Adding a Site

Each experiment is conducted at a unique site. In the context of BETY, the term 'site' refers to a specific location and it is common for many sites to be located within the same experimental station. By creating distinct records for multiple sites, it is possible to differentiate among independent studies.

1. Before adding a site, search to make sure that site is not already

   entered in the database.

2. Search for the site given latitude and longitude

   • If an institution name or city and state are given, try to

     locate the site on Google Maps

   • If a site name is given, try to locate the site using a

     combination of Google and Google Maps

   • If latitude and longitude are given in the paper, search by lat

     and lon, which will return all sites within $\pm$ 1 degree lat and

     long.

   • If an existing site is plausibly the same site as the one

     mentioned in the paper, it will be necessary to check other

     papers linked to the existing site.

     • Use the same site if the previous study uses the *exact same

       location* and experimental setup.

     • Create a new site if the study was conducted in a different

       field (i.e., not the exact same location).

     • Create a new site if one study was conducted in a greenhouse

       and another was conducted in a field.

     • Do not use distinct sites for seed source in a common garden

       experiment (see ’When not to enter a new site’ below)

3. To use an existing site, click Edit for the site, and then select

   current citation under Add Citation Relationships

4. If site does not exist, add a new site.

Interface for adding a new site:

Attributes of a site record

Descriptors	Notes
Site Name	Site identifier, sufficient to uniquely identify the site within the paper
City	Nearest city
State	State, if in the US
Country	Country
Longitude	Decimal Form. For conversion see the equation in table 9
Latitude	Decimal Form. For conversion see the equation in table 9
Greenhouse	TRUE if plants were grown in a greenhouse, growth chamber or pots.
Soil	By percent clay, sand, and silt if given
SOM	Soil organic matter (% by weight)
MAT	Mean Annual Temperature (°C)
MAP	Mean Annual Percipitation (mm)
MASL	Elevation (meters above sea level, m)
Notes	Site Details not included above
Soil Notes	Soil details not included above
Rooting Zone Depth	Measured in Meters (m)
Depth of Water Table	Measured in Meters (m)

1. Do not enter a new site When plants (or seeds) are collected from multiple locations and then grown in the same location, this is called 'common garden experiment'. In this case, the location of the study is included as site information. Information about the seed source can be entered as a distinct cultivar.

Site Location

Points can be added via the web interface; spatial geometries, e.g. a plot, site, or country boundary, must be entered via the PostgreSQL command line.

Point Locations

If latitude and longitude coordinates are not available, it is often possible to determine the site location based on the site name, city, and other information. One way to do this would be to look up a location name in Google Maps and then locate it on the embedded map. Google Maps can provide decimal degrees if the LatLng feature is enabled, which can be done here. Google Earth can be particularly useful in locating sites, along with their coordinates and elevation. Alternatively, the site website or address might be found through an internet search (e.g. Google).

Use Table \ref{tab:location_accuracy} to determine the number of significant digits to indicate the level of precision with which a study location is known.

Table \ref{tab:location_accuracy} \label{tab:location_accuracy} Level of accuracy to record in lat and lon fields.

Location Detail	Degree Accuracy
City	0.1
Mile	0.01
Acre	0.001
10 Meters	0.0001

Boundaries

A vector boundary must be obtained. Here is one way to obtain a site boundary using R:

A rectangular plot (with bounding box)

Here I set the bounding box for a plot by specifying the plot corners and elevation. Notice that it is necessary to specify the first point twice, once at the beginning and once at the end.

UPDATE sites
SET geometry = ST_Geomfromtext('POLYGON((-76.116081 42.794448 415, 
                                         -76.116679 42.794448 415, 
                                         -76.116679 42.79231 415, 
                                         -76.116081 42.79231 415,
                                         -76.116081 42.794448 415))', 4326)
WHERE
    ID = 1123;

A country boundary:

library(prevR)# for `create.boundary` function
library(sp)
library(rgeos)

UK_boundary <- create.boundary('United Kingdom')
writeLines(
  paste("insert into sites (country, sitename, geometry) values ('UK', 'United Kingdom', ST_GEOMFromText('",
         writeWKT(UK_boundary), "',4326)) ;"), con = 'uk.sql')

Then import at the command line (can also copy / paste to terminal, but this boundary is long)

psql -U bety -d bety < uk.sql

References

• PostGIS ST_GeomFromText documentation: http://www.postgis.org/docs/ST_GeomFromText.html

• gis.stackexchange: http://gis.stackexchange.com/q/111212/1239

• Github issues: https://github.com/PecanProject/pecan/issues/570