set_scientific_name#
One of the functions you can use to check certain columns of your data is set_scientific_name().
This function aims to check that you have the following Darwin Core Vocabulary Terms:
scientificName: the scientific name of the species you observed
It can also can check the following:
scientificNameRank(OPTIONAL): rank of the scientific name you are providing.scientificNameAuthorship(OPTIONAL): Authors of the species name you are using.
specifying scientificName#
Like with other set_* functions, to specify which column you want to rename or change, you
specify it with the Darwin Core term. In this case, it is scientificName.
>>> my_dwca.set_scientific_name(dataframe=occ,scientificName='Species')
>>> my_dwca.occurrences.head()
scientificName Latitude Longitude Collection_date
0 Corymbia latifolia -13.04 131.07 29/3/2022
1 Eucalyptus tectifica -13.04 131.07 13/9/2022
2 Banksia aemula -33.60 150.72 15/8/2022
3 Eucalyptus sclerophylla -33.60 150.72 16/6/2022
4 Persoonia laurina -33.60 150.72 19/10/2022
what does check_data and suggest_workflow say now?#
Note: each of the set_* functions checks your data for compliance with the
Darwin core standard, but it’s always good to double-check your data.
Now, we can check that our data column do comply with the Darwin Core standard.
>>> my_dwca.set_scientific_name(dataframe=occ,scientificName='Species')
>>> my_dwca.check_dataset()
Number of Errors Pass/Fail Column name
------------------ ----------- --------------
0 ✓ scientificName
══ Results ════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════════
Errors: 0 | Passes: 1
✗ Data does not meet minimum Darwin core requirements
Use corella.suggest_workflow()
However, since we don’t have all of the required columns, we can run suggest_workflow()
again to see how our data is doing this time round.
>>> my_dwca.suggest_workflow()
── Darwin Core terms ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── All DwC terms ──
Matched 1 of 4 column names to DwC terms:
✓ Matched: scientificName
✗ Unmatched: Collection_date, Latitude, Longitude
── Minimum required DwC terms occurrences ──
Type Matched term(s) Missing term(s)
------------------------- ----------------- ------------------------------------------------
Identifier (at least one) - occurrenceID OR catalogNumber OR recordNumber
Record type - basisOfRecord
Scientific name scientificName -
Location - decimalLatitude, decimalLongitude, geodeticDatum
Date/Time - eventDate
── Suggested workflow ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
── Occurrences ──
To make your occurrences Darwin Core compliant, use the following workflow:
corella.set_occurrences()
corella.set_coordinates()
corella.set_datetime()
Additional functions: set_abundance(), set_collection(), set_individual_traits(), set_license(), set_locality(), set_taxonomy()
Other functions#
To learn more about how to use other functions, go to
Optional functions:
Creating Unique IDs:
Passing Dataset: