download taxon tree?
Rick Levy
Thanks
Rick
Mary Barkworth
Would love to be able to download, preferably as a csv file (about all I can handle). Perhaps separate files for accepted names and synonyms (to assist those of us who are IT challenged).
Mary
Robert Pace
Mary Barkworth
My interest is in downloading trees, or at least names, from one Symbiota network for use in another. I invested considerable effort in looking up names and authors several insect names not in Scan. I do not want to have to repeat that work in order to b able to use them in another network. Nor do I want to overwrite names I have obtained from reputable sources (e.g., International Ornithological Union or whatever it is called) with names in ITIS. So – I really want to be able to download at least the names from one Symbiota network to use in another, possibly using a different taxonomy.
Mary
Robert Pace
Herrick Brown
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Mary Barkworth
Yes. But new feature – the ability to download from a Symbiota site. Seriously, having added names, including author names for many taxa that were not available in ITIS, I really want to avoid redoing that work. IT IS is very American (North, Central, and South) centric.
Herrick Brown
Yes. But new feature – the ability to download from a Symbiota site. Seriously, having added names, including author names for many taxa that were not available in ITIS, I really want to avoid redoing that work. IT IS is very American (North, Central, and South) centric.
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Mary Barkworth
Good point. How about the ability to download, for example, scarab names from SCAN.
Might be a more reasonable size. Then I could download other insect groups as needed. Not ideal – but better than redoing all that work.
Mary
Robert Pace
egbiodi...@gmail.com
Portal managers can pass you a flat CSV download of the taxa data using the SQL statement below. They can also run a MySQL dump of the taxa tables, but installing the dump files will copy over any other taxa data previously loaded into your system. You will need to contact them directly for this info.
Not all portals want to make their taxonomic data available as a pubic download. There are numerous taxonomic authorities that are better resourced to play that role. I only know of 2 Symbiota portals that are being used to in an attempt to establish a taxonomic authority. Most just use their internal thesaurus as a method to quickly resolve taxonomic discrepancies commonly associated with specimen data, which is the original primary purpose of the internal Symbiota thesaurus. Most thesauri are not maintained regularly enough to merit authoritative status. For this reason, using one portal’s thesaurus to create another might not be the best options (e.g. propagating error).
For various reasons, the ITIS import has been problematic to maintain and thus is being replaced with some new tools (note: ITIS imports will still be possible through the generic flat-file taxonomic import tool). An alternative method of building your thesaurus is to load your collection data (does not initially require a taxonomic thesaurus to exist) and then use the taxonomic cleaning tools (made available within collection management menu as of Sept 2017) to evaluate the names associated with specimen data. This tool makes use of web services available from Catalog of Life, WoRMS, TROPICOS, and/or EOL to validate and import scientific names, authors, acceptance status, and full taxonomic hierarchy. These resources tend to be more actively maintained, and thus are often a better taxonomic data source for setting up a new portal. The preferred taxonomic authorities can be activated within the portal’s configuration file ($TAXONOMIC_AUTHORITIES variable). TROPICOS web services requires an API key that needs to be requested from them. Once the tool has been fully tested, it will be integrate into the checklist module and the taxonomic import tool. We are also planning on soon adding Index Fungorium or MycoBank as an authority option.
SELECT t.tid, t.kingdomName, ts.family, t.sciname, t.author, t.unitname1, t.UnitInd1, t.unitname2, t.UnitInd2, t.unitind3, t.unitname3,
t.rankid, t.SecurityStatus, ts.parenttid, t2.sciname as parentStr, ts.tidaccepted, t3.sciname as acceptedStr
FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid
INNER JOIN taxa t2 ON ts.parenttid = t2.tid
INNER JOIN taxa t3 ON ts.tidaccepted = t3.tid
WHERE ts.taxauthid = 1;
-Ed
Mary Barkworth
The problem I had in the early days of creating a network was that uploading a new taxonomy did not overwrite the existing one, it often created a second usage of a name that was then in conflict with the previous usage – but both were in the system. In the end, I had Curtis delete all names that had two different parent taxa.
As I noted earlier, it is subsets of taxa that I want to be able to copy, those that I have added to one portal by consulting other sources such as those suggested by Ed. I would add one other source – Wikipedia – particularly for authors of higher level taxa of animals. The times that I checked, it was reliable.
Mary