How to aquire and add 'Aphia' taxon tree

Home Forums User Forum How to aquire and add 'Aphia' taxon tree

This topic contains 3 replies, has 3 voices, and was last updated by Norine Spears Norine Spears 1 month, 2 weeks ago.

Viewing 4 posts - 1 through 4 (of 4 total)
  • Author
    Posts
  • #3181
    Avatar
    NZmollusca

    Hello,
    I am a new user and I will be using Specify 6 for New Zealand Mollusc databasing only.
    I have been advised that the best taxon catalogue (if that’s the right term) is called ‘Aphia’ which uses the WoRms (World registar of Marine species) taxa / taxon tree. I have been advised that it is also self updating via Specify 6. I have done some google searching and have searched the forums here but I can’t seem to find where I can download or implement the ‘Aphia’ system into Specify 6. Can anyone help with this please?

    many thanks,
    Jason

    #3187
    Avatar
    Plarson

    I don’t know anything about the self-updating, but you can upload a taxon tree structure of your choosing when you initialize your collection, and whatever other corresponding data you wish to include. When I moved to Specify, I was only switching platforms, so I used the taxon tree from my former database. There is also a ready-to-go taxon tree you can use when you set up the database, but I don’t know if it includes AphiaID (or the related WoRMS LSID).

    Also know that Specify forces you to have a complete taxon tree for all the major ranks (KPCOFGS) – so with mollusks you’re going to have to make some dummy taxa for ranks where there’s no agreement on placement (e.g., in WoRMS, Family Patellidae has no Order, but Specify will force you to put in an ordinal name).

    -Paul

    #3188
    Avatar
    Plarson

    Sorry, I didn’t actually answer your question on how to get the tree.

    There doesn’t seem to be a way (that I can find) to download the taxon tree or any parts of it from WoRMS. If the built-in tree in Specify doesn’t contain AphiaID, then there’s one other way I can think of.

    If you have a list of all the species you will be cataloging in your database, you can use the MatchTaxa tool in WoRMS to compare your species against the species names listed in WoRMS. When you select your outputs, make sure you check AphiaID, and Classification. Then, even if you start with just species names, you will get the higher classification for those species and when you create your taxon tree in the Workbench in Specify, you can assign AphiaID to a field of your choosing in your database.
    -Paul

    #3201
    Norine Spears
    Norine Spears

    Hi all,

    Thank you for posting answers Paul! I just want to add that we have had users upload their Taxon Authority from WoRMS through the WorkBench using spreadsheets. If you email us at support@specifysoftware.org I will be happy to send you an example. Also, it is possible to ‘un-enforce’ any level of the trees through MySQL and ,Paul, since we host your data we can do that for you at any time, please email if this is appealing.

    Sincerely,
    – Norine

Viewing 4 posts - 1 through 4 (of 4 total)

You must be logged in to reply to this topic.