The GBIFTaxa worksheet

This worksheet exists to record taxonomic in information for organisms referred to in the Data worksheets. This taxonomic information should be recorded in a format that can be validated against the GBIF backbone taxonomy. Generally the GBIF backbone taxonomy is most suitable for taxa discovered via direct observation (rather than sequencing), so this worksheet is most appropriate for storing the details of directly observed taxa. If taxa are used anywhere in the dataset either this worksheet or the NCBITaxa worksheet must be included. It is also an option to provide both a GBIFTaxa worksheet and a NCBITaxa worksheet, e.g. in cases where both sequencing and direct observational data are being reported.

GBIF Taxon validation

In order to help keep the taxonomy as clean as possible and to allow us to index the taxonomic coverage of datasets, we will check all taxon names in GBIFTaxa worksheet against the GBIF backbone taxonomy database. If you want to check your taxon names and ranks, then the search engine is here:

https://www.gbif.org/species/search

No online taxonomy is ever going to be 100% up to date (or 100% agree with your taxonomic usage!) but the GBIF backbone has very good taxonomic coverage and is well curated.

Taxon table layout

The table format looks like this:

Name	Taxon name	Taxon type	Taxon ID	Ignore ID	Parent name	Parent type	Comments
crbo	Crematogaster borneensis	Species
dolic_sp	Dolichoderus	Genus
gannets	Morus	Genus	2480962
lost_orang	Pongo tapanuliensis	Species			Pongo	Genus	New species
morpho1	NA	Morphospecies			Formicidae	Family
bombines	Bombini	Tribe			Apidae	Family
micr_hid	Microcopris hidakai	Species		1090433	Microcopris	Genus

The table must contain column headers in the first row of the worksheet. The first three columns (Name, Taxon name and Taxon type) are mandatory and contain the following:

Name: This column must contain a local name for all of the taxa that you are going to use in the rest of the dataset. You cannot have duplicated names! Note that these can be abbreviations or codes: if you want to use Crbe in your data worksheets, rather than typing out Crematogaster borneensis every time, then that is fine.

Note

These are the names that you are going to use in your data worksheet. The other columns are to help us validate the taxonomy of your names.

Taxon name: This column must contain the scientific name of the taxon, which will be used for taxon validation via GBIF. Note that this should not include any taxon authority, so Panthera tigris not Panthera tigris (Linnaeus, 1758).
Taxon type: This column must provide the taxonomic type of the named taxon, which is usually the taxonomic rank. For example, the taxon Pongo pygmaeus would be of type Species and the taxon Formicidae would be of type Family. If the taxon type is not one of the core GBIF backbone ranks ( Kingdom, Phylum, Order, Class, Family, Genus, Species and Subspecies), or is one of the special values Morphospecies or Functional group, then you will need to provide a parent taxon (see below).
Comments: This is entirely optional - if you have a fairly standard set of taxa with no serious issues then you can leave it out entirely or it can be empty. If you do have particular notes that you want to make - explaining disagreements with GBIF taxonomy, new species notes and the like - then these can be very useful for future researchers trying to place taxa.

The other fields are optional and are used to handle the following taxonomic issues. You only need to put anything in these optional fields for the rows they apply to: leave them blank for all other rows as in the example table above.

Ambiguous taxon names

Some taxon names map to more than one taxon. For example, the genus Morus can refer to either mulberries or gannets. The checking code will raise an error if it encounters an ambiguous name. In these rare cases, you will need to look up the taxon in GBIF and provide the GBIF ID number in the Taxon ID field.

The example in the table allows us to confirm that you mean this Morus: https://www.gbif.org/species/2480962.

Incorrect GBIF taxonomy

In general, we follow the GBIF 'accepted usage' of a taxon name and this includes following when GBIF say a taxon is a synonym. We include your taxon name in our taxonomic indices, but under the taxonomic hierarchy suggested by GBIF.

In the example in the table, GBIF asserts that Microcopris hidakai is a synonym of Onthophagus hidakai and so our taxonomic index will include both those names under the parent genus Onthophagus. The taxon validation of your dataset does warn about this in the output:

? Row 7 (micr_hid): considered a homotypic_synonym of Onthophagus hidakai (1090433) in GBIF backbone

If you strongly disagree with that accepted usage, then you can use the Ignore ID field to explicitly ignore the GBIF match. You will need to insert the GBIF ID number of the accepted usage (reported in the warning message) in this field. You will then need to provide a parent taxon (see below)

Parent taxon details

If a taxon name cannot be matched against GBIF, then you will need to provide details of a parent taxon. This is a taxon that can be validated in GBIF and provides a hook to allow us to place the child taxon in the backbone taxonomy. Note that you should still provide the taxon information as usual.

In these cases, the next three columns (Parent name, Parent type and Parent ID) are used to provide a parent taxon. They are used in exactly the same way as the Taxon columns: the only restriction is that the Parent type must be one of core ranks used in the GBIF backbone: Kingdom, Phylum, Order, Class, Family, Genus, Species and Subspecies. Again Parent ID is only needed to resolve ambiguous taxon names.

The table shows examples for the following cases:

New and unrecognized taxa

If a taxon is new or not recognized by GBIF (and you're sure it isn't just a typo!) then provide a parent name and type to allow us to hook the taxon into the index. For example, before Pongo tapanuliensis was recognised as a species, you would need to provide Pongo as a parent name of type 'genus',

You would then get a message in the file validation report saying:

- Row 4 (lost_orang): not found in GBIF but has valid parent information

Morphospecies and Functional groups

For morphospecies and functional groups, the Taxon type should be specified as 'Morphospecies' or 'Functional group'. The Name field should be filled in with whatever name is used to label it in the dataset. In this case, the Taxon name field is not checked or used anywhere in the validation process, so can be filled in with whatever you wish. However, this the field still has to be filled out. If you do not wish to provide a name here, we recommend just filling it in with 'NA'.

Now you need to provide a parent taxon and type. The level of taxonomic certainty for morphospecies and functional groups is quite variable, but we'd like the finest taxonomic level you can provide. As an example, in the table above, 'Morphospecies #1' is simply identified as being an ant. The validation report will show:

- Row 5 (morpho1): Morphospecies with valid parent information

Less common taxonomic levels

If you want to use taxa defined at any intermediate taxonomic levels that are not included in the GBIF backbone, then you will again need to provide a parent taxon. In the example in the table, taxa identified to tribe level (Bombini) are hooked in as being in the family Apidae. The subfamily Apinae would be more precise, but subfamily isn't one of the backbone taxonomic levels.

Ignored taxa

If you have set an Ignore ID value for a taxon, then that is explicitly rejecting the parent taxon that we would naturally use from GBIF and so you will need to provide a replacement. The example in the table is explicitly saying that Microcopris hidakai is not a synonym but is a separate taxon that belongs in Microcopris.

Deleted taxa

The GBIF backbone also includes a large number of deleted taxon ids: these are a mix of duplicated names, typos in the database and other errors. The GBIF ID of these taxa are preserved, along with some information, but we do not allow deleted taxa to be used in the GBIFTaxa worksheet.

My data doesn't contain taxa

Fine. You can omit either or both of the GBIFTaxa and NCBITaxa worksheets!