1. How to create a database (Version ModestR v6.5 or higher)

Step by step tutorial:
How to create a
ModestR database
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/

What do you need for this tutorial:
1. ModestR v.6.5 or higher
software installed
2. Internet connection
3. About 15 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR

We’ll describe how to create a new
ModestR database, how to populate it
using taxonomic data stored in a CSV
file. Follow the next steps!

1. Run ModestR DataManager, go to the File/New Taxonomy database menu option and create a new database called
“MymodestRDatabase”.
Create a new database

The next step is creating a new taxonomy in the database. There are two options to do that:
a) Importing a CSV file that contains the taxonomy we want to add to the database.
or
b) Importing a taxonomy range from GBIF Backbone taxonomy.
In the next step of this tutorial we’ll explain the option a).
But you also use the option b) which is explained in the tutorial ModestR tools to work with GBIF and ITIS taxonomy
databases.

2. Import taxonomy data from a CSV file using the menu Import/Import taxonomy/From CSV file. Select the wanted CSV
file to be imported. For this example, you can download the sample file Ipez.CSV from the ModestR website (see
Help&Doc/Manual and tutorials section).
A CSV file with taxonomy data to
be imported. Columns should be:
class, order, family, genus and
species

3. A dialog box will ask you about the format of the CSV file to be imported. Accept defaults if you are using the sample
CSV file provided for this tutorial. If not, adjust the settings according to your CSV file format.
Set importation format settings
(accept defaults if you are using the
sample CSV file provided)

4. Once the importation ended, you will see a taxonomy structure in DataManager:
Click on any node to expand it

Now, let’s suppose you want to
download occurrence data from GBIF
online database for all species of
Callorhinchidae family. Then follow the
next steps!

1. Go to Search page on the right panel to easily search for the wanted taxon, just by entering part of its name:
1. Go to Search page
2. Write the first letters of the taxon (“Callo”)
3. Search results will appear by levels. Just
click on the wanted taxon to see it selected
in the tree
4. Check this node, to work
just with this branch.

2. Select to import data from GBIF for all the species of the wanted taxon
1. Check the “Callorhinchidea”
branch
2. Go to menu “Import” and select the option
“Import presence data for this branch”
3. Then select “From online GBIF database”

3. As a security measure, DataManager will warn you that this operation will modify database contents and therefore
propose you to do a backup. But for this example it is not necessary, so we’ll say “No”.
For this example, answer
“No” to the message box.
But for real usage, it may be
prudent to answer “Yes” to
make a backup copy of a
database before doing an
important modification

4. You may accept GBIF terms.

5. Then you’ll have to
set GBIF
importation
options. But for
this example, you
can just indicate
the valid habitats
and accept the
other default
settings.
Note: You may find detailed information
about all options in the ModestR User
Manual available on the ModestR
Website
Remember that you
can obtain a short help
of any option just by
placing the mouse
cursor over the
corresponding
element.
Select valid habitats
for the species. In this
case, just check “Sea”
and click on “Accept”
button

6. Downloading will start automatically. Data for each species will be downloaded and stored in the database. Just wait
for the task to be finished.
Species currently being
downloaded
If a species is considered a
synonyms according to GBIF,
the main species is
automatically found and used

7. When download task is completed, the list of imported species maps is displayed, as well as an importation log that
you can save to a file to keep information about data sources, rights and citations. Here we have downloaded data
for all the species of a whole family. But you can do the same for any taxonomic level, from class to species.
List of imported species maps
is displayed
You can copy or save the
importation log to keep
information about synonyms
used, data downloaded, and
data sources.

8. You can click on one download species to see it in the tree and open it in MapMaker.
Globe icon aside the species indicates
that this species has a distribution map
stored in the database
1. Click on one species in the
list of downloaded species
(you can also search it in the
Search page or go to it
directly in the tree)
2. In the tree, click with the
right mouse button over the
wanted species to see
contextual menu, and select
Open map in MapMaker

9. MapMaker will be ran and automatically displays the selected species.
Occurrences are shown on the map in
different colors depending on whether
they are located in a valid or an invalid
habitat.

10. Close MapMaker and go back to DataManager. You can filter database records to only see the species that have
distributions maps. This is usually the default filtering when you open DataManager.
Note: remember to verify those settings when
you open DataManager. Some taxons may be
hidden because of those settings , leading to
wrongly think that they are missing.
Only the species with maps will be shown.
Go to “Search page” and check options “Show only
branches with maps” and “Show only species with maps”

11. You can just close DataManager. Data are automatically stored in the database. Remember that the next time you are
running DataManager it will automatically try to open the last database you used, and usually filter species to only
show those which have maps. To permanently change the filters settings go to “Options”-”Preferences” menu. That’s
all for now!
1. Go to “Options”-”Preferences” menu
Select both filters
and click on
“Accept” button

It was the
Step by step tutorial:
How to create a ModestR database
Thank you for your interest.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/º
You can find this one and other tutorials in
http://www.ipez.es/ModestR
By the ModestR team
Colaborators:
Estefanía Isaza Toro

1. How to create a database (Version ModestR v6.5 or higher)

Recommended

Recommended

More Related Content

What's hot

What's hot (11)

Similar to 1. How to create a database (Version ModestR v6.5 or higher)

Similar to 1. How to create a database (Version ModestR v6.5 or higher) (20)

Recently uploaded

Recently uploaded (20)

1. How to create a database (Version ModestR v6.5 or higher)