step by step tutorial- modestr tools for taxonomy

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Step by step tutorial: ModestR tools to work with taxonomic data

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

What do you need for this tutorial:

1. ModestR v3.2 or higher2. Internet connection3. About 20 minutes

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


http://www.ipez.es/ModestR



We’ll describe some tools provided by ModestR to work with taxonomic data. ModestR can use ITIS

taxonomic database to explore and export taxonomic data.

It can also use GBIF to check and complete taxonomic data from a list of species.

Follow the next steps!



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:

1. Go to http://www.itis.gov/ , the web site of the Integrated Taxonomic Information System2. In the left side menu, select Get ITIS Data / Full Database Download / Database Files



3. Download the Full ITIS Data Set (SQLite) --itisSqlite.zip to a folder of your computer

4. Uncompress 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.



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 right panel, a tree allows you to easily explore ITIS database.

In the left panel, two tabs allow to go to export feature, and to search tool


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 itfaster 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 datato 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 taxonsthat 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.

Just click on the Export button.


The exported file, opened with a worksheet application, will look like this:


The selected levels are included in the exportation


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.



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.



Once finished, the exported file will contain several columns:• Class, order, family, genus, species, for each original species of the input file.• Accepted: indicates using a 1 (=yes) or a 0 (=no) if the original species is a species flagged as accepted by GBIF.• 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)• Corrected: indicates if yes (=1) or a no (=0) GBIF returned a correction for the original species name.• Confidence: when a correction has been suggested, this indicates its % confidence according to GBIF• IsSynonym: indicates if yes (=1) or a no (=0) GBIF considered that the original species name was a synonym of the returned species

name.• 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.



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.


http://www.slideshare.net/modestrsoftware/step-by-step-tutorial-1-how-to-create-a-database

http://www.slideshare.net/modestrsoftware/step-by-step-tutorial-1-how-to-create-a-database


It was theStep by step tutorial:

ModestR tools to work with taxonomic data

Thank you for your interest.

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You can find this one and other tutorials in http://www.ipez.es/ModestR



step by step tutorial- modestr tools for taxonomy

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