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 150349915
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 115267430
1 Archaea 14989
2 Bacteria 463591
3 Bamfordvirae 526
4 Chromista 1101637
5 Fungi 2745670
6 Helvetiavirae 1
7 Heunggongvirae 509
8 Loebvirae 3
9 Orthornavirae 6680
10 Pararnavirae 308
11 Plantae 29060762
12 Protista 390672
13 Shotokuvirae 1114
14 Trapavirae 3
15 Viroid 143
16 Virus 4273
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/a6a91fbd-77f4-4440-ba66-7d043f27a297 Pseudomys delicatulus (Gould, 1842) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Delicate Mouse
1 https://biodiversity.org.au/afd/taxa/d3d03db1-3305-4f09-9f3f-64d8c512ee8c Mesembriomys gouldii (J.E. Gray, 1843) species Animalia Chordata Mammalia Rodentia Muridae Mesembriomys Black-footed Tree-rat
2 https://biodiversity.org.au/afd/taxa/936ee591-1e1a-4f9e-934e-4bc174c54414 Zyzomys argurus (Thomas, 1889) species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Common Rock-rat
3 https://biodiversity.org.au/afd/taxa/635a8ab7-774e-4676-9e75-8dc31333cab1 Pseudomys hermannsburgensis (Waite, 1896) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Sandy Inland Mouse
4 https://biodiversity.org.au/afd/taxa/20ca6a48-09d2-4f05-ba8e-bbae4fa40175 Melomys burtoni (Ramsay, 1887) species Animalia Chordata Mammalia Rodentia Muridae Melomys Grassland Melomys
5 https://biodiversity.org.au/afd/taxa/53115180-4024-4d50-baf7-edc4556b89f7 Notomys alexis Thomas, 1922 species Animalia Chordata Mammalia Rodentia Muridae Notomys Spinifex Hopping-mouse
6 https://biodiversity.org.au/afd/taxa/952ae705-57e2-43d1-9a06-b35498202469 Mus musculus Linnaeus, 1758 species Animalia Chordata Mammalia Rodentia Muridae Mus House Mouse
7 https://biodiversity.org.au/afd/taxa/6a01d711-2ac6-4928-bab4-a1de1a58e995 Conilurus penicillatus (Gould, 1842) species Animalia Chordata Mammalia Rodentia Muridae Conilurus Brush-tailed Tree-rat
8 https://biodiversity.org.au/afd/taxa/c1817333-9c62-4a05-af03-fe5fb9c9a0ce Rattus rattus (Linnaeus, 1758) species Animalia Chordata Mammalia Rodentia Muridae Rattus Black Rat
9 https://biodiversity.org.au/afd/taxa/ffcb9f84-c70f-4bc3-af9d-4f37a5a07e3f Rattus tunneyi (Thomas, 1904) species Animalia Chordata Mammalia Rodentia Muridae Rattus Pale Field-rat
10 https://biodiversity.org.au/afd/taxa/cbaf1515-df15-49ec-be06-36058183644b Rattus villosissimus (Waite, 1898) species Animalia Chordata Mammalia Rodentia Muridae Rattus Long-haired Rat
11 https://biodiversity.org.au/afd/taxa/1c2e0a49-5530-48a2-83f3-2d853c89ab03 Pseudomys desertor Troughton, 1932 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Desert Mouse
12 https://biodiversity.org.au/afd/taxa/eb140ad3-776d-4294-bd33-6464097bfff3 Pseudomys nanus (Gould, 1858) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Western Chestnut Mouse
13 https://biodiversity.org.au/afd/taxa/da75e4fd-b02b-4f5c-9f7c-e835633b18a2 Rattus colletti (Thomas, 1904) species Animalia Chordata Mammalia Rodentia Muridae Rattus Dusky Rat
14 https://biodiversity.org.au/afd/taxa/d02be481-91a1-4b33-a7a5-0e73f995c71c Zyzomys maini Kitchener, 1989 species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Arnhem Land Rock-rat
15 https://biodiversity.org.au/afd/taxa/25ad81dd-0bd0-4fe5-94d7-1ec605bbf8b0 Zyzomys palatalis Kitchener, 1989 species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Carpentarian Rock-rat
16 https://biodiversity.org.au/afd/taxa/5e54144e-c15e-4906-a20c-ab076696c35c Leggadina lakedownensis Watts, 1976 species Animalia Chordata Mammalia Rodentia Muridae Leggadina Lakeland Downs Mouse
17 https://biodiversity.org.au/afd/taxa/2843e4d8-931a-41f0-875e-f6756f44088f Hydromys chrysogaster Geoffroy, 1804 species Animalia Chordata Mammalia Rodentia Muridae Hydromys Water-rat
18 https://biodiversity.org.au/afd/taxa/298a7b7a-96c0-4b48-8746-ea9ad8590fe5 Pseudomys australis J.E. Gray, 1832 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Plains Rat
19 https://biodiversity.org.au/afd/taxa/dd6aca04-8169-46e4-955b-06cbe831efdf Zyzomys pedunculatus (Waite, 1896) species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Central Rock-rat
20 https://biodiversity.org.au/afd/taxa/e56ebe66-5dbd-4b63-b8fc-95b67ac9411a Leggadina forresti (Thomas, 1906) species Animalia Chordata Mammalia Rodentia Muridae Leggadina Forrest's Mouse
21 https://biodiversity.org.au/afd/taxa/ac8c37b1-2543-4bc2-b55d-b97cbbefefbf Notomys aquilo Thomas, 1921 species Animalia Chordata Mammalia Rodentia Muridae Notomys Northern Hopping-mouse
22 https://biodiversity.org.au/afd/taxa/43ef1334-3aba-483f-ba1f-c0407e3cc847 Pseudomys johnsoni Kitchener, 1985 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Central Pebble-mound Mouse
23 https://biodiversity.org.au/afd/taxa/39ea6204-ab1b-469e-b107-b64d24c4903f Pseudomys calabyi Kitchener & Humphreys, 1987 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Kakadu Pebble-mound Mouse
24 https://biodiversity.org.au/afd/taxa/958ed049-9bca-4c65-a720-9e16e1b7434c Rattus sordidus (Gould, 1858) species Animalia Chordata Mammalia Rodentia Muridae Rattus Canefield Rat
25 https://biodiversity.org.au/afd/taxa/327e0ec3-8efa-43c5-9bc9-867d3082ed88 Notomys longicaudatus (Gould, 1844) species Animalia Chordata Mammalia Rodentia Muridae Notomys Long-tailed Hopping-mouse
26 https://biodiversity.org.au/afd/taxa/61403a2b-8537-46e1-91cf-672d02be62b3 Leporillus apicalis (Gould, 1853) species Animalia Chordata Mammalia Rodentia Muridae Leporillus Lesser Stick-nest Rat
27 https://biodiversity.org.au/afd/taxa/3a840ca2-936e-4075-a622-f0d628bace31 Notomys amplus Brazenor, 1936 species Animalia Chordata Mammalia Rodentia Muridae Notomys Short-tailed Hopping-mouse
28 https://biodiversity.org.au/afd/taxa/1745e7b1-6f91-47a9-baf4-c56f0643cb05 Notomys cervinus (Gould, 1853) species Animalia Chordata Mammalia Rodentia Muridae Notomys Fawn Hopping-mouse
29 https://biodiversity.org.au/afd/taxa/54222852-0af1-4e1f-b45b-175ed441d015 Notomys mitchellii (Ogilby, 1838) species Animalia Chordata Mammalia Rodentia Muridae Notomys Mitchell's Hopping-mouse
30 https://biodiversity.org.au/afd/taxa/0553a58d-450b-455a-8844-62d5e5d14774 Xeromys myoides Thomas, 1889 species Animalia Chordata Mammalia Rodentia Muridae Xeromys False Water-rat
31 https://biodiversity.org.au/afd/taxa/e169b779-e4e4-411f-95e0-b21d4b4c6060 Notomys fuscus (Jones, 1925) species Animalia Chordata Mammalia Rodentia Muridae Notomys Dusky Hopping-mouse
32 https://biodiversity.org.au/afd/taxa/9f22993a-86b0-4003-9df4-4565d66de008 Pseudomys gracilicaudatus (Gould, 1845) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Eastern Chestnut Mouse
33 https://biodiversity.org.au/afd/taxa/1d179abb-b688-4242-989f-9a1a6d90f0b4 Mesembriomys macrurus (Peters, 1876) species Animalia Chordata Mammalia Rodentia Muridae Mesembriomys Golden-backed Tree-rat
34 https://biodiversity.org.au/afd/taxa/15e09f34-5033-424e-a37c-d6bb55f30b26 Rattus norvegicus (Berkenhout, 1769) species Animalia Chordata Mammalia Rodentia Muridae Rattus Brown Rat
35 https://biodiversity.org.au/afd/taxa/d9528b07-2a62-4120-b946-edab67821b44 Melomys cervinipes (Gould, 1852) species Animalia Chordata Mammalia Rodentia Muridae Melomys Fawn-footed Melomys
36 https://biodiversity.org.au/afd/taxa/dcf73c10-5e05-4b59-9d4e-2682ef369e5e Zyzomys woodwardi (Thomas, 1909) species Animalia Chordata Mammalia Rodentia Muridae Zyzomys Kimberley Rock-rat
37 https://biodiversity.org.au/afd/taxa/288dcc0f-822d-43e4-b31d-82edd9b11f00 Pseudomys gouldii (Waterhouse, 1839) species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Shark Bay Mouse (djoongari)
38 https://biodiversity.org.au/afd/taxa/3ca6b7e9-9862-48ac-b457-0e705dda1c75 Rattus leucopus (J.E. Gray, 1867) species Animalia Chordata Mammalia Rodentia Muridae Rattus Cape York Rat
39 ALA_DR24112_241 Cavia porcellus NaN species Animalia Chordata Mammalia Rodentia Caviidae Cavia Animals
40 https://biodiversity.org.au/afd/taxa/6983ebaa-1c9d-4b4d-a0fa-8c673d0248ef Pseudomys occidentalis Tate, 1951 species Animalia Chordata Mammalia Rodentia Muridae Pseudomys Western Mouse
41 https://biodiversity.org.au/afd/taxa/9a9f3fa9-ca3b-4a15-b25b-d291c9f504b5 Uromys caudimaculatus (Krefft, 1867) species Animalia Chordata Mammalia Rodentia Muridae Uromys Giant White-tailed 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 BASIS_OF_RECORD_INVALID CONTINENT_COORDINATE_MISMATCH COORDINATE_PRECISION_INVALID COORDINATE_ROUNDED COORDINATE_UNCERTAINTY_METERS_INVALID COUNTRY_DERIVED_FROM_COORDINATES FIRST_OF_MONTH FIRST_OF_YEAR GEODETIC_DATUM_ASSUMED_WGS84 GEODETIC_DATUM_INVALID ID_PRE_OCCURRENCE INDIVIDUAL_COUNT_INVALID MISSING_GEODETICDATUM MISSING_GEOREFERENCEDBY MISSING_GEOREFERENCEPROTOCOL MISSING_GEOREFERENCESOURCES MISSING_GEOREFERENCEVERIFICATIONSTATUS MISSING_GEOREFERENCE_DATE MISSING_TAXONRANK MODIFIED_DATE_INVALID MULTIMEDIA_DATE_INVALID OCCURRENCE_STATUS_INFERRED_FROM_INDIVIDUAL_COUNT RECORDED_DATE_INVALID STATE_COORDINATE_MISMATCH TAXON_MATCH_FUZZY
0 NaN -35.262050 149.068500 2016-12-05T18:10:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 98fc7e11-9064-4c0f-8bad-53485c421f88 eBird Australia PRESENT False False False False True False False False True False False False True True True True True True True False False True False False False
1 NaN -35.326399 149.067593 2020-11-11T17:17:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 40104e2d-2e95-4889-8bc5-76248457a82c eBird Australia PRESENT False False False True True False False False True False False False True True True True True True True False False True False False False
2 NaN -35.262050 149.068500 2015-12-07T16:30:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea ec682a25-dfbd-48b9-8a51-53356e52f1ff eBird Australia PRESENT False False False False True False False False True False False False True True True True True True True False False True False False False
3 NaN -35.317036 149.079250 2019-06-13T16:13:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 3ec71547-adda-4207-9386-c03ec6eb22bf eBird Australia PRESENT False False False True True False False False True False False False True True True True True True True False False True False False False
4 NaN -35.335215 149.049740 2015-07-17T00:00:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea cc91ef46-3bda-4920-8b36-61c24a293f9c Garden Bird Surveys PRESENT False False False False False False False False False False False True False False False False True True False False False False False False False
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
96396 NaN -35.329288 149.139065 2011-12-18T00:00:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 8d3a8ae4-4b4c-48f0-b352-331531a97203 Garden Bird Surveys PRESENT False False False False False False False False False False False True False False False False True True False False False False False False False
96397 NaN -35.313411 149.162326 2020-09-11T12:21:00Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea cb1c17d2-93e0-4ad8-8700-461d699aec66 eBird Australia PRESENT False False False False True False False False True False False False True True True True True True True False False True False False False
96398 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 False False False True True True False False True False False True True True True True True True True False False False False False True
96399 in1033 -35.276619 149.112914 2017-07-25T21:34:37Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 150d3252-111e-41ec-ab32-7f0567ac0330 ALA species sightings and OzAtlas PRESENT False False False True True True False False True False False True True True True True True True True False False False False False True
96400 in1033 -35.160122 149.140961 2018-07-05T06:30:46Z Eolophus roseicapilla https://biodiversity.org.au/afd/taxa/9b4ad548-8bb3-486a-ab0a-905506c463ea 59d49f01-33d2-46e2-92cb-f4c5f9ecd4fa ALA species sightings and OzAtlas PRESENT False False False True True True False False True False False True True True True True True True True False False False False False True
[96401 rows x 34 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 recordID dataResourceName occurrenceStatus multimedia images videos sounds creator license mimetype width height imageUrl
0 -35.327922 149.102528 2020-08-30T07:08:00Z Eolophus roseicapilla 89b44608-edbc-450e-aea5-c68b2b84a804 NatureMapr PRESENT Image 4fcf0397-8dc2-4647-b53c-48582c458852 NaN NaN None None image/jpeg 800 1199 https://images.ala.org.au/store/2/5/8/8/4fcf0397-8dc2-4647-b53c-48582c458852/original
1 -35.317800 149.146261 2020-01-06T12:00:00Z Eolophus roseicapilla b03e670c-29d4-44e4-b0b4-d698b7a00581 Earth Guardians Weekly Feed PRESENT Image 3e220765-bdec-4804-8015-4763e3b36bb3 NaN NaN None None image/jpeg 1001 750 https://images.ala.org.au/store/3/b/b/6/3e220765-bdec-4804-8015-4763e3b36bb3/original
2 -35.317737 149.161550 2020-05-01T13:40:00Z Eolophus roseicapilla ca1f9727-9d8e-4e79-b92c-d10e285b2c15 iNaturalist Australia PRESENT Image 7b95197f-2520-4167-980a-7b8dfc395952 NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/2/5/9/5/7b95197f-2520-4167-980a-7b8dfc395952/original
3 -35.316870 149.160586 2020-07-20T14:28:00Z Eolophus roseicapilla 4426ea86-f5f3-4c92-97fb-9f6afc25e1c5 iNaturalist Australia PRESENT Image f84a964a-0eb8-4eb5-9c67-e5bcd50e0d64 NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/4/6/d/0/f84a964a-0eb8-4eb5-9c67-e5bcd50e0d64/original
4 -35.316857 149.162818 2020-10-23T10:51:00Z Eolophus roseicapilla e0c904f7-ad62-46da-973e-f948bd36d8f5 iNaturalist Australia PRESENT Image cb82294a-cd01-4ca5-b841-5d6f6f853d2f NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/f/2/d/3/cb82294a-cd01-4ca5-b841-5d6f6f853d2f/original
.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
329 -35.408271 149.131080 2020-05-30T16:26:00Z Eolophus roseicapilla b3f8b976-7b50-4f2f-83a5-4ce96de0bf64 iNaturalist Australia PRESENT Image 2ef7e944-89b5-413b-a3b5-a40dec3ada2f NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/f/2/a/d/2ef7e944-89b5-413b-a3b5-a40dec3ada2f/original
330 -35.408271 149.131080 2020-05-30T16:26:00Z Eolophus roseicapilla b3f8b976-7b50-4f2f-83a5-4ce96de0bf64 iNaturalist Australia PRESENT Image 651aa84d-703a-4564-8b10-230c83809046 NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/6/4/0/9/651aa84d-703a-4564-8b10-230c83809046/original
331 -35.408271 149.131080 2020-05-30T16:26:00Z Eolophus roseicapilla b3f8b976-7b50-4f2f-83a5-4ce96de0bf64 iNaturalist Australia PRESENT Image ae88ae92-0398-4f0b-95ae-1135e40f8dbc NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/c/b/d/8/ae88ae92-0398-4f0b-95ae-1135e40f8dbc/original
332 -35.408271 149.131080 2020-05-30T16:26:00Z Eolophus roseicapilla b3f8b976-7b50-4f2f-83a5-4ce96de0bf64 iNaturalist Australia PRESENT Image e59c3aa1-cd66-4c5d-9aff-aa31c9da2d5f NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/f/5/d/2/e59c3aa1-cd66-4c5d-9aff-aa31c9da2d5f/original
333 -35.408271 149.131080 2020-05-30T16:26:00Z Eolophus roseicapilla b3f8b976-7b50-4f2f-83a5-4ce96de0bf64 iNaturalist Australia PRESENT Image f779de33-c76b-4ead-9682-d2153feec9fc NaN NaN deborod http://creativecommons.org/licenses/by-nc/4.0/ image/jpeg 1800 1200 https://images.ala.org.au/store/c/f/9/c/f779de33-c76b-4ead-9682-d2153feec9fc/original
[334 rows x 17 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.