SEEKing our way to better presentation of data and models from scientific investigations.
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"SEEKing our way to better presentation of data and models from scientific investigations." At ICSB/NormSys workshop Melbourne 2014.
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SEEKing our way to better presentation of data and models from scientific investigations.
- 1. @nataliestanford natalie.stanford@manchester.ac.uk SEEKing our way to better presentation of data and models from scientific investigations.
- 2. Carole Goble Stuart Owen Jacky Snoep Wolfgang Mueller Olga Krebs Quyen Nguyen Natalie Stanford Katy WolstencroftPeter Kunszt Bernd Rinn also contributing: VLN SEEK team also contributing: UK SEEK team
- 3. Systems biology projects produce complex and heterogeneous datasets.
- 4. The data is saved and stored in convenient, but non-standard formats.
- 5. This is the case for each researcher within groups across large consortia projects. Consortia Grp 3 Grp 1 Grp 2
- 6. The data contained within the files can be very ambiguous.
- 7. Sharing within labs, across projects, and publicly becomes difficult.
- 8. The availability and reusability of the data in the long-term is compromised.
- 9. This all leads to issues with conveying what a project has achieved to funders. • Papers? • Data produced? • Discoveries? • Presentations? • Workshops? • Tutorials? Defining success and impact of project.
- 10. We need better ways of formatting, storing, and sharing data and models.
- 11. SEEK is a commons originally designed for centralizing information and assets for large consortia projects.
- 12. Each user has their own profile.
- 13. …and their data and models are uploaded to projects within the SEEK database.
- 14. SEEK has varied functionality. Yellow pages, manage SOPs and link to investigations, studies, assays, specimens and samples. Find my peers. Creating and sharing SOPs across projects. Track my specimens. Track different versions of my model. Data viewing functionality; ISA framework for linking studies to data, models, SOPs, samples, publications. Browse experimental data without downloading them. How data, models and SOPs fit together. Which data belong with which publication.
- 15. It works as aggregated asset manager, allowing storage on SEEK, or linking assets from disparate databases.
- 16. Investigation: Glucose metabolism in P. falciparum trophozoites Study: Model construction Study: Model validation Assay: LDH Assay: PK Assay: ENO Assay: PGM Assay: PGK Assay: GAPDH Assay: TPI Assay: ALD Assay: PFK Assay: PGI Assay: HK Assay: GLCtr Assay: PYRtr Assay: LACtr Assay: G3PDH Assay: GLYtr Assay: ATPase Data: GLCtr Model: GLCtr Data: HK Model: HK Steady state Incubation penkler1 Validation data penkler2 Validation data ... ... SOP: GLCtr SOP: HK ... SOP: Validation Assay: Culturing Assay: Lysate prep. SOP: Culturing SOP: Lysate prep. It allows published work and all associated data and files to be organised in an ISA (Investigation, Study, Assay) format.
- 17. Construction Validation Metabolomics Metabolomics Mass SpecTranscriptomics Proteomics Fluxomics Investigations Studies AssaysTowards Interoperable Bioscience Data, Nature Genetics, 2012 Assays The ISA structure reflects an intuitive structure and storage of scientific findings.
- 18. SEEK also integrates with other tools.
- 19. Have now set up FAIRdom to further develop SEEK as an open platform where all assets can be uploaded and linked to with DOI.
- 20. “There is no greater impediment to the advancement of knowledge than the ambiguity of words.” -Thomas Reid + Natalie Stanford
- 21. The data contained within the files can be very ambiguous.
- 22. There are many Systems Biology standards available. Minimal Information Models Standard Formats Ontologies Data Models Simulation Results [Nicolas Le Novere] MAGE-TABStandard Formats RDF annotations
- 23. ..But, the barrier to standard formats and annotation usage by researchers can seem great.
- 24. There are tools available to assist users.
- 25. We develop RightField, a semantic annotation tool for data files.
- 26. We use it to generate templates for different types of assay data. Excel workbook loaded into RightField with multiple worksheets
- 27. Suitable ontologies are selected and used to annotate cells for associated data input. Selected parent term from the ontology Methods for specifying ontology terms Term lists for selected cells Value Type and Property
- 28. Scientists are able to use the templates in Excel, where the annotations take the form of drop down menus or data entry cells.
- 29. The usage of tools like RightField are reducing the uptake barriers for generating formatted and annotated data and models.
- 31. “Ruin is the destination toward which all men rush, each pursuing his own best interest in a society that believes in the the freedom of the commons.” - Garrett Hardin, The Tragedy of the Commons.
- 32. To find out more about FAIRdom please visit our website. www.fair-dom.org
Notes de l'éditeur
- What doesn’t this data tell us? Whether it is experimental data or model data. What the reactions/species mean. If it is an experiment what type of experiment was used. Was there an SOP associated with it? Etc.
- What doesn’t this data tell us? Whether it is experimental data or model data. What the reactions/species mean. If it is an experiment what type of experiment was used. Was there an SOP associated with it? Etc.
- Linking methods with data and linking models with data We adopted the ISA framework – Investigation, Study and Assay – which provides a scaffold and experimental context for linking data and models. We also include and link Standard Operating Procedures (SOPs). We currently don’t do any RDF generation from the contents of these, but hope to in the future. Lots of use of spreadsheets “Schema.org for Systems Biology”
- What doesn’t this data tell us? Whether it is experimental data or model data. What the reactions/species mean. If it is an experiment what type of experiment was used. Was there an SOP associated with it? Etc.
- RightField is an Adminstrator’s tool to be used by an informatician. The user of the spreadsheets need never see this and the scary ontology stuff. Uses OWL API there is an upper memory limit on the size of an ontology RightField can open, due to limitations in the OWL API we use. However, once the ontology is open in RightField it doesn't have an impact on the saved spreadsheet. RF doesn't store the entire ontology inside the spreadsheet, but just the sets of terms used for the annotations and reference to the originating ontology and version. When the list of terms for a given cell becomes very long, we do have a problem with the dropdown box becoming unmanageable. To solve this we are looking at adding a feature that converts it into an auto-completion type cell rather than a dropdown box. Since this would involve a macro or plugin (which we like to avoid) we would make this an optional and explicit option by the user.
- Multiple ontologies
- Scientist never sees RightField, but just your normal basic Excel spreadsheet – with dropdown boxes for controlled terms (or text boxes for literals). By default we highlight the marked up cells in yellow, but this can be changed, and even the cells moved about without affecting the tracking of the ontologies or terms used. Value proposition to users