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Electronic labnotes

Electronic labnotes. Mari Wigham. Commit /. Information Management @ WUR. Organising , sharing , finding and reusing data Expertise in: Modelling data and how people work with it

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Electronic labnotes

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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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