curation-friendly tools for the scientific researcher

Curation-Friendly Tools for the Scientific Researcher

Brian WestraUniversity of Oregon

bwestra@uoregon.edu

Data services needs assessment: 2009-2010

Interviewed 25 faculty:

BiologyCenter for Advanced Materials Characterization at OregonChemistryComputer & Information ScienceGeological SciencesHuman PhysiologyInstitute for a Sustainable EnvironmentMuseum of Natural and Cultural HistoryPhysicsPsychology

Some background

o Connecting data sources to data viewing and usage

o Data organizationo Metadata/annotation of fileso Recording workflow, procedures,

provenance

Preservation, archiving and publishing data were farther down the list

Primary issues/needs

Clearly articulated need and opportunity; also tie-in to data management plan implementations

Logical extension of the role for libraries beyond traditional services

Support for e-Science is a goal

Working in the data lifecycle/ecosystem is more robust than ‘just’ archiving/preservation

Why we’re involved…

Maintaining, preserving and adding value to digital research data throughout its lifecycle.

http://www.dcc.ac.uk/digital-curation/what-digital-curation

What is digital curation?

File management tools: i.e., Sharepoint

Best practices: naming conventions, version control software

Are there other solutions or services?

What might meet these needs?

Going beyond file management systems to embedded, more holistic tools/systems:

o Electronic Lab Notebooks

o Content/format-specific data management software

What might meet these needs?

“…how a laboratory tracks and manages its information resources, particularly the data that represents the laboratory’s product.” (Avery, McGee, & Falk, 2000)

“a data and sample management system that is designed to improve the management of laboratory workflow” (“Clinical LIMS,” 2011)

Most basic function: sample handling and reporting.

LIMS – Lab Info Mgmt System

Data (create, store, share, organize, analyze) +

information (notes)

May include: sample handling, storeroom inventory, signatures, collaboration, protocols and SOPs, embedded workflows, data analysis and visualization

LIMS and ELN functions and features often overlap

ELN – Electronic Lab Notebook

Many of them! UWisconsin-Madison RFI responses included these vendors:

o Accelryso Agilento Amphorao Axiopeo Conturo IDBSo Kinematiko Labtracko Notebookmakero Rescentriso Waters

ELN options

Continuously changing field of vendors and products

o Nature article

o Other options: open source, or a mix of basic tools, often used in open science

ELN options

Some UO considerations:

o Academic audience (vs. FDA compliance)o Cost – S/W, hardware, sys-admin, trainingo Interface and ease of useo Account managemento Platformo Research domain integration*o Metadata support*o Data file management*

*curation characteristics

Narrowing the field

o Research domaino Workflow integration with analytical tools, methodso Data capture from typical hardware/sourceso Ontologies

o Metadatao Capture/extractiono Representation, standardso Export with files

o Data file managemento File format standards, transformationso Export optionso Metadatao Provenance, version controlo Archiving raw and derivatives

Curation-friendly: compatible with or supporting:

Wisconsin-Madison RFI

o Some highlights from an excellent list of considerations

o Good process

o Plan to field test with 60 participants

Narrowing the field

What might be your “make or break” issues?

How would you assign weights or ranking to the metrics?1. Costs2. Platform3. Product lock-in4. etc.

Narrowing the field

‘Ground truth’ the metrics and values/comparators

Satellite or high-altitude (pre-pilot) might not conform to on the ground (during the pilot)

Thoughts on evaluation

http://www.seawead.org/index.php?option=com_content&view=article&id=29:ground-truthing&catid=9&Itemid=9

Have realistic team work load and timeline expectations

It’s progress! It may be difficult to apply measures of curation capacity to an ELN

oArchiving and preservation capacityoExportable relational (semantic) representationoPublication of data

Thoughts & observations

It may be more realistic to ask:

o Will this help you (the PI) find and understand the data and notes this week/ next year/after the student is gone?

o Can this improve your ability to do data management (and write a better plan for the next grant proposal)?

o Is it simple enough that it will become part of the routine? i.e., folklore: info everyone knows but no one records

Thoughts & observations

Example: publish direct to ChemSpider

Chemspider record

ELN data exchange project: Dial-a-molecule

Thoughts & observations

A compelling reason for faculty to participate

Collaboration and coordination with stakeholders (Office of Research, IT, Libraries, research faculty, Tech Transfer)

Champion(s) – these are usually not easy or inexpensive to implement, in the lab or with limited budgets

Characteristics of a good pilot study

What is the scope of a “pilot case”?o Durationo Number of participantso Hardware capacityo Level of training and supporto Evaluation criteria and roleso Exit strategy – and dealing with success

Who’s going to pay for this (right now)?

Might anticipate who is going pay for this (if it works well and goes to production)

Set expectations and build concensus

“Data you enter in the ELN software will be stored in a secure

location, however; at the end of the pilot period, the data will

be removed and we cannot guarantee that it can be recovered

fully from the ELN. Therefore, we very strongly encourage you

to keep an additional copy of all data and notebook entries in

electronic and/or hard copy format during the pilot as a backup

measure and as a means of keeping a complete and continuous

record of your work during the pilot period.”

https://academictech.doit.wisc.edu/informed-consent-electronic-lab-notebook-pilot

Expectations

Many biology labs produce a lot of still images and video

Image management

Cresko lab - UO

Open Microscopy Environment (OME)-developed system for image file management

OMERO

Embeds/supports curation:

o Uses a metadata standard for description (OME XML)

o Employs file format standards (import to tiff) o Can archive raw and derivative fileso Provides intuitive organizational schemao Annotation and description support on

multiple levelso Export of files with metadata

OMERO strengths

video

Annotation

It’s open source – what is the level of support/installation base? Longevity/stability?

How well does it fit into the workflow of the lab?

Can it support the proprietary formats generated in the labs?

What are the IT/systems requirements?

Primary evaluation questions

Finding a host and participants

Establishing realistic expectationso Host obligationso Project scope

Barriers to the pilot study

DCXL: Digital Curation for Excel

Discussion: what other options are you exploring?

Other projects and ideas:

Thank you!

ReferencesAvery, G., McGee, C., & Falk, S. (2000). Product Review: Implementing LIMS: A “how-to” guide. Analytical Chemistry, 72(1), 57 A-62 A. American Chemical Society. doi:10.1021/ac0027082

CIO Office, U. of W.-M. (n.d.). Charter 6.7: eLab Notebooks | CIO Office | UW-Madison. Retrieved February 9, 2012, from http://www.cio.wisc.edu/plan-docs-Charter6-7.aspx

Clinical LIMS. (2011). Retrieved from http://www.scientificcomputing.com/product-IN-Clinical-LIMS-072811.aspx?terms=LIMS

Giles, J. (2012). Going paperless: The digital lab. Nature, 481(7382), 430-1. doi:10.1038/481430a

PerkinElmer. (n.d.). PerkinElmer Informatics. Retrieved February 9, 2012, from http://www.cambridgesoft.com/?l=en

Rescentris. (n.d.). Rescentris | CERF Software. Retrieved February 9, 2012, from http://rescentris.com/cerf-software/

University of Dundee & Open Microscopy Environment. (n.d.). About OMERO — OME. Retrieved February 9, 2012, from http://www.openmicroscopy.org/site/products/omero

University of Wisconsin-Madison. (2012). Informed Consent for Electronic Lab Notebook Pilot | Technology Solutions for Teaching and Research. Retrieved February 9, 2012, from https://academictech.doit.wisc.edu/informed-consent-electronic-lab-notebook-pilot

University of Wisconsin-Madison. (n.d.-a). Electronic Lab Notebooks | Technology Solutions for Teaching and Research. Retrieved February 9, 2012, a from http://academictech.doit.wisc.edu/ideas/electronic-lab-notebooks

University of Wisconsin-Madison. (n.d.-b). Electronic Lab Notebook Request for Information - University of Wisconsin-Madison. Retrieved February 9, 2012, b from https://academictech.doit.wisc.edu/files/115349rfi.pdf