Oct
20

DPO’s new software tool wins award for promoting open science

A new open-source application developed by Luis Villanueva gives collections managers an easy way to detect and correct errors uploaded to the Global Biodiversity Information Facility.

The Global Biodiversity Information Facility (GBIF) Secretariat announced Oct. 17 that the Smithsonian’s Digitization Program Office was selected by an expert jury as a winner in the 2018 Ebbe Nielsen Challenge. The entry, submitted by DPO Informatics Program Officer Luis J. Villanueva, the GBIF Issues Explorer, won a Second Place award among 23 entries from countries around the world. The Challenge was open to software tools that used GBIF data or tools to promote open science and open biodiversity data. The prize includes a monetary award of €3,500 (about $4,000). DPO will use the prize to expand the informatics efforts it is providing to the Smithsonian units and the community.

Screenshot of web page

Screenshot of web application

head shot

Luis J. Villanueva

The GBIF Issues Explorer web application was developed to provide collection managers at the Smithsonian with an easy way to explore the issues identified in their data uploaded to GBIF. These issues can include taxonomy problems, errors in coordinates, or invalid dates in the records. Due to the large size of the data (e.g., Paleobiology has over 660,000 records in GBIF), exploring these issues is a time-consuming task. The GBIF Issues Explorer allows researchers to use an easy web interface that displays the most relevant information to determine how to fix any problems in the records. Links to the collection database, inline images, and a map can help to improve the quality in the data for future updates. Researchers can also use the application to check GBIF data before running their analyses.

The GBIF Issues Explorer application was written for R/Shiny and is available with an open source license in Github. Villanueva developed the application after conversations with Holly Little, Informatics Specialist in the Department of Paleobiology at the Natural History Museum.

The Office of Research Computing provided the Shiny server. The Digitization Program Office is a program in the Smithsonian’s Office of the Chief Information Officer (OCIO).

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Posted: 20 October 2018
About the Author:

Alex di Giovanni is primarily responsible for "other duties as assigned" in the Office of Communications and External Affairs. She has been with the Smithsonian since 2006 and plans to be interred in the Smithson crypt.