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Importing Taxa
layout: post title: “Importing taxa (taxonomic tree)” author: “Laura” tags: —
When uploading taxa to Symbiota using the “batch upload” tool, the spreadsheet to be uploaded may include the following fields:
| FRONT-END (taxaloader.php) | FRONT-END explanation |
|---|---|
| acceptance | 0 = not accepted, 1 = accepted (default 1) |
| acceptedstr | accepted name (if 1, it will be equal to sciname) |
| author | RECOMMENDED, author of sciname |
| class | |
| errorstatus | ? |
| family | |
| genus | |
| hybrid | |
| infraauthor | author of infraspecific epithet |
| infraspecificepithet | |
| initialtimestamp | |
| kingdom | |
| notes | |
| order | |
| organism | ? |
| parentstr | RECOMMENDED, parent taxon (literal name of taxon, for instance, Mollusca) |
| phylum | |
| rankid | id of rank found in table taxonunits (i. e. Kingdom = 10, Species = 220) |
| rankname | i. e. species, genus, class, etc. |
| sciname | only full scientific name (without author) |
| scinameinput | REQUIRED, full scientific name with or without author |
| section | |
| securitystatus | |
| source | |
| sourceacceptedid | |
| specificepithet | |
| subclass | |
| subfamily | |
| subgenus | |
| subkingdom | |
| suborder | |
| subphylum | |
| subsection | |
| subtribe | |
| superclass | |
| taxonrank | |
| tribe | |
| unacceptabilityreason | |
| vernacular | |
| vernlang |
A great number of taxonomic fields can be uploaded for a single record. Taxonomic fields, ordered by level of inclusion (greater to lower):
- organism
- kingdom
- subkingdom
- phylum
- subphylum
- superclass
- class
- subclass
- order
- suborder
- tribe
- subtribe
- family
- subfamily
- section
- subsection
- genus
- subgenus
- sciname/scinameinput
- specificepithet
- infraspecificepithet
The uploaded taxa are then processed into different tables, to generate/rearrange the taxonomic tree:
- Table
taxa: information about one particular taxon, with theirSciName,KingdomName,RankID,SecurityStatus, etc. - Table
taxaenumtree: relationships between taxa, established pair-to-pair, by theirTIDs (taxaauthidandparenttid).
Therefore, the minimum taxonomic levels required for Symbiota to generate a taxonomic tree are the full species name (least inclusive name, could be Genus + Specific epithet or even any taxonomic level), and Kingdom, and preferrably their parent taxon name (field parentstr).
For some groups, records can be uploaded with the full taxonomic information (when available), and then cleaned up using the Data Cleaning Tools. For other groups (namely those without a robust electronic Taxonomic Authority such as ITIS/EOL), it’s better if the taxonomic trees are uploaded first, with the more inclusive levels being added also first.