Import Data

Title  Import Data

Summary

This script tool: (1) creates a File Geodatabase if one does not exist, (2) imports spatially referenced genetic data from a simple flat file format (SRGD.csv) to a new Feature Class located in the File Geodatabase, and (3) creates a copy of the input data in a table located in the File Geodatabase.

Required Inputs:

  • Spatially referenced genetic data formatted according to the SRGD.csv file format. Data can be for identified individuals or for genetic samples.

    Data will be automatically sorted into the categories Genetic, Identification, Location and Other. The user should look to make sure the appropriate fields are categorized correctly. If changes are needed, the user can un-check and/or re-check data fields where appropriate.

    NOTE: The SRGD.csv format includes the minimum data requirements for basic geneGIS functionality. Additional data can be included.

Optional Inputs:

  • If known, a spatial reference for the point data (recommended).

    NOTE: The default spatial reference is Geographic WGS 1984.

Outputs:

  • A new file geodatabase (if one does not already exist).

  • A new feature class located within the file geodatabase.

  • A copy of the data in a table located within the file geodatabase.


Usage

This script tool can be used to import spatially referenced genetic data into a feature class that is viewable in ArcGIS.


Syntax

ClassifiedImport (SRGD_Input_File, {Spatial_Reference}, File_Geodatabase_Location, File_Geodatabase_Name, Genetic_Columns, Identification_Columns, Location_Columns, {Other_Columns})

Parameter Explanation Data Type
SRGD_Input_File Dialog Reference

The following data fields for the SRGD input file MUST be formatted as follows:

  • Sample_ID (required)

    A unique identifier for each data record or encounter with an animal that has an associated spatial (latitude, longitude) and temporal element (date, time) resulting in the collection of a sample (e.g., biopsy, skin, ear tag) and/or a photograph, tag or band that will allow the same individual to be resighted or recaptured. This information may have been used to determine an individual’s identity.

  • Individual_ID

    A unique identifier for each known individual in the dataset. This information may have been derived from some previous type of analysis (e.g., determination of identity using genotyping or photo-identification methods).

  • Latitude (required)

    The latitude, in decimal degrees, where the sample or photograph was collected. Latitudes are positive north of the equator and negative south of the equator.

  • Longitude (required)

    The longitude, in decimal degrees, where the sample or photograph was collected. Longitudes are positive east of the Prime Meridian and negative west of the Prime Meridian.

    NOTE: the default spatial reference, unless indicated by the user during data import, is Geographic (WGS84).

    Alternatively, data can specify X and Y columns for projected datasets, such as coordinates stored in UTM.

  • Date_Time(Date required; Time optional)

    The date and time for when the sample or photograph was collected. We recommend ISO 8601 date format (YYYY/MM/DD hh:mm:ss).

  • Region

    The general region from where the sample or photograph was collected. This can be based on political or geographic boundaries (e.g., oceans, countries, states, etc.) or the study design (e.g., a specific quadrat or plot).

  • Sex (*)

    The genetic sex (e.g., M, F, U) of the sample or individual, if known.

  • Haplotype(*)

    The mitochondrial haplotype of the sample or individual, if known.

  • L_YourLocusName(*)

    The name of a specific locus. For biallelic data (microsatellites, SNPs), there should be 2 columns with the same locus name. Each column should hold a value for each of the alleles for that locus.

    Include as many loci and allelic values as necessary for your data.

    The L_ prefix will allow the Import Tool to recognize correctly the loci.

    ArcGIS does not allow more than one field with the same name. Upon import into ArcGIS, the name for each locus will be appended as follows: L_YourLocusName_1, L_YourLocusName_2.

    * NOTE: These fields are considered optional because any combination of Sex, Haplotype and Loci data are possible. However, at least one is requiredto make use of the intended geneGIS functionality.

Additional fields can be included as needed.

File
Spatial_Reference (Optional) Dialog Reference

The default spatial reference is Geographic WGS 1984.

If data were collected with another spatial format, specify it here.

Spatial Reference
File_Geodatabase_Location Dialog Reference

The location where the new file geodatabase will be placed or the location of an already existing file geodatabase.

Folder
File_Geodatabase_Name Dialog Reference

The name of the new or already existing file geodatabase.

String
Genetic_Columns Dialog Reference

This section should include any relevant genetic data (Sex, Haplotype, Loci) within the dataset being imported. The user should ensure all appropriate fields are checked and/or un-checked.

For loci data, ArcGIS does not allow more than one field with the same name. Upon import into AcGIS, the name for each locus will be appended as follows: L_YourLocusName_1, L_YourLocusName_2.

Multiple Value
Identification_Columns Dialog Reference

This section should include any relevant indentification data (Sample_ID, Individual_ID) within the dataset being imported. The user should ensure all appropriate fields are checked and/or un-checked.

Multiple Value
Location_Columns Dialog Reference

This section should include the latitude and longitude data for the dataset being imported or X and Y columns for projected data.

Multiple Value
Other_Columns (Optional) Dialog Reference

This section can include any other relevant data that the user wants to include in the import by either checking and/or un-checking appropriate fields.

Multiple Value

Code Samples

Tags

import spatially explicit genetic data, creates file geodatabase, creates feature class

Credits

Created by the geneGIS team: Dori Dick, Shaun Walbridge, Scott Baker, Dawn Wright


Use limitations