 5

Example GSK Global Analytical http://www.acdlabs.

5 Example GSK Global Analytical 3/30/2016 6

6 ACD/Labs Approach Data should be accessible with the simplest effort possible No barriers between vendors Differences between techniques should be minimized Why are processing modalities different for NMR & MS? Similar digital data should share interpretive tools 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 7

7 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 8

8 ACD/Labs Approach Time with labs helping solve problems: Value is best created when labs can capture data speed interpretation improve accuracy of answers for the organization share knowledge created move forward with results in confidence 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 9

9 Architecture Approaches Big Data Architectures in Scientific Innovation Workflows Consolidate Data Locations Maximize Presentation Flexibility Graphic courtesy of Michael Elliott. 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 10

10 Knowledge Management Standards Chemical Structures All formats! Analytical data Proprietary formats (see above) Open (galactic, jdx, NetCDF, AnML, Allotrope, ) Metadata (analytics, search/mining, ChAMP, Allotrope taxonomies) 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 11

11 Knowledge Management Standards Analytical data Proprietary formats (as above) Open Galactic, ANDI (NetCDF), JCAMP-DX (.jdx), SpectroML, mzml, AnIML.ADF (Allotrope) 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 12

12 Knowledge Management Standards Chemical Structures.mol,.sdf,.sk2,.cdx,.skc, SMILES, INCHI Sequence representation of biomolecular sequences HELM Both sequence and structure Names! Markush 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 13

13 Knowledge Management Standards Metadata Value regularly underestimated Standardized taxonomies Support for analytics, search, data mining, semantic web 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 14

14 Integration Modern decentralized laboratory informatics environment Externalization - Support for outsourcing Overlap and similarities with internal but diverse geographic locations 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 15

15 Integration Unify data from distinct formats and types databases, formats Use common exchange protocols SOAP, RESTful, API, data/structure,.jdx, JSON Incorporate tools friendly to data pipes Compatibility with web based presentation layers browser independence java/javascript 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 16

16 Advanced Chemistry Development, Inc. (ACD/Labs) 17

17 Example RTI Forensic Database Database structure and functionality from a community-oriented collection of instrumental analytical data with a central curation model Expansion of a Cheminformatic Database of Spectral Data for Forensic Chemists and Toxicologists, 18

18 Example 3M Global Analytical Advanced Chemistry Development, Inc. (ACD/Labs) 19

19 Application Case Study CMO/Lab 1 CRO/Lab 2 Sponsor Company Method Transfer and Translation CMO/Lab 3

20 Technologies for Live Data Interoperability

21 Spectrus Portal: Search, Retrieve and Browse Metadata; Link to archive File Metadata Browse results Search metadata Link to archived raw data here Download links 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 22

22 Spectrus Portal Live, Assembled Data 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 23

23 Presentation Interoperability

24 Presentation Interoperability 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 25

25 A Universal Live Data Language CMO/Lab 1 CRO/Lab 2 Sponsor Company CMO/Lab 3

26 Platform for Chemical Intelligence CMO/Lab 1 CH 3 O H 3 C CH 3 O NH NH N CH 3 OH O O N H Automated Compound Verification CRO/Lab 2 Sponsor Company X CMO/Lab 3

27 ACD/Labs Externalization Platform CH 3 O H 3 C CH 3 O NH NH N CH 3 O N H Traditional Scattered Dead Data Transfer Manual Data Transcription Documents, spreadsheets, PDF ACD/Labs Approach Immediate Access Translated Live Data Actionable Data Chemical Insights Structured Formats Business Rules

28 3/30/2016 Advanced Chemistry Development, Inc. (ACD/Labs) 29

ACD/Labs Software Impurity Resolution Management. Presented by Peter Russell

ACD/Labs Software Impurity Resolution Management Presented by Peter Russell Impurity Resolution Process Chemists Method Development Specialists Toxicology Groups Stability Groups Analytical Chemists 7/8/2016