�ݺ�ߣ

MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/
Step by step tutorial:
ModestR tools to work with GBIF and ITIS
taxonomy databases

What do you need for this tutorial:
1. ModestR 6.5 or higher
2. Internet connection
3. About 20 minutes
ModestR software can be freely downloaded from http://www.ipez.es/ModestR

We��ll describe 3 tools provided by ModestR to work
with taxonomic data. (1) ModestR can use GBIF or (2)
ITIS taxonomic database to explore and export
taxonomic data.
(3) It can also use GBIF to check and complete
taxonomic data from a list of species.

1. Explore GBIF taxonomy database
and export data.
Optionally, import those data to
DataManager

One feature provided by ModestR is a simple GBIF Backbone Taxonomy explorer.
This feature is included in the DataManager application. Therefore, to test it, we��ll start by running ModestR DataManager.
If you already have created a ModestR database, you can open it. Otherwise, just go to the File >> New Taxonomy database
menu option and create a new database called ��MymodestRDatabase��. This is just because some DataManager menus are
enabled only if a ModestR database is opened.

Now we��ll explore the GBIF Backbone Taxonomy (from now on GBIFBT). A selection of this database that mainly includes
accepted taxa is distributed with ModestR (later we��ll explain how to download new updates of this database from GBIF
and import them to ModestR).
Go to menu Import >> Import Taxonomy >> From GBIF Backbone Taxonomy. Then wait for a moment while data are
loaded��. (this is a large database!).

A browser integrated in DataManager will appear, allowing you to explore GBIFBT. You can eventually export data to a CSV
file (easily read by worksheets such as Excel), or use the search tool to find specific taxons.
In the left panel, two
tabs allow to go to
export feature, and to
search tool
In this panel, a
tree allows you to
easily explore
GBIFBT database.

To use the search tool, select the Search tool tab. You can write the first letters (at least 3 letters are required) of a taxon to
search for it in the database. Take into account that this can require some time.
Select the Search tool tab.
Then write the first letters (at
least 3 letters are required) of a
taxon to search and click on
��Update results��
Result will appear on this list.
Clicking on any of the results, it
will be highlighted in the left
tree (this can require some
time)
To limit a search and make it
faster, you can first uncheck
the kingdoms you want to
exclude from the search.

Once found the taxa you are interested in, you may export them to a CSV file. To do that, just check the wanted taxa in the
left tree. You can check any rank (classes, families��.). Then select the levels to be exported on the right panel and click the
��Export to file�� button. Or you can directly import them to the current database clicking on ��Add to database��.
Select the Export options tab.
Check on the left tree the taxa
that contain the species to be
exported.
Select the levels to be exported.
By default, class, order, family,
genus and species are selected. If
you don��t include a level, the
information for this level for each
species will not be included in the
exported result.
You can eventually want to directly
import selected taxonomic data to the
current ModestR database. But this
option will only be enabled if
exclusively class, order, family, genus
and species are exported, because
they are the ranks supported by
ModestR.

The exported file, opened with a worksheet application, will look like this:
The selected levels
are included in the
exportation
If you optionally choose to directly
import taxa to the current database,
they will appear in the taxonomic tree
of Datamanager.

As explained before, ModestR includes a selection of the GBIFBT database that mainly includes accepted taxa. This
database is regularly updated, so you may eventually want to download the last version from GBIF and import it to
ModestR. To do that you can go to menu Import >> Import Taxonomy >> From GBIF Backbone Taxonomy, then click on the
button ��Taxonomy website��. This will open a web browser and go to GBIF Backbone Taxonomy site.

In this page, search for a link to the page where you can download GBIF Backbone Taxonomy site.
When this tutorial was done, this link was http://rs.gbif.org/datasets/backbone/

Then locate and download the file ��backbone-current-simple.txt.gz��. It is a large file so this may require some time.

The next step is to uncompress the file ��backbone-current-simple.txt.gz��. You will obtain a file named ��backbone-
simple.txt�� that can have a size of more than 2 Gb.

Now go back to DataManager, where we have left the GBIF taxonomy browser opened. Then click on the button ��Import
new version�� and, in the dialog that will appear, select the file ��backbone-simple.txt�� you have downloaded and
uncompressed previously.

The importation process will start. This can take several minutes, as the GBIFBT contains several millions of species.
If all goes well, the new database will be imported and stored into ModestR and shown in the GBIFBT browser.
The date of the last imported file is shown at the bottom of the GBIFBT browser.

2. Explore ITIS taxonomy database and
export data.
Optionally, import those data to
DataManager

One feature provided by ModestR is a simple ITIS database explorer. ITIS is and Integrated Taxonomic Information System,
online at http://www.itis.gov/ . But to use those data, you should first download them, following those steps:
2. In the left side menu, select
Get ITIS Data >> Full Database
Download >> Database Files
1. Go to http://www.itis.gov/
the web site of the Integrated
Taxonomic Information System

4. Uncompressed the downloaded
file, you��ll obtain a file named
��ITIS.sqlite��
5. Now you can explore and import
taxonomic data from the ITIS
database using ModestR
DataManager.
3. Download the Full ITIS Data Set (SQLite) --
itisSqlite.zip to a folder of your computer

ModestR can help users to explore taxonomic data and to check or complete it. Those features are gathered in the
DataManager application. Therefore, to test them, we��ll start by running ModestR DataManager. If you already have
created a ModestR database, you can open it. Otherwise, just go to the File >> New Taxonomy database menu option and
create a new database called ��MymodestRDatabase��. This is just because some DataManager menus are enabled only if a
ModestR database is opened.

Now we��ll explore the ITIS taxonomic database we have previously downloaded. Go to menu Import >> Import Taxonomy
>> From ITIS database >> ITIS database browser tool. A dialog box will be shown, where you should select the previously
uncompressed file ��ITIS.sqlite��. Then wait for a moment while data are loaded��. (this is a large database!).

A browser integrated in DataManager will appear, allowing you to explore ITIS database. You can eventually export data to
a CSV file (easily read by worksheets such as Excel), or use the search tool to find specific taxons.
In the left panel, two
tabs allow to go to
export feature, and to
search tool
In this panel, a
tree allows you to
easily explore ITIS
database.

To use the search tool, select the Search tool tab. You can write the first letters (at least 3 letters are required) of a taxon to
search for it in the database. Take into account that this can require some time (occasionally a long time��). You can make it
faster by firstly unchecking the kingdoms you want to exclude from the search.
Select the Search tool tab.
Then write the first letters (at
least 3 letters are required) of a
taxon to search
Result will appear on this list.
Clicking on any of the results, it
will be highlighted in the left
tree (this can require some
time)
To limit search and make it
faster, you can first uncheck
the kingdoms you want to
exclude from the search.

Once found the taxons you are interested in, you may want to export the corresponding data to a CSV file. To do that, just
check the wanted taxons in the left tree. You can check any rank (classes, families��.). Then select the levels to be exported
on the right panel and click the Export button.
Select the Export options tab.
Check on the left tree the
taxons that contain the species
to be exported.
Select the levels to be exported.
By default, class, order, family,
genus and species are selected. If
you don��t include a level, the
information for this level for each
species will not be included in the
exported result.
You can eventually want to directly
reimport exported taxonomic data to
the current ModestR database. But
this option will only be enabled if
exclusively class, order, family, genus
and species are exported, because
they are the ranks supported by
ModestR.

The exported file, opened with a worksheet application, will look like this:
The selected levels
are included in the
exportation

3. Using GBIF to check and complete
taxonomic data from a list of species.

Now we��ll see another feature provided by ModestR to work with taxonomic data. That is a tool that can complete
taxonomic data from a list of species (only species are currently supported), and check them to detect synonyms or
probably inappropriate names. This feature uses GBIF online database. To use this tool, the first step is to create a CSV file
with the list of species to be checked. This can be done in a worksheet, then saved as CSV file, or even in a simple text
editor such as Notepad, and saved with the ��CSV�� extension.
Worksheet saved as CSV file

Now go to menu Import >> Import Taxonomy >> GBIF taxonomy search tool. A dialog box will be shown, where you should
select the previously created CSV file with the list of species.

In the next dialog box, select if the file contains a header (in this case first line it will be skipped), and the field separator
(this only be used when using files with more than one column). Most of the times, default options will be OK and you just
have to click the Accept button.

The a dialog box will allow you to select the target file where result will be saved. Once accepted, the checking process will
start. You need to be connected to Internet because this tool uses GBIF web services to retrieve taxonomic data.

1. Class, order, family, genus, species, for each original species of the input file.
2. Accepted: indicates using a 1 (=yes) or a 0 (=no) if the original species is a species flagged as accepted by GBIF.
3. OriginalName: is the original species name of the input file (that can be different from the name returned by GBIF, in case of
synonyms or corrections)
4. Corrected: indicates if yes (=1) or a no (=0) GBIF returned a correction for the original species name.
5. Confidence: when a correction has been suggested, this indicates its % confidence according to GBIF
6. IsSynonym: indicates if yes (=1) or a no (=0) GBIF considered that the original species name was a synonym of the returned species
name.
7. Observations: other observations, if any. They can indicate that this species may not be considered as the most appropriate by GBIF.
If eventually a species was not found in GBIF, it is also indicated here.
Once finished, the exported file will contain several columns with different information

The results returned by this tool are not intended to be absolutely authoritative, thus it is very recommended to carefully
review them. But this can be a useful tool to help checking species names and to easily obtain for the higher ranks.
The returned file, once reviewed, can be directly imported by DataManager to add those species to a ModestR database.
See the tutorial How to create a ModestR database for more information.

It was the
Step by step tutorial:
ModestR tools to work with taxonomic data
Thank you for your interest.
MODESTR QUICK TUTORIALS HTTP://WWW.IPEZ.ES/MODESTR/?
You can find this one and other tutorials in
http://www.ipez.es/ModestR
By the ModestR team
Colaborators:
Estefan��a Isaza Toro

�ݺ�ߣ

7.- ModestR tools for taxonomy (Version ModestR v6.5 or higher)

More Related Content

7.- ModestR tools for taxonomy (Version ModestR v6.5 or higher)