Data Usage
@Prajjwal Bhattarai
Objective
- Stage 1: Develop a Database and API that takes in input from the hardware device
- Stage 2: Use data for prediction, analysis and modeling to contribute to the field
Questions
- What type of variables would you want to log from the field (weather/climatic conditions, attitude, habitat, amphibian characteristics, etc) given no hardware constraints?
- Use variables from the genome upload
- Linking data like temperature from other databases is an option
- How is this data collected from the engineering team?
- What type of genetic data would you want logged in the database?
- How is this data collected from the bio team?
Amphibian Disease Portal Current Usage
- Submitting collected samples to the portal. Vredenburg, 2019, Jongsma,2016,, Parrott, 2017, Catenazzi,2017
- Genus
- Species
- Location
- Type of test performed
- Test result
- Mortality
- Sampling type
- External swab
- Isolate
- Swabbing
- Whole-genome data
- Testing method
Upload sheet to geome
https://s3-us-west-2.amazonaws.com/secure.notion-static.com/3fa460b4-3afc-4dd6-9fba-a691e345453b/AmphibiaWeb_Disease_Portal_(1).xlsx
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- General reviews, either of the current state of research in the amphibian world (the portal gets mentioned as a collaborative tool but no data is submitted to or retrieved) Olson, 2019, Adams, 2018, (Allain et al., 2019)
- Elementary data (total number of cases, no. of species affected, etc) De la Riva, 2011, Montori, 2019,
- Basic mapping; just taking the latitude-longitude data from the portal and plotting it in a simple map. Watts, 2019
- Meta-analysis for the prevalence of bd, comparing the results from in-site testing to previous tests from the portal. Compares presence of bd across amphibian genus, species and sex. Courtois, 2015
- Xie, 2016 creates a binary classification model for predicting the presence of bd in a region based on climate and precipitation data. Uses the portal diagnostic data as a label for whether or not bd is present in a region. Olson, 2013 has a similar, simpler approach that includes creating correlative charts with climate, precipitation, and habitat (tundra, tropical, subtropical, etc)