how to create a modestr database

Step by step tutorial: How to create a

ModestR database

MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/

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

What do you need for this tutorial:

1. ModestR v.4 or higher software installed

2. Internet connection3. About 15 minutes

ModestR software can be freely downloaded from http://www.ipez.es/ModestR


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


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 Documentation section), or using this link.


A CSV file with taxonomy data to be importedColumns 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. Justclick on the wanted taxon to see it selectedin 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. Once checked the “Callorhinchidea” branch…

2. Go to menu “Import” and 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.


Note: You may find detailed informationabout all options in the ModestR Tutorialavailable 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 a synonyms according to GBIF, main

species is 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, 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 downloadedspecies (you can also search it in the Searchpage or go to it directly in the tree)

2. In the tree, click with the right mouse buttonover the wanted species to see contextualmenu, 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.


Note: remember to verify those settingswhen you open DataManager. It is becauseof them that some taxons can be hidden.

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”


10. 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. 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 theStep 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



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