THE LAB NOTEBOOKA critical tool for scientific data management

Kristin Briney

Data Management BootcampUW-Madison Libraries22 February 2012

Pre-publication v. Post-publication Data

• Lot of management work done in second area• This talk focuses on first area• Data management very important in pre-publication

• Help scientists find their own data, saving time and effort• Help scientist share data

• Even within a lab this is important!

• Help PI’s keep track of data-long term as students leave• Makes post-publication management smoother

The Scientific Process• Literature review• Experiment design and grant writing• Acquire raw data• Data analysis• Repeat acquisition and analysis• (Maybe share data)• Make data presentational and write paper• Submit paper and eventually publish it• [Post-publication]

Data and Metadata Historically

Starkey, G., Newman, W. Royall, & Principe, L. (2004). Alchemical laboratory notebooks and correspondence. Chicago: University of Chicago Press.

Data and Metadata Currently

Flickr: proteinbiochemisthttp://www.flickr.com/photos/proteinbiochemist/3167660996/

Flickr: jurvetsonhttp://www.flickr.com/photos/jurvetson/4918852870/in/photostream/

Current Data and Metadata Problems• Pointing metadata to data• Long-term concerns with keeping data and metadata

together• Back-ups are an issue• No standard for digital file organization

Current Data and Metadata Practices• Practices vary lab-to-lab AND researcher-to-researcher• Sometimes PI’s enforce order but often not• Very difficult to locate another’s data currently• Common practice in lab is to test an experiment against

another’s data• (Intra-lab sharing a good selling point for data management!)

• Big need for education here

Data and Metadata in the Future• Metadata are digital in an electronic lab notebook• Data are digital and stored on computer• Electronic lab notebook stores or points to data

• More on e-notebooks later

Ideal Lab Notebook Contents• Raw data• Experimental metadata

• Equipment used, set-up, etc• Drawings/photos of set-up

• Worked-up data• Analysis tools used• Graphs and figures

• Cross-references and citations• Journal article, previous experiment in notebook, MSDS, etc.

• Research ideas• E-mails, letters, other discussions about research• Table of contents and/or index

(2009). Guide for keeping laboratory records. Rockville, MD: National Cancer Institute, Technology Transfer Center.

Ideal Lab Notebook Contents• All contents should be dated and initialed

• Some notebooks need second signature

• There should be standards in each lab

• Obviously, very few scientists actually keep this type of notebook

Common Lab Notebook Contents

• Experimental metadata• Can include drawings

• Usually figures of analyzed data

• Some cross-references and citations

• If you are lucky, a table of contents

Flickr: julia_manzerovahttp://www.flickr.com/photos/julia_manzerova/4022055109/in/photostream/

Ideal Lab Notebook Format• Electronic lab notebook

• Metadata and copies of data embedded in same file• Integration of outside material/files• Plugins like a chemical structure creator• Digital signatures and date stamps

• Easily searchable• Shareable, but control who has access to data

• Other issues here like de-identifying data, etc

How Librarians Can Help• Libguide on organizing digital files and recording this info

in lab notebook• Outline creating surrogate records in lab notebook for digital files

• Suggest file naming and organization conventions• Avoid “ / \ : * ? ‘ < > [ ] & $ characters• Use underscores not spaces• Date files and do it consistently (YYYY-MM-DD)• Label folders with reference to notebook

• Example: C:\Documents\BrineyNotebookIV\2012-02-22

• Outline metadata requirements to point to file• Names of file, folder, computer, etc.

http://researchdata.wisc.edu/manage-your-data/file-naming-and-versioning/

How Librarians Can Help

• Add lab notebooks to collection• Example: Laura

Kiessling of UW Chemistry Department

• What do retiring professors do with their notebooks?

Flickr: mabelsoundhttp://www.flickr.com/photos/mabelsound/4827325346/

How Librarians Can Help• Put together resources on proper lab notebook skills

• Short term goal is to have resources available• Print or online resources

• Long term goal focuses on instruction

• Target intro courses where most notebook ed happens• Point out resources during literacy instruction

• Target grad students• Focus on research groups

• Workshops on electronic lab notebooks• Slip in data management training during software training• DoIT a good resource

Future Things to Keep an Eye On• Lab notebooks are critical important tools, but they’re

changing• I expect everything to be electronic by the end of my career

• No clear winner yet for e-notebook software• Keep an eye on DoIT’s e-notebook pilot

Summary• Identify areas in the pre-publication data cycle where

scientists need help• Recognize why lab notebooks are an important data

management tool• Evaluate how lab notebooks are changing and how this

affects management of data• Understand the scope of usual and ideal notebook

practices• Outline ways that librarians can help in both the short-

term and long-term

Resources• (2009). Guide for keeping laboratory records. Rockville,

MD: National Cancer Institute, Technology Transfer Center.

• Kanare, H. M. (1985). Writing the laboratory notebook. Washington, D.C.: American Chemical Society.

• UW-Madison Research Data Services (RDS)• UW-Madison Division of Information Technology (DoIT)

Thank You!

• This presentation available under a Creative Commons Attribution-NonCommercial 3.0 license