TAXREF Taxonomic Referencing made easy
TaxRef is designed to meet three needs:
For now, TaxRef is in a very early pre-release. Please use the following steps to try TaxRef.
1. Check if you have Java installed: http://www.java.com/en/download/installed.jsp
Mac OS X 10.6 and below: Java should be pre-installed.
Mac OS X 10.7 (Lion) and above: Java is not pre-installed.
Windows: depends on your computer manufacturer.
Linux: probably not, but should be available from your package manager.
If not, you should be able to install a version of Java for your
operating system from: http://www.java.com/en/download/manual.jsp
2. Download TaxRef for Windows from:
https://github.com/gaurav/taxref/blob/master/releases/build/TaxRef-devel.zip?raw=true
3. Choose a CSV dataset to validate. If you can't come up with one,
download the DwC-A file from
http://ipt.pensoft.net/ipt/resource.do?r=neembucu and unzip it. Find the
"taxon.txt" file in the unzipped directory.
4. TaxRef doesn't yet support files without a header line; however, it does
support tab-delimited files! If you're using your own checklist, make
sure that it's either tab-delimited or CSV with a header as the first
line of the line.
5. Download the ITIS DwC taxa.txt file from
http://gaurav.github.com/itis-dwca/ (right-click on
http://gaurav.github.com/itis-dwca/latest/taxa.txt and do a Save-As).
6. In TaxRef, select menu item "File" -> "Open tab-delimited" and choose
the taxon.txt.
- TaxRef automatically extracts a canonicalName (monomial, binomial
or trinomial) from the scientificName, unless a "canonicalName"
column is already defined in the input file.
- In some cases (e.g. id #1776), TaxRef cannot extract a canonical
name (from "H. leucophlaeos (Mart. ex DC.) Mattos"). However, this
is a fully editable work environment -- you can enter the correct
name into the canonicalName column if you like.
7. Select menu item "Match" -> "Match against CSV", and choose the ITIS
CSV file (I'm calling these file "DarwinCSV" files for convenience)
- The "Match" -> "Match against ITIS" menu option will automatically
download the ITIS DwC file you downloaded above and run the match.
- All matched names -- scientific names and canonical names -- will
light up in red (not matched) or green (matched).
8. If you want, you can save this file as a CSV -- the red/green match
status isn't exported yet, but the canonical name is. I hope to have it
set up so that it adds the taxonId for matched names, which can then be
exported to indicate that the name was successfully matched.
Copyright (C) 2012 Gaurav Vaidya.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.