Step by step tutorial: How to create a ModestR database · 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

Step by step tutorial: How to create a

ModestR database

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http://www.ipez.es/ModestR/





What do you need for this tutorial:

1. ModestR software installed 2. Internet connection 3. About 15 minutes

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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”.



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. You can download the sample file Ipez.CSV from the ModestR website, or using this link.


A CSV file with taxonomy data to be imported Columns should be: class, order, family, genus and species

http://www.ipez.es/ModestR/Documents/Tutorial_stepbystep/IPez.csv


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 Callorinchidae family. Then follow the

next steps!


http://www.gbif.org/


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


2. Select to import data from GBIF for all the species of the wanted taxon


1. In the tree, click with the right mouse

button over the wanted taxon

“Callorinchidae” to see contextual menu

2. Select the option Import presence data

for this branch

3. Then select “From GBIF samples”


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.


Select valid habitats for the species. In this case, just check Sea and click

on Accept button

Remember that you can obtain a short help of

any option just by placing the mouse

cursor over the corresponding element.

You may find detailed information about all

options in the ModestR Tutorial available on

the ModestR Website


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

Synonyms for the species that are

automatically found and used


7. When downloading 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 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, data sources, rights

and citations.


8. You can click on one download species to see it in the tree and open it in MapMaker.


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)

Globe icon aside the species indicates that

this species has a distribution map

stored in the database

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.


Samples (occurrence records) are shown

on the map in different colors

depending on if they are located in a valid or an invalid habitat.


9. 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.


Go to Search page and check options Show only branches with maps and Show only species with

maps.

Note: remember to verify those settings when you open

DataManager. It is because of them that some taxons can be hidden.

Only the species with maps will be shown.


10. That’s all for now. You can just close DataManager. Data are automatically stored in the database. Remember that the next time you run DataManager it will automatically try to open the last database you used, and usually filter species to only show those which have maps. But now you already know how to change those settings!



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




