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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetics and Genomics of Tropical Fruit, Sugarcane and Grasses

Location: Subtropical Horticulture Research

Project Number: 6038-21000-022-04
Project Type: Specific Cooperative Agreement

Start Date: Jun 04, 2013
End Date: Sep 30, 2015

Objective:
1. Develop a method to acquire location data and make it available for mapping and spatial querying of the database. Methods and procedures will be evaluated and optimal practices will be suggested and upon approval implemented for existing accessions for future additions to the database. 2. Develop less time intensive and partially automated routines that can streamline and simplify data curation in preparation for submission to standardized global databases (GRIN) while minimizing human error and saving time and effort, by reducing repetitive operations at multiple steps along the data preparation process. Scripts to transform raw field data sheets to comply with the GRIN database schema will be developed. 3. Develop a simple method that will allow the merging of map accession data with the geographic location information using open source and GIS capable software. Develop scripts and design template map layers that will allow for thematic mapping and querying of all attributes associated to accessions in the database. 4. Implement data storage and back-up procedures and design training material for employees and host a training workshop for USDA personnel.

Approach:
(1) We will evaluate existing workflows and data collection procedures. In order to develop appropriate method to gather location information we will visit the USDA SHRS and accompany a trained person from USDA during data acquisition. Based on procedures, plant distribution and density we will make recommendations on location attribute collection. (2) We will acquire spatial information for all accessions based on method developed in (1). Data will be stored as flat files and a database tables linked to accession data. Methods will primarily depend on the existing GRIN database structure and flexibility of expansion. (3) We will get familiar with the GRIN database schema - local installation and experimenting with existing tools (e.g., Curator Tool, Import Wizards, etc.). The data structure of all existing accessions in spreadsheet format will drive the scripting effort to convert all data to compliance with the GRIN database schema and loading tools. We will work in close collaboration with USDA Scientists and Systems Administrators to guarantee compliance with software standards and limitations of the agency. (4) We will batch process all existing data into a local database. Upon quality control of results data will be committed to the global GRIN database. (5) We will develop map templates that are most useful for data collection planning assistance and mapping of attribute data. For this task we will consult with data managers, campaign planners and scientists. The goal is to develop simple procedures within open source software environments that are GIS capable. We will consult with USDA personnel on preferences and current software use and compliance. (6) We will document all procedures and detailed method steps. Training material for a workshop will be prepared and one on-site workshop will be conducted. (7) For the second year we will provide consultation services, additional training and advising in continuation of accession collections.

Last Modified: 11/23/2014
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