Look Up Information#
There are two simplified functions to look up information:
galah.show_all()
galah.search_all()
galah.show_values()
galah.search_values()
These are individual functions that are able to return all types of information in one place, rather than using specific sub-functions to look up information.
For example, to show all available Living Atlases supported:
>>> galah.show_all(atlases=True)
atlas institution acronym url
0 Australia Atlas of Living Australia ALA https://www.ala.org.au
1 Austria Biodiversitäts-Atlas Österreich BAO https://biodiversityatlas.at
2 Brazil Sistemas de Informações sobre a Biodiversidade Brasileira SiBBr https://sibbr.gov.br
3 Flanders Vlaams Biodiversiteitsportaal VBP https://natuurdata.inbo.be
4 France Portail français d'accès aux données d'observation sur les espèces OpenObs https://inpn.mnhn.fr
5 Global Global Biodiversity Information Facility GBIF https://gbif.org
6 Guatemala Sistema Nacional de Información sobre Diversidad Biológica de Guatemala SNIBgt https://snib.conap.gob.gt
7 Kew Kew Data Portal KDP https://data.kew.org
8 Portugal GBIF Portugal GBIF.pt https://www.gbif.pt
9 Spain GBIF Spain GBIF.es https://www.gbif.es
10 Sweden Swedish Biodiversity Data Infrastructure SDBI https://biodiversitydata.se
11 United Kingdom National Biodiversity Network NBN https://nbn.org.uk
To search for a specific available Living Atlas:
>>> galah.search_all(atlases="Spain")
atlas institution acronym url
0 Spain GBIF Spain GBIF.es https://www.gbif.es
To show all fields:
>>> galah.show_all(fields=True)
id description type link
0 abcdTypeStatus ABCD field in use by herbaria field NaN
1 acceptedNameUsage http://rs.tdwg.org/dwc/terms/acceptedNameUsage field NaN
2 acceptedNameUsageID http://rs.tdwg.org/dwc/terms/acceptedNameUsageID field NaN
3 accessRights NaN field NaN
4 annotationsDoi NaN field NaN
... ... ... ... ...
1100 multimediaLicence Media filter field media
1101 images Media filter field media
1102 videos Media filter field media
1103 sounds Media filter field media
1104 qid Reference to pre-generated query other
[1105 rows x 4 columns]
And to search for a specific field:
>>> galah.search_all(fields="Australian States",column_name="description")
id description type link
0 cl22 Australian States and Territories Australian States and Territories layers
1 cl2013 ASGS Australian States and Territories ASGS Australian States and Territories layers
Here is a list of information types that can be used with galah.show_all() and galah.search_all():
Information type |
Description |
|---|---|
Configuration |
|
|
Show what living atlases are available |
|
Show what APIs & functions are available for each atlas |
|
Show what values are acceptable as ‘download reasons’ for a specified atlas |
Taxonomy |
|
|
Take a universal identifier and return taxonomic information |
|
Show valid taxonomic ranks (e.g. Kingdom, Class, Order, etc.) |
Filters |
|
|
Show fields that are stored in an atlas |
|
Show results of data quality checks run by each atlas |
Group filters |
|
|
Show what data quality profiles are available |
|
Show what species lists are available |
Data providers |
|
|
Show which institutions have provided data |
|
Show the specific collections within those institutions |
|
Shows all the data groupings within those collections |
_values functions#
Sifting through the output of galah.show_all(fields=True) to find a specific field can be inefficient.
Instead, we might wish to use search_fields to look for specific fields that match a search, and get
their possible values to filter our results.
If we want to know what kinds of fields describe the basis of how an occurrence was recorded, you can
search for the keyword “basis” using galah.search_all():
>>> galah.search_all(fields="basis")
id description type link
0 raw_basisOfRecord The basis of record as supplied by the data publisher field NaN
1 basisOfRecord What this is a record of e.g. specimen, human observation, fossil http://rs.tdwg.org/dwc/terms/basisOfRecord field https://github.com/AtlasOfLivingAustralia/ala-dataquality/wiki/basisOfRecord
Once a desired field is found, you can use show_values to understand the information contained within that field, e.g.
>>> galah.show_values(field="basisOfRecord")
field category
0 basisOfRecord HUMAN_OBSERVATION
1 basisOfRecord PRESERVED_SPECIMEN
2 basisOfRecord OCCURRENCE
3 basisOfRecord MACHINE_OBSERVATION
4 basisOfRecord OBSERVATION
5 basisOfRecord MATERIAL_SAMPLE
6 basisOfRecord LIVING_SPECIMEN
7 basisOfRecord FOSSIL_SPECIMEN
8 basisOfRecord MATERIAL_CITATION
You can even narrow down your search by searching for matching values:
>>> galah.search_values(field="basisOfRecord",value="SPECIMEN")
field category
0 basisOfRecord LIVING_SPECIMEN
1 basisOfRecord FOSSIL_SPECIMEN
2 basisOfRecord PRESERVED_SPECIMEN
This provides the information you need to pass meaningful queries to galah_filter.
>>> galah.atlas_counts(filters="basisOfRecord=LIVING_SPECIMEN")
totalRecords
0 133650