Curation-Friendly Tools for the Scientific Researcher

Transcription

1 Portland State University PDXScholar Online Northwest Online Northwest 2012 Feb 10th, 2:10 PM - 2:55 PM Curation-Friendly Tools for the Scientific Researcher Brian Westra University of Oregon Let us know how access to this document benefits you. Follow this and additional works at: Westra, Brian, "Curation-Friendly Tools for the Scientific Researcher" (2012). Online Northwest This Presentation is brought to you for free and open access. It has been accepted for inclusion in Online Northwest by an authorized administrator of PDXScholar. For more information, please contact pdxscholar@pdx.edu.

2 Brian Westra University of Oregon

3 Data services needs assessment: Interviewed 25 faculty: Biology Center for Advanced Materials Characterization at Oregon Chemistry Computer & Information Science Geological Sciences Human Physiology Institute for a Sustainable Environment Museum of Natural and Cultural History Physics Psychology

4 o o o o Connecting data sources to data viewing and usage Data organization Metadata/annotation of files Recording workflow, procedures, provenance Preservation, archiving and publishing data were farther down the list

5 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

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

7 File management tools: i.e., Sharepoint Best practices: naming conventions, version control software Are there other solutions or services?

8 Going beyond file management systems to embedded, more holistic tools/systems: o Electronic Lab Notebooks o Content/format-specific data management software

9 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.

10 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

11 Many of them! UWisconsin-Madison RFI responses included these vendors: o Accelrys o Agilent o Amphora o Axiope o Contur o IDBS o Kinematik o Labtrack o Notebookmaker o Rescentris o Waters

12 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

13 Some UO considerations: o Academic audience (vs. FDA compliance) o Cost S/W, hardware, sys-admin, training o Interface and ease of use o Account management o Platform o Research domain integration* o Metadata support* o Data file management* *curation characteristics

14 o o o Research domain o Workflow integration with analytical tools, methods o Data capture from typical hardware/sources o Ontologies Metadata o Capture/extraction o Representation, standards o Export with files Data file management o File format standards, transformations o Export options o Metadata o Provenance, version control o Archiving raw and derivatives

15 Wisconsin-Madison RFI o Some highlights from an excellent list of considerations o Good process o Plan to field test with 60 participants

16 What might be your make or break issues? How would you assign weights or ranking to the metrics? 1. Costs 2. Platform 3. Product lock-in 4. etc.

17 Ground truth the metrics and values/comparators Satellite or high-altitude (pre-pilot) might not conform to on the ground (during the pilot) om_content&view=article&id=29:groundtruthing&catid=9&itemid=9

18 Have realistic team work load and timeline expectations It s progress! It may be difficult to apply measures of curation capacity to an ELN o Archiving and preservation capacity o Exportable relational (semantic) representation o Publication of data

19 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

20 Example: publish direct to ChemSpider Chemspider record ELN data exchange project: Dial-a-molecule

21 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

22 What is the scope of a pilot case? o Duration o Number of participants o Hardware capacity o Level of training and support o Evaluation criteria and roles o 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)

23 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.

24 Many biology labs produce a lot of still images and video Cresko lab - UO

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

26 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 files o Provides intuitive organizational schema o Annotation and description support on multiple levels o Export of files with metadata

27 video

28 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?

29 Finding a host and participants Establishing realistic expectations o Host obligations o Project scope

30 DCXL: Digital Curation for Excel Discussion: what other options are you exploring?

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32 Avery, 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: /ac CIO Office, U. of W.-M. (n.d.). Charter 6.7: elab Notebooks CIO Office UW-Madison. Retrieved February 9, 2012, from Clinical LIMS. (2011). Retrieved from aspx?terms=LIMS Giles, J. (2012). Going paperless: The digital lab. Nature, 481(7382), doi: /481430a PerkinElmer. (n.d.). PerkinElmer Informatics. Retrieved February 9, 2012, from Rescentris. (n.d.). Rescentris CERF Software. Retrieved February 9, 2012, from University of Dundee & Open Microscopy Environment. (n.d.). About OMERO OME. Retrieved February 9, 2012, from University of Wisconsin-Madison. (2012). Informed Consent for Electronic Lab Notebook Pilot Technology Solutions for Teaching and Research. Retrieved February 9, 2012, from University of Wisconsin-Madison. (n.d.-a). Electronic Lab Notebooks Technology Solutions for Teaching and Research. Retrieved February 9, 2012, a from University of Wisconsin-Madison. (n.d.-b). Electronic Lab Notebook Request for Information - University of Wisconsin- Madison. Retrieved February 9, 2012, b from