Traits Standards Committee Meeting Notes

By David LeBauer; ARPA-E TERRA Reference Data and Computing Team Comment

Participants

David LeBauer, Max Burnette, Cheryl Porter, Shawn Serbinm David Lee, Noah Fahlgren, Mitch Tuinstra, Yuhao Chen (Delp lab), Justin McGrath, Jeff White, Craig Willis, Eric Lyons

Data Pipeline overview

Accessing data

Production data: https://terraref.ncsa.illinois.edu/bety/

Test data: https://terraref.ncsa.illinois.edu/bety-test/

documentation: https://pecan.gitbooks.io/betydb-data-access/content/

API documentation https://pecan.gitbooks.io/betydb-data-access/content/API/beta_API.html

Data Samples

Traits:

Web interface: https://terraref.ncsa.illinois.edu/bety-test/traits

API: https://terraref.ncsa.illinois.edu/bety-test/api/beta/traits?key=9999999999999999999999999999999999999999&limit=5

Shared Field Measurement Protocols

  • Review draft document of sampling protocols
  • Interest in sharing across teams? Dave Lee can circulate among the other TERRA teams and work to get feedback after the Traits Standards Committee and the Cat5 team are satisfied with the document.
  • Interest in additional measurements at MAC?

Data and meta-data formats

Shared Protocols

NIH protocol database - Zoe Lacroix

Example pub at: http://www.ncbi.nlm.nih.gov/pubmed/26673793:

Scientific legacy workflows are often developed over many years, poorly documented and implemented with scripting languages. In the context of our cross-disciplinary projects we face the problem of maintaining such scientific workflows. This paper presents the Workflow Instrumentation for Structure Extraction (WISE) method used to process several ad-hoc legacy workflows written in Python and automatically produce their workflow structural skeleton. Unlike many existing methods, WISE does not assume input workflows to be preprocessed in a known workflow formalism. It is also able to identify and analyze calls to external tools. We present the method and report its results on several scientific workflows.

Prometheus wiki for plant protocols: http://prometheuswiki.publish.csiro.au/tiki-custom_home.php

PĂ©rez-Harguindeguy et al (2013) New handbook for standardised measurement of plant functional traits worldwide. Australian Journal of Botany, 61, 167-234. http://dx.doi.org/10.1071/BT12225 http://www.nucleodiversus.org/index.php?mod=page&id=79

http://earthcube.org/group/geosemantics

Austrailian group has workflow software + standards

Rothamstead data

INRA France

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