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https://github.com/gaurav/taxref

TaxRef, a basic taxon name validator
https://github.com/gaurav/taxref

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TaxRef, a basic taxon name validator

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README 

        
TAXREF

Taxonomic Referencing made easy



1. INTRODUCTION



TaxRef is designed to meet three needs:

    1.  Taxonomic validation: given a list of potentially correct

        taxon names, identify the currently accepted name corresponding

        to that taxon name, or record the name as being invalid.

        e.g. given "Fellis tigris", validate the name as a mistype of

        "Felis tigris", which is a junior synonym of "Panthera tigris".

    2.  Taxonomic referencing: given a valid taxon name, fill in

        higher taxonomy corresponding to that name. Note that this

        will need to be against a particular taxonomic checklist.

        e.g. given "Panthera tigris", identify the family ("Felidae"),

        order ("Carnivora"), class ("Mammalia"), phylum ("Chordata"),

        kingdom ("Animalia") and optionally domain ("Eukarya").

    3.  Checklist comparison: given multiple taxonomic checklists,

        identify differences between them and provide summaries as

        to those differences.

        e.g. one checklist might have "80% (n=4) of the names in

        genus 'Panthera'" as the other checklist.



2. HOW TO USE IT



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.



3. COPYRIGHT



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 .