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sbtools: An R package for ScienceBase

Completed
By Community for Data Integration (CDI) April 7, 2015

Science is an increasingly collaborative endeavor. In an era of Web-enabled research, new tools reduce barriers to collaboration across traditional geographic and disciplinary divides and improve the quality and efficiency of science. Collaborative online code management has moved project collaboration from a manual process of email and thumb drives into a traceable, streamlined system where code can move directly from the command-line onto the Web for discussion, sharing, and open contributions. Within the USGS, however, data have no such analogous system. To bring data collaboration and sharing within the USGS to the next level, we are missing crucial components.



The sbtools project team built sbtools, an R interface to ScienceBase (fig. 17). To build this package, the team organized a diverse group representing experts in data management, science, and research-software development domains. This interface provides scripted R access to ScienceBase to manage metadata and data files, to search the catalog of datasets, and to view and modify data in formats familiar to R users. The package is designed to keep most interactions simple and includes internal handling of complex Web service interactions (for example, authentication) to simplify use for end-users. With its release, sbtools enables rapid and reproducible access to one of the single largest repositories of Earth-science data and an advanced cloud-based data collaboration platform.  sbtools will add value to ScienceBase for scientists, developers, and users of R in the USGS. The project team will release and distribute the code via the Comprehensive R Archive Network (CRAN) and USGS-R repositories. 

Accomplishments

The following accomplishments have been made or are in progress as of September 2015:



Note:  This description is from the Community for Data Integration 2015 Annual Report.

sbtools: A package connecting R to cloud-based data for collaborative online research

The adoption of high-quality tools for collaboration and reproducible research such as R and Github is becoming more common in many research fields. While Github and other version management systems are excellent resources, they were originally designed to handle code and scale poorly to large text-based or binary datasets. A number of scientific data repositories are coming online and are often f
Authors
Luke Winslow, Scott Chamberlain, Alison P. Appling, Jordan S. Read
By
Community for Data Integration (CDI)

sbtools: USGS ScienceBase Tools

Tools for interacting with U.S. Geological Survey ScienceBase https://www.sciencebase.gov interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
By
Water Resources Mission Area, Community for Data Integration (CDI)

Jordan S Read, PhD (Former Employee)

Chief, Data Science Branch
Water Resources Mission Area

Science is an increasingly collaborative endeavor. In an era of Web-enabled research, new tools reduce barriers to collaboration across traditional geographic and disciplinary divides and improve the quality and efficiency of science. Collaborative online code management has moved project collaboration from a manual process of email and thumb drives into a traceable, streamlined system where code can move directly from the command-line onto the Web for discussion, sharing, and open contributions. Within the USGS, however, data have no such analogous system. To bring data collaboration and sharing within the USGS to the next level, we are missing crucial components.



The sbtools project team built sbtools, an R interface to ScienceBase (fig. 17). To build this package, the team organized a diverse group representing experts in data management, science, and research-software development domains. This interface provides scripted R access to ScienceBase to manage metadata and data files, to search the catalog of datasets, and to view and modify data in formats familiar to R users. The package is designed to keep most interactions simple and includes internal handling of complex Web service interactions (for example, authentication) to simplify use for end-users. With its release, sbtools enables rapid and reproducible access to one of the single largest repositories of Earth-science data and an advanced cloud-based data collaboration platform.  sbtools will add value to ScienceBase for scientists, developers, and users of R in the USGS. The project team will release and distribute the code via the Comprehensive R Archive Network (CRAN) and USGS-R repositories. 

Accomplishments

The following accomplishments have been made or are in progress as of September 2015:



Note:  This description is from the Community for Data Integration 2015 Annual Report.

sbtools: A package connecting R to cloud-based data for collaborative online research

The adoption of high-quality tools for collaboration and reproducible research such as R and Github is becoming more common in many research fields. While Github and other version management systems are excellent resources, they were originally designed to handle code and scale poorly to large text-based or binary datasets. A number of scientific data repositories are coming online and are often f
Authors
Luke Winslow, Scott Chamberlain, Alison P. Appling, Jordan S. Read
By
Community for Data Integration (CDI)

sbtools: USGS ScienceBase Tools

Tools for interacting with U.S. Geological Survey ScienceBase https://www.sciencebase.gov interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.
By
Water Resources Mission Area, Community for Data Integration (CDI)

Jordan S Read, PhD (Former Employee)

Chief, Data Science Branch
Water Resources Mission Area
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