Download Data#
The atlas_ functions are used to return data from the atlas chosen using galah_config(). They are:
atlas_counts()
atlas_occurrences()
atlas_species()
atlas_media()
Record counts#
galah.atlas_counts() provides summary counts on records in the specified atlas, without needing to download all the records.
>>> galah.galah_config(atlas="Australia")
>>> galah.atlas_counts()
totalRecords
0 167267751
In addition to filters arguments, galah.atlas_counts() has an optional group_by argument, which provides counts grouped
by the requested field.
>>> galah.atlas_counts(group_by="kingdom")
kingdom count
0 Animalia 131317918
1 Archaea 15109
2 Bacteria 458328
3 Chromista 1066058
4 Fungi 1909315
5 Plantae 30914478
6 Protista 480194
7 Viruses 13662
Species lists#
A common use case of atlas data is to identify which species occur in a specified region, time period,
or taxonomic group. galah.atlas_species() is similar to search_taxa, in that it returns taxonomic information and
unique identifiers in a dataframe. It differs in not being able to return information on taxonomic levels other
than the species; but also in being more flexible by supporting filtering:
>>> galah.atlas_species(taxa="Rodentia",filters="stateProvince=Northern Territory")
Species Species Name Scientific Name Authorship Taxon Rank Kingdom Phylum Class Order Family Genus Vernacular Name
0 https://biodiversity.org.au/afd/taxa/b6045bad-6c5e-46ba-8644-15c0bd6320bb Pseudomys delicatulus (Gould, 1842) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Delicate Mouse
1 https://biodiversity.org.au/afd/taxa/4797cf4c-db5c-48d6-9524-3330cb78cfda Mesembriomys gouldii (J.E. Gray, 1843) species Animalia Chordata Mammalia Rodentia Muridae Mesembriomys Black-footed Tree-rat
2 https://biodiversity.org.au/afd/taxa/07c52a7f-f529-4137-b41f-3052aeca60b5 Zyzomys argurus (Thomas, 1889) species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Common Rock-rat
3 https://biodiversity.org.au/afd/taxa/c7a6c8d8-ab20-456e-bc9c-538720409b70 Pseudomys hermannsburgensis (Waite, 1896) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Sandy Inland Mouse
4 https://biodiversity.org.au/afd/taxa/5b6226c0-b579-4d59-8d66-f23bd328b9dd Melomys burtoni (Ramsay, 1887) species Animalia Chordata Mammalia Rodentia Muridae Melomys Grassland Melomys
5 https://biodiversity.org.au/afd/taxa/c1063f9b-5a3b-4dc4-a430-6568b5088579 Notomys alexis Thomas, 1922 species Animalia Chordata Mammalia Rodentia Muridae Notomys Spinifex Hopping-mouse
6 https://biodiversity.org.au/afd/taxa/0a444981-cf13-484c-81b5-9313d5851c4e Mus musculus Linnaeus, 1758 species Animalia Chordata Mammalia Rodentia Muridae Mus House Mouse
7 https://biodiversity.org.au/afd/taxa/9bb1445f-39e4-417e-b384-60a277447a4a Conilurus penicillatus (Gould, 1842) species Animalia Chordata Mammalia Rodentia Muridae Conilurus Brush-tailed Tree-rat
8 https://biodiversity.org.au/afd/taxa/575ddf45-3127-4e8f-bb75-efdd6468a571 Rattus rattus (Linnaeus, 1758) species Animalia Chordata Mammalia Rodentia Muridae Rattus Black Rat
9 https://biodiversity.org.au/afd/taxa/958c426a-21be-4389-84c5-9c227a0ce8a6 Rattus tunneyi (Thomas, 1904) species Animalia Chordata Mammalia Rodentia Muridae Rattus Pale Field-rat
10 https://biodiversity.org.au/afd/taxa/5733f8c9-38f9-4a17-a2ee-f793fa70ed98 Rattus villosissimus (Waite, 1898) species Animalia Chordata Mammalia Rodentia Muridae Rattus Long-haired Rat
11 https://biodiversity.org.au/afd/taxa/e7703da0-c258-413b-8578-e2dfade1591f Pseudomys desertor Troughton, 1932 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Desert Mouse
12 https://biodiversity.org.au/afd/taxa/93b9afae-579d-4181-9fae-501230f0b0d8 Pseudomys nanus (Gould, 1858) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Western Chestnut Mouse
13 https://biodiversity.org.au/afd/taxa/4e9a6d73-a015-4aea-948c-8fc3eae46c1c Rattus colletti (Thomas, 1904) species Animalia Chordata Mammalia Rodentia Muridae Rattus Dusky Rat
14 https://biodiversity.org.au/afd/taxa/dab6e02d-b4a5-4009-81ea-14b9f139b910 Zyzomys maini Kitchener, 1989 species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Arnhem Land Rock-rat
15 https://biodiversity.org.au/afd/taxa/2595dcfd-30f7-48f6-a50e-af3551bd9cc8 Zyzomys palatalis Kitchener, 1989 species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Carpentarian Rock-rat
16 https://biodiversity.org.au/afd/taxa/cc2d4c74-8072-487e-a47f-9747806dc34a Leggadina lakedownensis Watts, 1976 species Animalia Chordata Mammalia Rodentia Muridae Leggadina Lakeland Downs Mouse
17 https://biodiversity.org.au/afd/taxa/e985914e-3435-4f6b-9978-2cbb19d29fee Pseudomys australis J.E. Gray, 1832 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Plains Rat
18 https://biodiversity.org.au/afd/taxa/7f791f55-1d6f-4448-91a0-996daa72081c Hydromys chrysogaster Geoffroy, 1804 species Animalia Chordata Mammalia Rodentia Muridae Hydromys Water-rat
19 https://biodiversity.org.au/afd/taxa/90c13414-5069-4125-8b56-0b5c59a752e3 Zyzomys pedunculatus (Waite, 1896) species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Central Rock-rat
20 https://biodiversity.org.au/afd/taxa/4b5e599e-70af-40a6-b4bb-13cfdb98c23f Leggadina forresti (Thomas, 1906) species Animalia Chordata Mammalia Rodentia Muridae Leggadina Forrest's Mouse
21 https://biodiversity.org.au/afd/taxa/b5981535-b6c0-41e3-b573-9e383b91a9a4 Notomys aquilo Thomas, 1921 species Animalia Chordata Mammalia Rodentia Muridae Notomys Northern Hopping-mouse
22 https://biodiversity.org.au/afd/taxa/f44806fd-7802-45d7-bb10-774ecc577c7d Pseudomys johnsoni Kitchener, 1985 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Central Pebble-mound Mouse
23 https://biodiversity.org.au/afd/taxa/e59c9613-14d2-4d2f-8b19-3b165a6ed11e Pseudomys calabyi Kitchener & Humphreys, 1987 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Kakadu Pebble-mound Mouse
24 https://biodiversity.org.au/afd/taxa/ff0f2d1f-3abf-4288-8365-ee6c6be17b38 Rattus sordidus (Gould, 1858) species Animalia Chordata Mammalia Rodentia Muridae Rattus Canefield Rat
25 https://biodiversity.org.au/afd/taxa/66b0dc84-12dd-4aca-a7b8-82d1ae89bc18 Notomys longicaudatus (Gould, 1844) species Animalia Chordata Mammalia Rodentia Muridae Notomys Long-tailed Hopping-mouse
26 https://biodiversity.org.au/afd/taxa/9daf14f2-931d-44a6-8537-5127c56ab950 Leporillus apicalis (Gould, 1853) species Animalia Chordata Mammalia Rodentia Muridae Leporillus Lesser Stick-nest Rat
27 https://biodiversity.org.au/afd/taxa/356745c1-ce6d-42f1-935c-9098261cd81f Pseudomys mimulus Thomas, 1926 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys NaN
28 https://biodiversity.org.au/afd/taxa/2da4cbaa-005f-4346-8e11-6a1e5ddd0444 Notomys amplus Brazenor, 1936 species Animalia Chordata Mammalia Rodentia Muridae Notomys Short-tailed Hopping-mouse
29 https://biodiversity.org.au/afd/taxa/77c6c9f3-40d3-48da-96f5-d80e402ad18d Notomys cervinus (Gould, 1853) species Animalia Chordata Mammalia Rodentia Muridae Notomys Fawn Hopping-mouse
30 https://biodiversity.org.au/afd/taxa/c4bfec0f-0137-49a1-84bb-c088e99844b8 Notomys mitchellii (Ogilby, 1838) species Animalia Chordata Mammalia Rodentia Muridae Notomys Mitchell's Hopping-mouse
31 https://biodiversity.org.au/afd/taxa/b042c17d-27fd-4154-8bdf-519aeb952836 Xeromys myoides Thomas, 1889 species Animalia Chordata Mammalia Rodentia Muridae Xeromys False Water-rat
32 https://biodiversity.org.au/afd/taxa/c0e8f4ca-3c7e-4b71-9d8f-992e3e3b07b9 Notomys fuscus (Jones, 1925) species Animalia Chordata Mammalia Rodentia Muridae Notomys Dusky Hopping-mouse
33 https://biodiversity.org.au/afd/taxa/f6168080-2649-4d2e-ad43-5b852bc5913d Pseudomys gracilicaudatus (Gould, 1845) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Eastern Chestnut Mouse
34 https://biodiversity.org.au/afd/taxa/3694beb2-9b22-4e79-9373-5d0d887be69b Mesembriomys macrurus (Peters, 1876) species Animalia Chordata Mammalia Rodentia Muridae Mesembriomys Golden-backed Tree-rat
35 https://biodiversity.org.au/afd/taxa/e5b3ef22-25f4-48f6-95f2-2bd384b8efe7 Rattus norvegicus (Berkenhout, 1769) species Animalia Chordata Mammalia Rodentia Muridae Rattus Brown Rat
36 https://biodiversity.org.au/afd/taxa/59b21252-19fe-4fc3-85d4-ddb6a7e49e78 Melomys cervinipes (Gould, 1852) species Animalia Chordata Mammalia Rodentia Muridae Melomys Fawn-footed Melomys
37 https://biodiversity.org.au/afd/taxa/2eef1990-96e3-498a-887a-f1dfa334b218 Rattus leucopus (J.E. Gray, 1867) species Animalia Chordata Mammalia Rodentia Muridae Rattus Cape York Rat
38 https://biodiversity.org.au/afd/taxa/b9b253e9-a56c-4a72-8ce3-15de06ef8417 Pseudomys gouldii (Waterhouse, 1839) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Shark Bay Mouse (djoongari)
39 https://biodiversity.org.au/afd/taxa/cce5d053-414a-40e0-87bd-ab8012287068 Leporillus conditor (Sturt, 1848) species Animalia Chordata Mammalia Rodentia Muridae Leporillus Greater Stick-nest Rat
40 ALA_DR30477_78 Cavia porcellus NaN species Animalia Chordata Mammalia Rodentia Caviidae Cavia Guinea Pig
41 https://biodiversity.org.au/afd/taxa/35a0671a-e449-4581-aeac-510ea2f251ea Zyzomys woodwardi (Thomas, 1909) species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Kimberley Rock-rat
42 https://biodiversity.org.au/afd/taxa/3b31abbc-6b8a-4fbf-aed6-f614dbb51cb8 Rattus lutreolus (J.E. Gray, 1841) species Animalia Chordata Mammalia Rodentia Muridae Rattus Swamp Rat
43 https://biodiversity.org.au/afd/taxa/83049628-f180-4a3f-9f48-af5cee08d818 Pseudomys occidentalis Tate, 1951 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Western Mouse
44 https://biodiversity.org.au/afd/taxa/0058f9b2-a9c1-49a2-811b-9b2efcc8e279 Pseudomys novaehollandiae (Waterhouse, 1843) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys New Holland Mouse
45 https://biodiversity.org.au/afd/taxa/07e98c03-3739-4779-bfbd-ae4d930dad7a Uromys caudimaculatus (Krefft, 1867) species Animalia Chordata Mammalia Rodentia Muridae Uromys White-tailed Uromys
46 https://biodiversity.org.au/afd/taxa/6a5c25e0-3b06-4ae2-8069-b4c1350c4365 Mastacomys fuscus Thomas, 1882 species Animalia Chordata Mammalia Rodentia Muridae Mastacomys Broad-toothed Rat
Occurrence data#
To download occurrence data you will need to specify your email in galah.galah_config(). This email must be
associated with an active account on your chosen atlas. See more information in the config section.
>>> galah_config(email = "your_email@email.com", atlas = "Australia")
After specifying your email, you can download occurrence records of, for example, Eolophus roseicapilla:
>>> galah.atlas_occurrences(taxa="Eolophus roseicapilla",filters=["stateProvince=Australian Capital Territory","year>=2010"],fields=["institutionID","basic"])
institutionID decimalLatitude decimalLongitude eventDate scientificName taxonConceptID recordID dataResourceName occurrenceStatus
0 NaN -35.342500 149.167500 2023-08-25T12:06:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 82e202e5-890e-4a3a-8846-83aa27bf75b3 eBird Australia PRESENT
1 NaN -35.310240 149.137645 2017-03-02T10:22:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 7b3222d7-36f4-4b97-8366-e79061cfb65b eBird Australia PRESENT
2 NaN -35.324650 149.051771 2017-10-29T17:00:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 6f355836-2373-4d51-b486-31817473fdae eBird Australia PRESENT
3 NaN -35.227600 149.143790 2023-02-12T07:28:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 30d771b6-f1be-4755-ab90-45e17521005f eBird Australia PRESENT
4 NaN -35.350302 149.029458 2016-02-26T00:00:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 2089f87e-ec0b-4678-af6f-dc3fb9e6983e Garden Bird Surveys PRESENT
... ... ... ... ... ... ... ... ... ...
107962 in1033 -35.386879 149.097992 2011-08-15T04:45:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 0764df7e-9f59-4599-9683-851dbf63f7f2 ALA species sightings and OzAtlas PRESENT
107963 in1033 -35.226993 149.020481 2017-06-25T14:00:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 32735c4a-bb78-4ffe-b7c1-7a7b7cc599ce ALA species sightings and OzAtlas PRESENT
107964 in1033 -35.751461 148.964401 2015-01-06T02:55:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 326e6431-6ea5-45a8-82dd-53ad9ad85a9b ALA species sightings and OzAtlas PRESENT
107965 in1033 -35.347511 149.044907 2013-08-07T23:57:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 0a6d58bc-ecbe-4133-9319-33a645c1b5d6 ALA species sightings and OzAtlas PRESENT
107966 in550 -35.322672 149.092483 2021-02-16T00:00:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 738123d4-dd65-4fe8-b449-796598a2233a Entangled Wildlife Australia PRESENT
[107967 rows x 9 columns]
Media metadata#
In addition to text data describing individual occurrences and their attributes, ALA stores images, sounds and videos
associated with a given record. Metadata on these records can be downloaded using galah.atlas_media() and the same set of
filters as the other data download functions.
>>> galah.atlas_media(taxa="Eolophus roseicapilla",filters=["year=2020","stateProvince=Australian Capital Territory"])
decimalLatitude decimalLongitude eventDate scientificName taxonConceptID recordID dataResourceName occurrenceStatus multimedia images videos sounds creator license mimeType width height imageUrl
0 -35.166122 149.166048 2020-11-07T12:29:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea c91faaef-1df3-41e6-a12e-c0dcd13e47b0 iNaturalist Australia PRESENT Image 9889254d-2a57-41dc-bc85-def7b8d3f0e0 NaN NaN David Cunningham http://creativecommons.org/licenses/by-nd/4.0/ image/jpeg 1947 1947 https://images.ala.org.au/store/0/e/0/f/9889254d-2a57-41dc-bc85-def7b8d3f0e0/original
1 -35.327922 149.102528 2020-08-30T07:08:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 89b44608-edbc-450e-aea5-c68b2b84a804 NatureMapr PRESENT Image 4fcf0397-8dc2-4647-b53c-48582c458852 NaN NaN image/jpeg 800 1199 https://images.ala.org.au/store/2/5/8/8/4fcf0397-8dc2-4647-b53c-48582c458852/original
2 -35.276720 149.178877 2020-10-12T21:21:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 3e1dd883-f0c3-4d58-bc7a-7af5a7b97887 NatureMapr PRESENT Image 266513f2-6d22-488b-847f-45fceb838393 NaN NaN image/jpeg 800 600 https://images.ala.org.au/store/3/9/3/8/266513f2-6d22-488b-847f-45fceb838393/original
3 -35.328299 149.101087 2020-04-02T06:06:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 14e3c386-a204-4221-88fe-2a71c3335fd8 NatureMapr PRESENT Image 5f4b7510-6c44-4e97-ad37-38177d85c75e NaN NaN image/jpeg 800 600 https://images.ala.org.au/store/e/5/7/c/5f4b7510-6c44-4e97-ad37-38177d85c75e/original
4 -35.328845 149.191573 2020-08-13T10:02:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 2b25fff2-cb89-45da-a860-e07436974280 iNaturalist Australia PRESENT Image a9084ee7-5ad7-478c-b4cb-634b087629b6 NaN NaN David Cunningham http://creativecommons.org/licenses/by-nd/4.0/ image/jpeg 2048 2048 https://images.ala.org.au/store/6/b/9/2/a9084ee7-5ad7-478c-b4cb-634b087629b6/original
.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
128 -35.236313 149.158740 2020-05-05T10:15:23Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea c13a86bf-f9e1-4d04-82f6-0faef3440d2c iNaturalist Australia PRESENT Image 9f683497-a08f-4a05-8f27-69e822d5eb03 NaN NaN d_and_c http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1536 2048 https://images.ala.org.au/store/3/0/b/e/9f683497-a08f-4a05-8f27-69e822d5eb03/original
129 -35.408220 149.131021 2020-02-12T18:41:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea b4dcd437-16b2-4f79-815c-0d75ddfcb200 iNaturalist Australia PRESENT Image a57d74a8-dbde-4aa2-8c48-072ed75d8d9a NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/a/9/d/8/a57d74a8-dbde-4aa2-8c48-072ed75d8d9a/original
130 -35.244163 148.980541 2020-09-14T13:25:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 39f6b583-bffe-4df6-bf31-e6231363d0be iNaturalist Australia PRESENT Image e2feb510-1e6f-4bf4-94a9-c1a8f36ba983 NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/3/8/9/a/e2feb510-1e6f-4bf4-94a9-c1a8f36ba983/original
131 -35.408250 149.131024 2020-07-31T15:32:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 707ae928-b495-4916-99d7-9b9d40f8abf9 iNaturalist Australia PRESENT Image 9bf68190-c34c-4d70-9165-903efab1cff3 NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/3/f/f/c/9bf68190-c34c-4d70-9165-903efab1cff3/original
132 -35.408263 149.131118 2020-04-07T16:04:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 92e78b1a-25d7-4ecb-9ed6-86edff3f5372 iNaturalist Australia PRESENT Image 04c6a10c-7b2c-422a-bcef-735c78b4caac NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/c/a/a/c/04c6a10c-7b2c-422a-bcef-735c78b4caac/original
[133 rows x 18 columns]
To actually download the media files to your computer, add the argument collect. By default, it downloads the data to your
current working directory, but you can specify the folder to download to with the path argument.
Configuring galah#
Various aspects of the galah package can be customized.
To download occurrence records, you will need to provide an email address registered with the ALA. You can create an account here. Once an email is registered with the ALA, it should be stored in the config:
>>> galah.galah_config(email = "myemail@gmail.com")
Setting a download reason
ALA requires that you provide a reason when downloading occurrence data (via the galah.atlas_occurrences() function).
The reason is set to 4 (scientific research) by default, but you can change this using galah_config(). See galah.show_all(reasons=True)
for valid download reasons.
>>> galah.galah_config(reason = 5)
Debugging#
If things aren’t working as expected, more detail (particularly about web requests)
can be obtained by setting the verbose option in many functions.