Integrative data management for reproducibility of microscopy experiments
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The document discusses ensuring reproducibility in microscopy experiments through integrative data management. It presents a data management platform called REPRODUCE-ME that uses semantic web technologies to capture experimental provenance. The platform extends the open-source OMERO platform to document experiments and correlate multi-device measurements and data. An ontology was also developed to represent experimental entities and execution conditions to improve data sharing and reproducibility. Future work involves enhancing semantic web languages for reproducibility and improving the system's scalability and performance.
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Integrative data management for reproducibility of microscopy experiments
- 1. Integrative Data Management for Reproducibility of Microscopy Experiments Sheeba Samuel Institute for Computer Science Friedrich-Schiller University, Jena, Germany May 29, 14th ESWC 2017 Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 1
- 2. Problem Reproducibility Repeatability Rerun Replicate Reuse Findable Accessible Interoperable Reliable Verification Validation Provenance Data Methods Workflow Sharing Experiment enviroment Version-control Machine-readable Parameters Annotations Documentation Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 2
- 3. Repeatability and Reproducibility of Experiments Repeatability: capability of getting the same results carried out by the same experimenter using the same conditions of measurement. [Taylor et al. 1994] Reproducibility: capability of getting the same results carried out by an independent experimenter using different conditions of measurement. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 3
- 4. Why Reproducibility is so important? Studies show only 10% of published science articles are reproducible. Scientists at the pharmaceutical company, Bayer, could reproduce only 14 out of 67 projects. [Prinz et al. 2011] Studies conducted by the biotech company, Amgen, reveals that only 6 of the 53 studies were reproduced in Cancer Research. [Begley et al. 2012] Image Source: http: // www. wakeupkiwi. com/ Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 4
- 5. Aim Design, Procedure Experiment Setup Results End-to-End Reproducibility of Experiments: Track Provenance of each step Perform Experiment Experiment Pipeline Publication (Text) Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 5
- 6. State of the Art Our research focus on: Scientific Data Management Semantic Web technologies for capturing provenance Scientific Workflows Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 6
- 7. Problem Statement The main goal of our research is to enable reproducibility by extending data management and Semantic Web technologies. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 7
- 8. Research Questions RQ-1 - How to capture the provenance of a scientific experiment through an integrative data management? RQ-2 - How to represent a scientific experiment and its execution environment with the help of Semantic Web technologies to enable reproducibility, data interoperability and reuse? RQ-3 - How to provide a scalable and high-performance platform to handle the experimental data and results? RQ-4 - How to enhance current Semantic Web languages with reproducibility qualifiers? Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 8
- 9. Preliminary Results A data management platform for experimental data. REPRODUCE-ME (Reproduce Microscopy Experiments) Ontology Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 9
- 10. Current Prototype The current prototype is developed based on OMERO. Features of OMERO Hierarchical organization of data Projects, Datasets and images Extended the OMERO server An “Experiment“ tab to document and view all the information regarding an experiment. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 10
- 11. Development Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 11
- 12. Current Prototype Developed a desktop client to deploy on workstations without internet. In the desktop client, a researcher while conducting an experiment can input all the data. upload the images, files and measurements obtained from the devices during the experiment to the server when an internet connection is available. Minimizing the loss of data naturally occurring when recording these things from memory. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 12
- 13. Current Prototype Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 13
- 14. Features of Current Prototype Retreive and correlate all measurements obtained from different devices belonging to one experiment. View the images and data of the experimental protocol at one place organized in a hierarchical manner. Provides access control. Different roles and permissions to restrict modification of data. Sharing of data between users. The version management of the scientific data. Track modifications Correction of mistakes revert back to previous versions if needed Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 14
- 15. Current Prototype Documentation of all necessary information regarding experiments while performing them. Sharing and Improvement of this information by other scientists. Extensible system - integration with less effort. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 15
- 16. First Results Manual validation by a group of biological scientists. Being continuously extended and improved with the feedback received from the scientists. 1 1 Image Source: https://pixabay.com Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 16
- 17. The Next Motivation My Lab Notebook I want to get the list of all the experiments performed in this research project ‘ReceptorLight’ which has used this protein structure cited in the Nature paper. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 17
- 18. Ontology Development Experiment Person Organization Software Activity designExperiment setupDevices analyseResult prepareExperimentMaterial recordData Material Device Plan Data File Image RawData Result Error Setting Version Publication Procedure Microscope License Measurement Experimenter Distributor Funding Agency Project Supervisor REPRODUCE-ME Entity 2 2 http://fusion.cs.uni-jena.de/fusion/repr Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 18
- 19. REPRODUCE-ME Ontology Experiment performingExperiment Vector Plasmid preparingExperiment Material prov:actedOnBehalfOf prov:wasStartedBy prov:wasEndedBy prov:used prov:used prov:wasGeneratedBy prov:wasGeneratedBy prov:wasGeneratedBy repr:verification verified repr:wasVerifiedBy prov:generated prov:startedAtTime= ”10-11-2016T03:23:45Z” ^^xsd:dateTime prov:endedAtTime= ”10-11-2016T10:30:15Z” ^^xsd:dateTime repr:Name=”20160406_bCNG1” repr:Type=”HeK293” ….. prov:wasAssociatedWith repr:hasEcoliStrain="HB101" repr:hasGrowthCondition=”o vernight,35°C” repr:referenceDOI=10.1038/nb t935 repr:Name="phCNGA3-TFP" repr:hascDNASource="K1-GEMHE- CNGA3" repr:referenceDOI=10.1371/journal. pgen.1003988 repr:ORCID="http://orcid.or g/0000-0002-2382-9722" Supervisor Experimenter X Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 19
- 20. System Architecture Ontop ReceptorLight Database OMERO Database PROV-O REPRODUCE-ME SPARQL Query OMERO Webclient Desktop Client Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 20
- 21. Conclusion The overall objective of our research is to extend data management and Semantic Web technologies to enable reproducibility. As a first step towards reproducibility, an integrative platform for the scientists to capture the provenance of the experiment is developed Can spend more time on their biological work rather than focusing on writing scripts and worrying about the storage of their huge data. Specifically designed keeping in mind the requirements of biological scientists working in the field of microscopy. We built an ontology for the microscopy experiments with a focus on capturing the description of experiment and execution environment conditions. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 21
- 22. Future Work This allows better interpretation of data from different scientists in a collaborative project. We will consider ways to enhance Semantic Web languages with reproducibility qualifiers. Scalability, performance and quality tests will be conducted to handle the sheer volume of data generated from each experiment. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 22
- 23. Acknowledgement This research is partially supported by the “Deutsche Forschungsgemeinschaft“ (DFG) of the CRC “High-end light microscopy elucidates membrane receptor function - ReceptorLight“. I thank Birgitta K¨onig-Ries and H. Martin B¨ucker for their guidance and feedback for the research plan. I thank Christoph Biskup and Kathrin Groeneveld from the Biomolecular Photonics Group at University Hospital Jena, Germany, for providing the requirements to develop the proposed approach and validating the system. Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 23
- 24. Thanks Questions??? Integrative Data Management for Reproducibility of Microscopy Experiments May 29, 14th ESWC 2017 24