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Electronic Lab Notes: Organizing, Sharing, & Finding Data Easily

Explore the benefits of structuring electronic lab notes for efficient data management. Learn how to organize data by researcher, year, and activity, increasing accessibility and traceability. Find out expert tips on tools and techniques for optimal data structuring.

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Electronic Lab Notes: Organizing, Sharing, & Finding Data Easily

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  1. Electronic labnotes Mari Wigham Commit/

  2. Information Management @ WUR • Organising, sharing, findingandreusing data • Expertise in: • Modelling data andhowpeopleworkwithit • Semantictechnology – making the data ‘understandable’ for computers sothattheycanbetter support the users • Emphasis on applicationsforuse in real life

  3. Information Management @ WUR

  4. Information Management @ WUR

  5. Mari Wigham • 5 years in the IM group • “R&D software developer” • Part of the Tiffany development team • I like the technicalchallengesinvolved but also building somethingthatmakessomeone’s job easier

  6. Thispresentation • What is anelectroniclabnote? • Example: Study on the effects of diet on health • What is anelectroniclabnote? – The Answer • (Tiffany) • (Storing data semantically) • Questions

  7. What do youthink of whenyouhear the term “Electronic lab note”?

  8. What is anelectroniclabnote?

  9. Why do you keep a lab notebook?

  10. For yourself • Noteresultsforfurther processing and analysis • Help in writingreportsand papers • Reference for later

  11. What is anelectroniclabnote?

  12. For others • Provenanceandtraceability • Journals are startingtodemand more thanjustthe paper • Research institutesandfundinginstitutionssuch as the EU and NWO are alsostartingtodemandmore fortheir money! • Your research colleagues – the ‘lone genius’ is very rare.

  13. Insightintoyour research • Papers

  14. Insightintoyour research • Explicatedknowledge • Materials • Methods • Data • Models • Results

  15. Sciencemethodology • Critical thinking, reproducibility, argumentation, collaboration • Scientific ‘workflow’ – a sequence of actions with inputs (e.g. observations) and outputs (e.g. data files) • For example: explicating research questions, preparing materials, experimenting, data analysis, reporting

  16. I don’t have time forthis!!!

  17. Example Studytoexamine the effects of diet on health There are manywaystoorganise the data. We will look at three: • By researcher • Byyear • Byactivity

  18. Example It is now the May holiday 2013. Peter and Anna are on holiday, and Lisa has received some urgent questions from the reviewers. They need to know: • the procedure used to produce the high protein diet • which bureau measured the data • what sort of preprocessing was carried out on the data.

  19. Organisationbyyear/researcher Needtoknowwhat was donewhen or bywho • the procedure usedtoproduce the high proteindiet • Thiscanbe found as it has a good name • which bureau measured the data • May beabletoguesswhich email gives the information • whatsort of preprocessing was carried out on the data. • NeedtoreadthroughPeter’slabnotes...

  20. Example – Organisingbyactivity Easy tonavigatethrough, foreach question youquicklyfind the right folder even ifyou had no prior knowledge. • the procedure usedtoproduce the high proteindiet • Thiscanbe found as it has a good name • which bureau measured the data • May beabletoguesswhich email gives the information • whatsort of preprocessing was carried out on the data. • NeedtoreadthroughPeter’slabnotes...

  21. Example – Organisingbyactivity plus extra structureandmetadata • Enter a brief description for each activity (folder) • It may help to identify inputs and outputs, or types of files (e.g. dataset, procedure, sample, document) • Linking to items produced in other activities allows you to follow the workflow and reuse items • How much or how little you do depends on your data

  22. Example – Organisingbyactivity plus extra structure Easy tonavigatethrough, foreach question youquicklyfind the right folder even ifyou had no prior knowledge. • the procedure usedtoproduce the high proteindiet • Thiscanbe found regardless of name as it is in the folder ‘procedures’ • which bureau measured the data • In description • whatsort of preprocessing was carried out on the data. • In description

  23. Example – Organisingbyactivity plus extra structure • Where are the labnotes? • Labnotes are most accessiblewhenyoustructure the information containedwiththem • There is room forall the information in the labnotes in the structuredescribed • How far youstructurethemdepends on yourowncircumstances. More structure = easiertounderstand but also = more time! • It canbeuseful (andsometimesnecessary) topreservethem in theirrough form • Sometimeshandyifyou split them up per activity

  24. What is anelectroniclabnote? The electronic bit is easy. But toreally benefit youneedtostructureyour data – that’s the hard part! • iPad, laptop, PC, smartphone... • Notepad, Word, PDF... • Dropbox, hard drive, website...

  25. Structuring data It takes time! But it’san investment – not time lost

  26. What tools shouldyouuse? There is no single best solution. Youneedtoconsider: • What are yougoingto store? • What do youneedto do yourwork? • What is requiredfromyouremployer, or yourfundinginstituition? • Whatsort of files, andhow large? • Is itconfidential? • Backupandarchiving • Is itbacked up, howoftenandhoweasilycanyou get it? • How long is the data kept? • Is there support?

  27. What tools shouldyouuse? • Security issues • Whocan access the data? • Caneveryonewith access seeall data? Alsoedit? • Regulatory issues – particularly ‘in the cloud’ • Where do youneed access? • Single location or multiple? • In the field? • Will you only share data or editittogether? • If editing thenyouneedtoconsider • howto manage different versions • Attributability of changes

  28. Tiffany

  29. Tiffany - context for research activities dataset person device statistical analysis e-note dataset my experiment model method person material method conference paper presentation

  30. Storing data semantically This is whatyour research data looks likefor a machine

  31. How do we improvethissituation? Notwords but ‘resources’ – with a strictdefinitionand a relationshipwithother resources http://name http://education http://cv http://work http://private

  32. ‘Semantic Web’

  33. Semantic Excel - Rosanne

  34. Semantic Excel - Rosanne

  35. Integrating data

  36. Sowhatcanelectroniclabnotes do foryou? In 2013 If you scan your lab book in... • Store your data electronically and make it available via email, website etc. If you create a searchable file... • Search for keywords in your labnotes If you store your files in a structure... • See your research in context • Find information more easily • Make your research more easily traceable • Make your research more easily reusable

  37. Sowhatcanelectroniclabnotes do foryou? In 2023 • Instead of just a literature search whenyou start a new project, do a ‘dataset’ and ‘method’ search? • Get automatic research creditswhensomeonereusesyour data? • Whilelisteningto a speaker at a conference, download his data andintegrateitwithyours, thendiscuss collaborating on a new paper to present the results over the wineandnibbles?

  38. Questions?

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