In [1]:
# lets work with the Cyprinus_carpio species
from pygbif.occurrences import search
In [2]:
# say we only select one dataset that we found before
res = search(taxonKey=4286975) # http://www.gbif.org/species/4286975
In [4]:
res['results'] # list of dictionaries
Out[4]:
[{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2573513',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'coordinateAccuracy': 0.013691,
'coordinateAccuracyInMeters': 1513.95,
'country': 'United States',
'countryCode': 'US',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-01-11T21:51:18.000+0000',
'day': 5,
'decimalLatitude': 34.06977,
'decimalLongitude': -118.34912,
'eventDate': '2016-01-04T23:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1229923598',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2573513',
'identificationID': '4790084',
'identifier': '2573513',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1229923598,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:32.993+0000',
'lastInterpreted': '2016-03-18T04:21:23.721+0000',
'lastParsed': '2016-03-18T04:06:17.125+0000',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'media': [{'created': '2016-01-04T23:00:00.000+0000',
'creator': 'NHM Citizen Science Program',
'format': 'image/png',
'identifier': 'http://static.inaturalist.org/photos/2871437/original.PNG?1452552740',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/2871437',
'rightsHolder': 'NHM Citizen Science Program',
'type': 'StillImage'}],
'modified': '2016-01-19T17:44:57.000+0000',
'month': 1,
'occurrenceID': 'http://www.inaturalist.org/observations/2573513',
'occurrenceRemarks': 'Observation and photo was submitted by @sabrina.mariee via Instagram #natureinla',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'NHM Citizen Science Program',
'references': 'http://www.inaturalist.org/observations/2573513',
'relations': [],
'rights': '© NHM Citizen Science Program some rights reserved',
'rightsHolder': 'NHM Citizen Science Program',
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': '53911',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'verbatimEventDate': '2016-01-05',
'verbatimLocality': 'La Brea Tar Pits',
'year': 2016},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': 'diveboard:297046_1242713_0',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Diveboard',
'coordinateAccuracy': 0.000904,
'coordinateAccuracyInMeters': 99.96,
'country': 'South Africa',
'countryCode': 'ZA',
'datasetID': 'http://ipt.diveboard.com/resource.do?r=diveboard-occurrences',
'datasetKey': '66f6192f-6cc0-45fd-a2d1-e76f5ae3eab2',
'datasetName': 'Diveboard - Scuba diving citizen science',
'dateIdentified': '2016-01-30T23:00:00.000+0000',
'day': 31,
'decimalLatitude': -26.5098,
'decimalLongitude': 28.0674,
'depth': 6.5,
'depthAccuracy': 6.5,
'elevation': 0.0,
'elevationAccuracy': 0.0,
'eventDate': '2016-01-31T07:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1248889687',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'georeferenceSources': 'Google Maps',
'identifiedBy': 'Orcadaniel',
'identifier': 'diveboard:297046_1242713_0',
'identifiers': [],
'infraspecificEpithet': 'carpio',
'institutionCode': 'Diveboard',
'issues': ['COORDINATE_REPROJECTION_SUSPICIOUS'],
'key': 1248889687,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-22T11:55:29.305+0000',
'lastInterpreted': '2016-02-24T14:35:40.246+0000',
'lastParsed': '2016-02-24T14:35:39.998+0000',
'locality': 'Bass Lake',
'modified': '2016-02-02T11:03:16.000+0000',
'month': 1,
'nameAccordingTo': 'EOL',
'order': 'Cypriniformes',
'orderKey': 1153,
'ownerInstitutionCode': 'Diveboard',
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'FR',
'publishingOrgKey': '1989b627-2a61-44db-83e4-392efc5da0a9',
'recordedBy': 'Orcadaniel',
'references': 'http://www.diveboard.com/orcadaniel/D1DR9Of',
'relations': [],
'rights': 'http://creativecommons.org/publicdomain/zero/1.0/',
'rightsHolder': 'Diveboard',
'samplingProtocol': 'citizen science scuba dive observation',
'scientificName': 'Cyprinus carpio carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': 'http://eol.org/pages/1242713',
'taxonKey': 7059109,
'taxonRank': 'SUBSPECIES',
'type': 'Event',
'verbatimLocality': 'Bass Lake, Henley on Klip, Randvaal',
'waterBody': 'Bass Lake',
'year': 2016},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2560728',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'country': 'Korea, Republic of',
'countryCode': 'KR',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-01-06T21:23:18.000+0000',
'day': 4,
'decimalLatitude': 33.24513,
'decimalLongitude': 126.55857,
'eventDate': '2016-01-03T23:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1227772620',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2560728',
'identificationID': '4758691',
'identifier': '2560728',
'identifiers': [],
'infraspecificEpithet': 'haematopterus',
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1227772620,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:31.454+0000',
'lastInterpreted': '2016-03-18T04:21:08.611+0000',
'lastParsed': '2016-03-18T04:06:10.746+0000',
'license': 'http://creativecommons.org/licenses/by/4.0/',
'media': [{'created': '2016-01-05T00:23:18.000+0000',
'creator': 'Kim, Hyun-tae',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/2852566/original.jpg?1452119000',
'license': 'http://creativecommons.org/licenses/by/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/2852566',
'rightsHolder': 'Kim, Hyun-tae',
'type': 'StillImage'},
{'created': '2016-01-05T00:23:21.000+0000',
'creator': 'Kim, Hyun-tae',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/2852567/original.jpg?1452119046',
'license': 'http://creativecommons.org/licenses/by/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/2852567',
'rightsHolder': 'Kim, Hyun-tae',
'type': 'StillImage'}],
'modified': '2016-01-06T22:21:43.000+0000',
'month': 1,
'occurrenceID': 'http://www.inaturalist.org/observations/2560728',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'Kim, Hyun-tae',
'references': 'http://www.inaturalist.org/observations/2560728',
'relations': [],
'rights': '© Kim, Hyun-tae some rights reserved',
'rightsHolder': 'Kim, Hyun-tae',
'scientificName': 'Cyprinus carpio haematopterus Martens, 1876',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': '326764',
'taxonKey': 6166576,
'taxonRank': 'SUBSPECIES',
'verbatimEventDate': '2016-01-04',
'year': 2016},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2702842',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'country': 'Australia',
'countryCode': 'AU',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-02-21T11:28:35.000+0000',
'day': 21,
'decimalLatitude': -33.88555,
'decimalLongitude': 151.19302,
'eventDate': '2016-02-21T05:21:36.000+0000',
'eventTime': '05:21:36Z',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1253304597',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2702842',
'identificationID': '5231231',
'identifier': '2702842',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1253304597,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:46.982+0000',
'lastInterpreted': '2016-03-18T04:23:38.205+0000',
'lastParsed': '2016-03-18T04:07:12.750+0000',
'license': 'http://creativecommons.org/licenses/by/4.0/',
'media': [{'created': '2016-02-22T00:21:36.000+0000',
'creator': 'sea-kangaroo',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/3043927/original.JPG?1456057717',
'license': 'http://creativecommons.org/licenses/by-nc-nd/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/3043927',
'rightsHolder': 'sea-kangaroo',
'type': 'StillImage'}],
'modified': '2016-03-07T22:21:24.000+0000',
'month': 2,
'occurrenceID': 'http://www.inaturalist.org/observations/2702842',
'occurrenceRemarks': 'Dark & gold koi coming up from the murk to dispatch bread with great efficiency.',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'sea-kangaroo',
'references': 'http://www.inaturalist.org/observations/2702842',
'relations': [],
'rights': '© sea-kangaroo some rights reserved',
'rightsHolder': 'sea-kangaroo',
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': '53911',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'verbatimEventDate': '2016-02-21 16:21:36',
'verbatimLocality': 'Victoria Park, Sydney, New South Wales, Australia',
'year': 2016},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2696995',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'coordinateAccuracy': 0.003228,
'coordinateAccuracyInMeters': 356.95,
'country': 'United States',
'countryCode': 'US',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-02-19T16:51:07.000+0000',
'day': 18,
'decimalLatitude': 34.14229,
'decimalLongitude': -118.34479,
'eventDate': '2016-02-17T23:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1253302326',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2696995',
'identificationID': '5217495',
'identifier': '2696995',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1253302326,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:46.008+0000',
'lastInterpreted': '2016-03-18T04:23:30.058+0000',
'lastParsed': '2016-03-18T04:07:09.767+0000',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'media': [{'created': '2016-02-17T23:00:00.000+0000',
'creator': 'NHM Citizen Science Program',
'format': 'image/png',
'identifier': 'http://static.inaturalist.org/photos/3035881/original.PNG?1455904270',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/3035881',
'rightsHolder': 'NHM Citizen Science Program',
'type': 'StillImage'}],
'modified': '2016-03-07T22:22:44.000+0000',
'month': 2,
'occurrenceID': 'http://www.inaturalist.org/observations/2696995',
'occurrenceRemarks': 'Observation and photo submission by @dankingbass via Instagram #LAriver ',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'NHM Citizen Science Program',
'references': 'http://www.inaturalist.org/observations/2696995',
'relations': [],
'rights': '© NHM Citizen Science Program some rights reserved',
'rightsHolder': 'NHM Citizen Science Program',
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': '53911',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'verbatimEventDate': '2016-02-18',
'verbatimLocality': 'la river, glendale',
'year': 2016},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2732895',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'country': 'Australia',
'countryCode': 'AU',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-02-29T22:56:39.000+0000',
'day': 24,
'decimalLatitude': -33.90381,
'decimalLongitude': 151.2266,
'eventDate': '2016-02-24T03:24:11.000+0000',
'eventTime': '03:24:11Z',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1253314297',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2732895',
'identificationID': '5298101',
'identifier': '2732895',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1253314297,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:51.191+0000',
'lastInterpreted': '2016-03-18T04:24:09.812+0000',
'lastParsed': '2016-03-18T04:07:25.318+0000',
'license': 'http://creativecommons.org/licenses/by/4.0/',
'media': [{'created': '2016-02-24T22:24:11.000+0000',
'creator': 'sea-kangaroo',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/3083408/original.JPG?1456790200',
'license': 'http://creativecommons.org/licenses/by-nc-nd/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/3083408',
'rightsHolder': 'sea-kangaroo',
'type': 'StillImage'},
{'created': '2016-02-24T22:22:01.000+0000',
'creator': 'sea-kangaroo',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/3083411/original.JPG?1456790259',
'license': 'http://creativecommons.org/licenses/by-nc-nd/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/3083411',
'rightsHolder': 'sea-kangaroo',
'type': 'StillImage'},
{'created': '2016-02-24T22:25:58.000+0000',
'creator': 'sea-kangaroo',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/3083412/original.JPG?1456790289',
'license': 'http://creativecommons.org/licenses/by-nc-nd/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/3083412',
'rightsHolder': 'sea-kangaroo',
'type': 'StillImage'},
{'created': '2016-02-24T22:25:23.000+0000',
'creator': 'sea-kangaroo',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/3083418/original.JPG?1456790384',
'license': 'http://creativecommons.org/licenses/by-nc-nd/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/3083418',
'rightsHolder': 'sea-kangaroo',
'type': 'StillImage'}],
'modified': '2016-03-07T22:17:17.000+0000',
'month': 2,
'occurrenceID': 'http://www.inaturalist.org/observations/2732895',
'occurrenceRemarks': 'When I came and stood on the footbridge, a very large number of hopeful mouths came speeding over! Carp, turtles, waterfowl, but mostly just huge carp. See 3rd photo for an overview. Some of the carp were more gold than others, and one looked like a koi (4th photo). A managed pest in the park: http://blog.centennialparklands.com.au/a-load-of-carp/',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'sea-kangaroo',
'references': 'http://www.inaturalist.org/observations/2732895',
'relations': [],
'rights': '© sea-kangaroo some rights reserved',
'rightsHolder': 'sea-kangaroo',
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': '53911',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'verbatimEventDate': '2016-02-24 14:24:11',
'verbatimLocality': 'Centennial Park, Sydney, New South Wales, Australia',
'year': 2016},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2741565',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'country': 'United States',
'countryCode': 'US',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-03-03T22:29:29.000+0000',
'day': 3,
'decimalLatitude': 30.18065,
'decimalLongitude': -97.72232,
'eventDate': '2016-03-03T15:59:28.000+0000',
'eventTime': '15:59:28Z',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1257410156',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2741565',
'identificationID': '5322052',
'identifier': '2741565',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1257410156,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:52.607+0000',
'lastInterpreted': '2016-03-18T04:24:19.699+0000',
'lastParsed': '2016-03-18T04:07:29.618+0000',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'media': [{'created': '2016-03-03T17:59:28.000+0000',
'creator': 'Rebecca Cowser',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/3096142/original.jpg?1457047133',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/3096142',
'rightsHolder': 'Rebecca Cowser',
'type': 'StillImage'}],
'modified': '2016-03-07T22:15:55.000+0000',
'month': 3,
'occurrenceID': 'http://www.inaturalist.org/observations/2741565',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
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'occurrenceRemarks': 'A group of four or five fishes found in Calleguas Creek next to CSUCI. They have a light green body heavily accented by black, which sharply defines their large scales. Their tail, pelvic and anal fins are slightly red. They appear to be a little over a foot in length. They are difficult to see from this iPhone camera, but let me emphasize, the black lines on their bodies are not lines or stripes or dots, but rather outlines of their scales, which make them difficult to find on any fish list. Their mouths may be below their body, possibly making them carps, but it is hard to definitively tell from observing then from above and they do not seem to match images for white or blue catfishes (found in this watershed)',
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'preparations': 'tissue (frozen); dissected whole animal (70% ethanol); tissue (95% ethanol); tissue (95% ethanol) sample',
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'occurrenceRemarks': 'Churning up the mud parts of the river bottom near shallow areas and emergent plants.',
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'occurrenceRemarks': "Common Carp (Cyprinus carpio) 2 August 2015: While walking the Bittern Marsh Trail we observed how the headless carcass of a large Common Carp (Cyprinus carpio), a common freshwater fish of Lake Lewisville and the Elm Fork Trinity River, was being washed back and forth by the wave action caused by the large volume of water being released just upstream not more than a quarter-mile at the Lake Lewisville dam's water outlet. At this particular point on the Bittern Marsh Trail at the Lake Lewisville Environmental Learning Area (LLELA) a portion of the river's bank and immediate area had been washed out by the historic spring and May 2015 rainfall in North Texas (and statewide) creating a temporary inlet of sorts. Here the voluminous water released from Lake Lewisville's dam by the authorities created waves like those of the ocean with a similar ebb and flow. This Common Carp carcass was coming and going with each wave but essentially remained in place ensconced on the sandy beach that had been created by this series of events. The Common Carp had met its fate and the waves would slowly but surely erode its tissue and return it from whence it came. No other fish in the Elm Fork Trinity River has this particular physical appearance even when deteriorated as in these images, the Common Carp's distinctive features continue to indicate its species. LLELA is administered jointly by the US Army Corps of Engineers, the City of Lewisville, Texas, the Lewisville Independent School District, and the University of North Texas.",
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'higherClassification': 'Animalia Chordata Craniata Gnathostomata Actinopterygii Neopterygii Ostariophysi Cypriniformes Cyprinoidea Cyprinidae Cyprinus carpio',
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'preparations': 'tissue (frozen); dissected whole animal (70% ethanol); tissue (95% ethanol); tissue (95% ethanol) sample',
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'verbatimEventDate': '2015-08-12',
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'locality': 'Fuik 2',
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'modified': '2015-08-11T22:00:00.000+0000',
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'type': 'event',
'verbatimCoordinateSystem': 'Belgium Lambert 72',
'verbatimEventDate': '2015-08-12',
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'modified': '2015-08-11T22:00:00.000+0000',
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'taxonRank': 'SPECIES',
'verbatimEventDate': '2014-04-26 14:47:51',
'verbatimLocality': 'Allegheny, Pennsylvania, United States',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-567210613',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 24,
'decimalLatitude': 49.99879,
'decimalLongitude': 8.57116,
'eventDate': '2014-04-23T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921373811',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921373811,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T19:00:35.798+0000',
'lastInterpreted': '2015-08-26T16:06:12.563+0000',
'lastParsed': '2015-08-26T16:06:12.319+0000',
'locality': 'Walldorf-Süd (Garten- u. Wohngebiet)',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '-1052402410',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-428424613',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Japan',
'countryCode': 'JP',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 13,
'decimalLatitude': 35.83212,
'decimalLongitude': 139.56282,
'eventDate': '2014-04-12T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921384823',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921384823,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T19:31:28.027+0000',
'lastInterpreted': '2014-11-14T21:14:18.749+0000',
'lastParsed': '2014-11-14T21:14:18.687+0000',
'locality': 'Yanasegawa',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '1739659602',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-1587263087',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 7,
'decimalLatitude': 51.92998,
'decimalLongitude': 10.48143,
'eventDate': '2014-04-06T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921389913',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921389913,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T19:45:58.678+0000',
'lastInterpreted': '2014-11-14T21:15:48.649+0000',
'lastParsed': '2014-11-14T21:15:48.549+0000',
'locality': 'Sechs Teiche bei Goslar',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '-701934471',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2059527282',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 12,
'decimalLatitude': 50.9408,
'decimalLongitude': 6.64621,
'eventDate': '2014-04-11T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921370754',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921370754,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T18:49:43.210+0000',
'lastInterpreted': '2015-08-26T16:00:06.039+0000',
'lastParsed': '2015-08-26T15:57:55.342+0000',
'locality': 'Erft bei Bergheim, renaturierter Abschnitt',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '1139381203',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-1101346575',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 26,
'decimalLatitude': 50.83641,
'decimalLongitude': 6.85307,
'eventDate': '2014-04-25T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921354586',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921354586,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T18:03:36.693+0000',
'lastInterpreted': '2014-11-14T21:06:27.201+0000',
'lastParsed': '2014-11-14T21:06:27.171+0000',
'locality': 'Bleibtreusee',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '1139381203',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-598460597',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 25,
'decimalLatitude': 50.98515,
'decimalLongitude': 6.84536,
'eventDate': '2014-04-24T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921377937',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921377937,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T19:10:39.637+0000',
'lastInterpreted': '2015-08-26T16:16:50.250+0000',
'lastParsed': '2015-08-26T16:16:50.119+0000',
'locality': 'Baadenberger Senke',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '1139381203',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-898440598',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 23,
'decimalLatitude': 50.90833,
'decimalLongitude': 6.35256,
'eventDate': '2014-04-22T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921370623',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921370623,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T18:49:43.067+0000',
'lastInterpreted': '2015-08-26T16:00:05.305+0000',
'lastParsed': '2015-08-26T15:57:55.133+0000',
'locality': 'Jülich-Kirchberg, Fischteiche',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '-178476598',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-1232470634',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 5,
'decimalLatitude': 51.54431,
'decimalLongitude': 9.90817,
'eventDate': '2014-04-04T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921386642',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921386642,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T19:36:22.023+0000',
'lastInterpreted': '2014-11-14T21:14:47.258+0000',
'lastParsed': '2014-11-14T21:14:47.214+0000',
'locality': 'Göttingen - Levinpark',
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '-675492344',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '-1696428425',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'naturgucker',
'country': 'Germany',
'countryCode': 'DE',
'datasetKey': '6ac3f774-d9fb-4796-b3e9-92bf6c81c084',
'day': 25,
'decimalLatitude': 48.72789,
'decimalLongitude': 9.10273,
'eventDate': '2014-04-24T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '921373362',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'identifiers': [],
'institutionCode': 'naturgucker',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 921373362,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-24T18:57:46.545+0000',
'lastInterpreted': '2015-08-26T16:04:51.838+0000',
'lastParsed': '2015-08-26T16:04:51.736+0000',
'locality': 'Stuttgart-Vaihingen Freibad',
'media': [{'format': 'text/html',
'references': 'http://www.enjoynature.net/?bild=-1484506967'}],
'month': 4,
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'BIOCASE',
'publishingCountry': 'DE',
'publishingOrgKey': 'bb646dff-a905-4403-a49b-6d378c2cf0d9',
'recordedBy': '323595770',
'relations': [],
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'year': 2014},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': 'diveboard:128159_985921_0',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Diveboard',
'country': 'United States',
'countryCode': 'US',
'datasetID': 'http://ipt.diveboard.com/resource.do?r=diveboard-occurrences',
'datasetKey': '66f6192f-6cc0-45fd-a2d1-e76f5ae3eab2',
'datasetName': 'Diveboard - Scuba diving citizen science',
'dateIdentified': '2014-04-16T22:00:00.000+0000',
'day': 17,
'decimalLatitude': 36.0361,
'decimalLongitude': -114.709,
'depth': 15.39,
'depthAccuracy': 15.39,
'elevation': 335.28,
'elevationAccuracy': 0.0,
'eventDate': '2014-04-17T11:46:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '896186097',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'georeferenceSources': 'Google Maps',
'identifiedBy': 'Michael Dyer',
'identifier': 'diveboard:128159_985921_0',
'identifiers': [],
'institutionCode': 'Diveboard',
'issues': ['COORDINATE_REPROJECTION_SUSPICIOUS'],
'key': 896186097,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-22T11:55:25.737+0000',
'lastInterpreted': '2015-05-27T14:22:33.019+0000',
'lastParsed': '2015-05-27T14:22:04.525+0000',
'locality': 'Kingman Wash',
'modified': '2015-04-29T11:49:21.000+0000',
'month': 4,
'nameAccordingTo': 'EOL',
'order': 'Cypriniformes',
'orderKey': 1153,
'ownerInstitutionCode': 'Diveboard',
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'FR',
'publishingOrgKey': '1989b627-2a61-44db-83e4-392efc5da0a9',
'recordedBy': 'Michael Dyer',
'references': 'http://www.diveboard.com/michaelrdyer/D5Nf1V',
'relations': [],
'rights': 'http://creativecommons.org/publicdomain/zero/1.0/',
'rightsHolder': 'Diveboard',
'samplingProtocol': 'citizen science scuba dive observation',
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': 'http://eol.org/pages/985921',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'type': 'Event',
'verbatimLocality': 'Kingman Wash, Arizona',
'waterBody': 'Lake Mead',
'year': 2014}]
In [5]:
res['count'] # how many records?
Out[5]:
76108
In [6]:
len(res['results'])
Out[6]:
300
In [7]:
res['results'][0]
Out[7]:
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2573513',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'coordinateAccuracy': 0.013691,
'coordinateAccuracyInMeters': 1513.95,
'country': 'United States',
'countryCode': 'US',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-01-11T21:51:18.000+0000',
'day': 5,
'decimalLatitude': 34.06977,
'decimalLongitude': -118.34912,
'eventDate': '2016-01-04T23:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1229923598',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2573513',
'identificationID': '4790084',
'identifier': '2573513',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1229923598,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:32.993+0000',
'lastInterpreted': '2016-03-18T04:21:23.721+0000',
'lastParsed': '2016-03-18T04:06:17.125+0000',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'media': [{'created': '2016-01-04T23:00:00.000+0000',
'creator': 'NHM Citizen Science Program',
'format': 'image/png',
'identifier': 'http://static.inaturalist.org/photos/2871437/original.PNG?1452552740',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/2871437',
'rightsHolder': 'NHM Citizen Science Program',
'type': 'StillImage'}],
'modified': '2016-01-19T17:44:57.000+0000',
'month': 1,
'occurrenceID': 'http://www.inaturalist.org/observations/2573513',
'occurrenceRemarks': 'Observation and photo was submitted by @sabrina.mariee via Instagram #natureinla',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'NHM Citizen Science Program',
'references': 'http://www.inaturalist.org/observations/2573513',
'relations': [],
'rights': '© NHM Citizen Science Program some rights reserved',
'rightsHolder': 'NHM Citizen Science Program',
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': '53911',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'verbatimEventDate': '2016-01-05',
'verbatimLocality': 'La Brea Tar Pits',
'year': 2016}
In [8]:
# another way, let's search for Cyprinus_carpio
from pygbif.species import *
In [9]:
result = name_backbone(name="Cyprinus", verbose=False)
In [10]:
result
Out[10]:
{'canonicalName': 'Cyprinus',
'class': 'Actinopterygii',
'classKey': 204,
'confidence': 94,
'family': 'Cyprinidae',
'familyKey': 7336,
'genus': 'Cyprinus',
'genusKey': 2347697,
'kingdom': 'Animalia',
'kingdomKey': 1,
'matchType': 'EXACT',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'rank': 'GENUS',
'scientificName': 'Cyprinus Linnaeus, 1758',
'status': 'ACCEPTED',
'synonym': False,
'usageKey': 2347697}
In [11]:
usageKey = result['usageKey']
res1 = search(taxonKey=usageKey) # same result as above
In [12]:
usageKey
Out[12]:
2347697
In [13]:
len(res1['results'])
Out[13]:
300
In [14]:
for res in res1['results']:
print(res['datasetKey'])
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50c9509d-22c7-4a22-a47d-8c48425ef4a7
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
6ac3f774-d9fb-4796-b3e9-92bf6c81c084
66f6192f-6cc0-45fd-a2d1-e76f5ae3eab2
In [15]:
res1['results'][0]
Out[15]:
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2573513',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'coordinateAccuracy': 0.013691,
'coordinateAccuracyInMeters': 1513.95,
'country': 'United States',
'countryCode': 'US',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2016-01-11T21:51:18.000+0000',
'day': 5,
'decimalLatitude': 34.06977,
'decimalLongitude': -118.34912,
'eventDate': '2016-01-04T23:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cyprinidae',
'familyKey': 7336,
'gbifID': '1229923598',
'genericName': 'Cyprinus',
'genus': 'Cyprinus',
'genusKey': 2347697,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2573513',
'identificationID': '4790084',
'identifier': '2573513',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1229923598,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:32.993+0000',
'lastInterpreted': '2016-03-18T04:21:23.721+0000',
'lastParsed': '2016-03-18T04:06:17.125+0000',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'media': [{'created': '2016-01-04T23:00:00.000+0000',
'creator': 'NHM Citizen Science Program',
'format': 'image/png',
'identifier': 'http://static.inaturalist.org/photos/2871437/original.PNG?1452552740',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/2871437',
'rightsHolder': 'NHM Citizen Science Program',
'type': 'StillImage'}],
'modified': '2016-01-19T17:44:57.000+0000',
'month': 1,
'occurrenceID': 'http://www.inaturalist.org/observations/2573513',
'occurrenceRemarks': 'Observation and photo was submitted by @sabrina.mariee via Instagram #natureinla',
'order': 'Cypriniformes',
'orderKey': 1153,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'NHM Citizen Science Program',
'references': 'http://www.inaturalist.org/observations/2573513',
'relations': [],
'rights': '© NHM Citizen Science Program some rights reserved',
'rightsHolder': 'NHM Citizen Science Program',
'scientificName': 'Cyprinus carpio Linnaeus, 1758',
'species': 'Cyprinus carpio',
'speciesKey': 4286975,
'specificEpithet': 'carpio',
'taxonID': '53911',
'taxonKey': 4286975,
'taxonRank': 'SPECIES',
'verbatimEventDate': '2016-01-05',
'verbatimLocality': 'La Brea Tar Pits',
'year': 2016}
In [16]:
for res in res1['results']:
if 'elevation' in res:
print(res['elevation']) # not all records have elevation
0.0
195.07
0.0
0.0
0.0
-1.0
-1.0
-1.0
0.0
-1.0
-1.0
0.0
335.28
In [17]:
for res in res1['results']:
if 'country' in res:
print(res['country'])
United States
South Africa
Korea, Republic of
Australia
United States
Australia
United States
United States
United States
United States
United States
Germany
Philippines
United States
United States
United States
United States
United States
United States
United States
Mexico
United States
United States
United States
United States
Japan
United States
Germany
Belgium
Belgium
Belgium
Belgium
Spain
Belgium
Singapore
Italy
Belgium
United States
United States
United States
Belgium
Japan
Norway
Germany
United States
Netherlands
Netherlands
United States
Sweden
Canada
United States
United States
Sweden
Belgium
Sweden
United States
United States
Germany
United States
United States
Germany
Japan
Belgium
Belgium
United States
Belgium
Belgium
Belgium
United States
United States
Belgium
United States
United States
United States
Belgium
New Zealand
United States
Belgium
Belgium
Belgium
Belgium
Norway
Belgium
Mexico
United States
Spain
Japan
Mexico
United States
Mexico
United States
United States
United States
United States
United States
United States
United States
United States
United States
United States
United States
Japan
United States
China
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Mexico
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Germany
Netherlands
Netherlands
United States
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Germany
Germany
Netherlands
Netherlands
Netherlands
Netherlands
United States
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Germany
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Germany
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
Netherlands
United States
Germany
Netherlands
Germany
Germany
Netherlands
Japan
Germany
New Zealand
United States
Netherlands
Germany
Netherlands
United States
Netherlands
Netherlands
Netherlands
United States
Netherlands
Netherlands
Netherlands
Germany
Netherlands
Netherlands
Germany
United States
Netherlands
Germany
Netherlands
Germany
Germany
Germany
Sweden
Sweden
Belgium
Germany
United States
Germany
Japan
Germany
Germany
Germany
Germany
Germany
Germany
Germany
United States
In [18]:
from mpl_toolkits.basemap import Basemap
In [19]:
%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np
In [27]:
lons = []
lats = []
for res in res1['results']:
if 'decimalLatitude' in res and 'decimalLongitude' in res:
lons.append(res['decimalLongitude'])
lats.append(res['decimalLatitude'])
In [97]:
x, y = my_map(lons, lats)
In [29]:
# changed projection from 'ortho' to 'robin'
my_map = Basemap(projection='robin', lat_0=50, lon_0=-100,
resolution='l', area_thresh=1000.0)
my_map.drawcoastlines()
my_map.drawcountries()
my_map.fillcontinents(color='coral')
# draw latitude and longitude
my_map.drawmeridians(np.arange(0, 360, 30))
my_map.drawparallels(np.arange(-90, 90, 30))
my_map.plot(x, y, 'bo', markersize=2)
plt.show()
In [30]:
# let's zoom in, we need lower/upper left/right latitude and longitude
llcrnrlon = min(lons)
llcrnrlat = min(lats)
urcrnrlon = max(lons)
urcrnrlat = max(lats)
In [31]:
# changed projection from 'ortho' to 'robin' to 'merc'
# Make this plot larger.
plt.figure(figsize=(16,12))
plt.title("Cyprinus_carpio occurence records from GBIF")
my_map = Basemap(projection='merc', lat_0=50, lon_0=-100,
resolution='c', area_thresh=1000.0,
llcrnrlon=llcrnrlon,
llcrnrlat=llcrnrlat,
urcrnrlon=urcrnrlon,
urcrnrlat=urcrnrlat)
my_map.drawcoastlines()
my_map.drawcountries()
my_map.drawmapboundary(fill_color='#649eff')
my_map.fillcontinents(color='#cc9955')
# draw latitude and longitude
my_map.drawmeridians(np.arange(0, 360, 30))
my_map.drawparallels(np.arange(-90, 90, 30))
my_map.plot(x, y, 'bo', markersize=5, color="#b01a1a")
plt.show()
In [32]:
cottus_bairdii = name_backbone(name="Cottus_bairdii", verbose=False)
In [33]:
usageKey = cottus_bairdii['usageKey']
res1 = search(taxonKey=usageKey, limit=100000) # same result as above
In [34]:
len(res1['results'])
Out[34]:
300
In [35]:
res1 # mind you, endOfRecords is FALSE
Out[35]:
{'count': 6458,
'endOfRecords': False,
'limit': 300,
'offset': 0,
'results': [{'accessRights': 'http://fieldmuseum.org/about/copyright-information',
'basisOfRecord': 'PRESERVED_SPECIMEN',
'catalogNumber': '126264',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Fishes',
'collectionID': 'Fishes',
'continent': 'NORTH_AMERICA',
'country': 'United States',
'countryCode': 'US',
'county': 'Door',
'datasetID': 'fishes-23-may-2016',
'datasetKey': 'afc30a94-6107-488a-b9c0-ba9c4fa68b7c',
'day': 16,
'decimalLatitude': 44.70465,
'decimalLongitude': -87.3599,
'depth': 0.7,
'depthAccuracy': 0.5,
'endDayOfYear': '16',
'eventDate': '2015-06-15T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cottidae',
'familyKey': 8621,
'fieldNumber': 'KAS15-14',
'gbifID': '1230322394',
'genericName': 'Cottus',
'genus': 'Cottus',
'genusKey': 2334066,
'geodeticDatum': 'WGS84',
'georeferenceProtocol': 'Google Earth',
'higherClassification': 'Animalia Chordata Actinopterygii Scorpaeniformes Cottidae',
'higherGeography': 'North America, U.S.A., Wisconsin, Door: Bear Creek half way up on Bear Creek Road at small bridge and east to County U.',
'identifiedBy': 'Mr. Thomas G. Anton : The Ecological Consulting Group, LLC',
'identifier': '58df7d71-382c-4093-abdd-b722884b0e1f',
'identifiers': [],
'individualCount': 19,
'institutionCode': 'FMNH',
'institutionID': 'FMNH',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1230322394,
'kingdom': 'Animalia',
'kingdomKey': 1,
'language': 'English',
'lastCrawled': '2016-03-23T21:32:16.516+0000',
'lastInterpreted': '2016-03-23T21:32:55.036+0000',
'lastParsed': '2016-03-23T21:32:16.545+0000',
'locality': 'Bear Creek half way up on Bear Creek Road at small bridge and east to County U.',
'media': [{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/475/IMG_4143.JPG',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/478/IMG_4146.JPG',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/481/IMG_4147.jpg',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/484/IMG_4154.JPG',
'type': 'StillImage'}],
'month': 6,
'nomenclaturalCode': 'ICZN',
'occurrenceID': '58df7d71-382c-4093-abdd-b722884b0e1f',
'order': 'Scorpaeniformes',
'orderKey': 590,
'organismID': '3363774',
'ownerInstitutionCode': 'FMNH',
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '7b8aff00-a9f8-11d8-944b-b8a03c50a862',
'recordedBy': 'K. Swagel',
'relations': [],
'rights': 'https://creativecommons.org/publicdomain/zero/1.0/',
'rightsHolder': 'The Field Museum of Natural History',
'scientificName': 'Cottus bairdii Girard, 1850',
'species': 'Cottus bairdii',
'speciesKey': 2334131,
'specificEpithet': 'bairdii',
'startDayOfYear': '16',
'stateProvince': 'Wisconsin',
'taxonKey': 2334131,
'taxonRank': 'SPECIES',
'type': 'PhysicalObject',
'year': 2015},
{'basisOfRecord': 'HUMAN_OBSERVATION',
'catalogNumber': '2021630',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Observations',
'coordinateAccuracy': 0.001655,
'coordinateAccuracyInMeters': 183.01,
'country': 'United States',
'countryCode': 'US',
'datasetKey': '50c9509d-22c7-4a22-a47d-8c48425ef4a7',
'datasetName': 'iNaturalist research-grade observations',
'dateIdentified': '2015-10-02T03:29:37.000+0000',
'day': 20,
'decimalLatitude': 45.47574,
'decimalLongitude': -123.19395,
'eventDate': '2015-09-19T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cottidae',
'familyKey': 8621,
'gbifID': '1227721754',
'genericName': 'Cottus',
'genus': 'Cottus',
'genusKey': 2334066,
'geodeticDatum': 'WGS84',
'http://unknown.org/occurrenceDetails': 'http://www.inaturalist.org/observations/2021630',
'identificationID': '3850203',
'identifier': '2021630',
'identifiers': [],
'institutionCode': 'iNaturalist',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1227721754,
'kingdom': 'Animalia',
'kingdomKey': 1,
'lastCrawled': '2016-03-29T17:17:03.160+0000',
'lastInterpreted': '2016-03-18T04:15:52.842+0000',
'lastParsed': '2016-03-18T04:04:09.698+0000',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'media': [{'created': '2015-09-20T08:13:16.000+0000',
'creator': 'camiewestfall',
'format': 'image/jpeg',
'identifier': 'http://static.inaturalist.org/photos/2464611/original.JPG?1443763779',
'license': 'http://creativecommons.org/licenses/by-nc/4.0/',
'publisher': 'iNaturalist',
'references': 'http://www.inaturalist.org/photos/2464611',
'rightsHolder': 'camiewestfall',
'type': 'StillImage'}],
'modified': '2015-12-05T23:52:11.000+0000',
'month': 9,
'occurrenceID': 'http://www.inaturalist.org/observations/2021630',
'order': 'Scorpaeniformes',
'orderKey': 590,
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '28eb1a3f-1c15-4a95-931a-4af90ecb574d',
'recordedBy': 'camiewestfall',
'references': 'http://www.inaturalist.org/observations/2021630',
'relations': [],
'rights': '© camiewestfall some rights reserved',
'rightsHolder': 'camiewestfall',
'scientificName': 'Cottus bairdii Girard, 1850',
'species': 'Cottus bairdii',
'speciesKey': 2334131,
'specificEpithet': 'bairdii',
'taxonID': '47636',
'taxonKey': 2334131,
'taxonRank': 'SPECIES',
'verbatimEventDate': '2015-09-20',
'verbatimLocality': 'Henry Hagg Lake, Scoggins Creek, Gaston OR',
'year': 2015},
{'accessRights': 'http://fieldmuseum.org/about/copyright-information',
'basisOfRecord': 'PRESERVED_SPECIMEN',
'catalogNumber': '126326',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Fishes',
'collectionID': 'Fishes',
'continent': 'NORTH_AMERICA',
'country': 'United States',
'countryCode': 'US',
'county': 'Kewaunee',
'datasetID': 'fishes-23-may-2016',
'datasetKey': 'afc30a94-6107-488a-b9c0-ba9c4fa68b7c',
'day': 22,
'decimalLatitude': 44.45704,
'decimalLongitude': -87.68428,
'depth': 0.55,
'depthAccuracy': 0.25,
'endDayOfYear': '22',
'eventDate': '2015-12-21T23:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cottidae',
'familyKey': 8621,
'fieldNumber': 'KAS15-29',
'gbifID': '1262186709',
'genericName': 'Cottus',
'genus': 'Cottus',
'genusKey': 2334066,
'geodeticDatum': 'WGS84',
'georeferenceProtocol': 'Google Earth',
'higherClassification': 'Animalia Chordata Actinopterygii Scorpaeniformes Cottidae',
'higherGeography': 'North America, U.S.A., Wisconsin, Kewaunee, Ellisville: East Twin River where it crosses County Road AB in Ellisville, WI (N3670 County Rd. AB, Town of Montpelier)',
'identifiedBy': 'Mr. Thomas G. Anton : The Ecological Consulting Group, LLC',
'identifier': '15af3b5e-6d33-45d7-bbec-dc687bf473cf',
'identifiers': [],
'individualCount': 12,
'institutionCode': 'FMNH',
'institutionID': 'FMNH',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1262186709,
'kingdom': 'Animalia',
'kingdomKey': 1,
'language': 'English',
'lastCrawled': '2016-03-23T21:32:16.593+0000',
'lastInterpreted': '2016-03-23T21:32:55.930+0000',
'lastParsed': '2016-03-23T21:32:16.873+0000',
'locality': 'Ellisville, East Twin River where it crosses County Road AB in Ellisville, WI (N3670 County Rd. AB, Town of Montpelier)',
'media': [{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1269/483/IMG_7039.JPG',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1269/484/IMG_7041.JPG',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1269/485/IMG_7043.JPG',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1269/486/IMG_7045.JPG',
'type': 'StillImage'}],
'month': 12,
'nomenclaturalCode': 'ICZN',
'occurrenceID': '15af3b5e-6d33-45d7-bbec-dc687bf473cf',
'order': 'Scorpaeniformes',
'orderKey': 590,
'organismID': '3369013',
'ownerInstitutionCode': 'FMNH',
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '7b8aff00-a9f8-11d8-944b-b8a03c50a862',
'recordedBy': 'K. Swagel',
'relations': [],
'rights': 'https://creativecommons.org/publicdomain/zero/1.0/',
'rightsHolder': 'The Field Museum of Natural History',
'scientificName': 'Cottus bairdii Girard, 1850',
'species': 'Cottus bairdii',
'speciesKey': 2334131,
'specificEpithet': 'bairdii',
'startDayOfYear': '22',
'stateProvince': 'Wisconsin',
'taxonKey': 2334131,
'taxonRank': 'SPECIES',
'type': 'PhysicalObject',
'year': 2015},
{'basisOfRecord': 'PRESERVED_SPECIMEN',
'catalogNumber': 'OSUMU 573110',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Fishes',
'country': 'United States',
'countryCode': 'US',
'county': 'Logan',
'datasetKey': '813b435e-f762-11e1-a439-00145eb45e9a',
'dateIdentified': '2013-12-31T23:00:00.000+0000',
'day': 19,
'decimalLatitude': 40.2531,
'decimalLongitude': -83.7488,
'eventDate': '2014-02-18T23:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cottidae',
'familyKey': 8621,
'fieldNotes': '; Group Number: 22; Preparation: ; Effort: 0915-1315, 1 mile; Length: ; Alch Storage: ; Comments:',
'gbifID': '1064530334',
'genericName': 'Cottus',
'genus': 'Cottus',
'genusKey': 2334066,
'geodeticDatum': 'WGS84',
'georeferenceRemarks': 'Locality: Fish; Drainage: Great Miami River - Ohio River; OSUM locality geocoordinate precision rating 1 (within 1000 feet)',
'georeferenceSources': 'Google Maps',
'identifiedBy': 'Kibbey, M. R. (Marc Randall)',
'identifier': 'urn:lsid:biosci.ohio-state.edu:osuc_occurrences:OSUMU__573110',
'identifiers': [],
'institutionCode': 'Ohio State University - Fish Division, Columbus, OH (OSUM)',
'issues': ['GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1064530334,
'kingdom': 'Animalia',
'kingdomKey': 1,
'language': 'en',
'lastCrawled': '2015-11-30T21:38:57.580+0000',
'lastInterpreted': '2015-11-30T21:38:57.888+0000',
'lastParsed': '2015-11-30T21:38:57.590+0000',
'lifeStage': 'ADULT',
'locality': 'Mad River, ust SR 245 and dst TR 174, in West Liberty Lions Park, in West Liberty OH, Liberty Township',
'modified': '2015-07-13T14:52:04.000+0000',
'month': 2,
'occurrenceID': 'urn:lsid:biosci.ohio-state.edu:osuc_occurrences:OSUMU__573110',
'order': 'Scorpaeniformes',
'orderKey': 590,
'phylum': 'Chordata',
'phylumKey': 44,
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'verbatimDepth': 'ca. 0.4 m',
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'fieldNotes': 'ACC: 2013:XII:15; Group Number: 22; Effort: 30 minutes; Length: 61.5mm SL; Comments: See OSUMU 438649 for Field Sample',
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'recordedBy': 'Zimmerman, B. J. (Brian J.) & Baker, J. (Justin)',
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'samplingProtocol': "8' seine",
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'decimalLatitude': 41.5913,
'decimalLongitude': -84.599,
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'verbatimLocality': 'Shocker time: 4718; Substrate = cobble, boulder, gravel, silt. Sampled 300 upstream, beginning at tributary on the right, ca. 50 ft. above low water bridge. Seine used ca. eight times. Only sampled 300 ft., so data were multiplied by 2. All run/riffle; no',
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'type': 'Physical Object',
'verbatimLocality': 'Type locality for Etheostoma kanawhae. Original road crossing of Raney (1941); original suspension bridge replaced with concrete bridge; road re-routed circa 1959 to new NC 16 location and new bridge built at the new NC 16 ca. 2003. Worked areas ca. 600 f',
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In [36]:
# later it's done more efficiently by loading the data in pd.DataFrame instead
lons1 = []
lats1 = []
for res in res1['results']:
if 'decimalLatitude' in res and 'decimalLongitude' in res:
lons1.append(res['decimalLongitude'])
lats1.append(res['decimalLatitude'])
In [41]:
x1, y1 = my_map(lons1, lats1)
# let's zoom in, we need lower/upper left/right latitude and longitude
llcrnrlon1 = min(lons1)
llcrnrlat1 = min(lats1)
urcrnrlon1 = max(lons1)
urcrnrlat1 = max(lats1)
In [42]:
# changed projection from 'ortho' to 'robin' to 'merc'
# Make this plot larger.
plt.figure(figsize=(16,12))
plt.title("Cyprinus_carpio occurence records from GBIF")
my_map = Basemap(projection='merc', lat_0=50, lon_0=-100,
resolution='l', area_thresh=1000.0,
llcrnrlon=llcrnrlon1,
llcrnrlat=llcrnrlat1,
urcrnrlon=urcrnrlon1,
urcrnrlat=urcrnrlat1)
my_map.drawcoastlines()
my_map.drawcountries()
my_map.drawmapboundary(fill_color='#649eff')
my_map.fillcontinents(color='#cc9955')
# draw latitude and longitude
my_map.drawmeridians(np.arange(0, 360, 30))
my_map.drawparallels(np.arange(-90, 90, 30))
my_map.plot(x1, y1, 'bo', markersize=5, color="#b01a1a")
plt.show()
In [43]:
usageKey
Out[43]:
2334131
In [44]:
type(res1['results'])
Out[44]:
list
In [45]:
res1['results'][0]
Out[45]:
{'accessRights': 'http://fieldmuseum.org/about/copyright-information',
'basisOfRecord': 'PRESERVED_SPECIMEN',
'catalogNumber': '126264',
'class': 'Actinopterygii',
'classKey': 204,
'collectionCode': 'Fishes',
'collectionID': 'Fishes',
'continent': 'NORTH_AMERICA',
'country': 'United States',
'countryCode': 'US',
'county': 'Door',
'datasetID': 'fishes-23-may-2016',
'datasetKey': 'afc30a94-6107-488a-b9c0-ba9c4fa68b7c',
'day': 16,
'decimalLatitude': 44.70465,
'decimalLongitude': -87.3599,
'depth': 0.7,
'depthAccuracy': 0.5,
'endDayOfYear': '16',
'eventDate': '2015-06-15T22:00:00.000+0000',
'extensions': {},
'facts': [],
'family': 'Cottidae',
'familyKey': 8621,
'fieldNumber': 'KAS15-14',
'gbifID': '1230322394',
'genericName': 'Cottus',
'genus': 'Cottus',
'genusKey': 2334066,
'geodeticDatum': 'WGS84',
'georeferenceProtocol': 'Google Earth',
'higherClassification': 'Animalia Chordata Actinopterygii Scorpaeniformes Cottidae',
'higherGeography': 'North America, U.S.A., Wisconsin, Door: Bear Creek half way up on Bear Creek Road at small bridge and east to County U.',
'identifiedBy': 'Mr. Thomas G. Anton : The Ecological Consulting Group, LLC',
'identifier': '58df7d71-382c-4093-abdd-b722884b0e1f',
'identifiers': [],
'individualCount': 19,
'institutionCode': 'FMNH',
'institutionID': 'FMNH',
'issues': ['COORDINATE_ROUNDED', 'GEODETIC_DATUM_ASSUMED_WGS84'],
'key': 1230322394,
'kingdom': 'Animalia',
'kingdomKey': 1,
'language': 'English',
'lastCrawled': '2016-03-23T21:32:16.516+0000',
'lastInterpreted': '2016-03-23T21:32:55.036+0000',
'lastParsed': '2016-03-23T21:32:16.545+0000',
'locality': 'Bear Creek half way up on Bear Creek Road at small bridge and east to County U.',
'media': [{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/475/IMG_4143.JPG',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/478/IMG_4146.JPG',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/481/IMG_4147.jpg',
'type': 'StillImage'},
{'format': 'image/jpeg',
'identifier': 'http://fm-digital-assets.fieldmuseum.org/1268/484/IMG_4154.JPG',
'type': 'StillImage'}],
'month': 6,
'nomenclaturalCode': 'ICZN',
'occurrenceID': '58df7d71-382c-4093-abdd-b722884b0e1f',
'order': 'Scorpaeniformes',
'orderKey': 590,
'organismID': '3363774',
'ownerInstitutionCode': 'FMNH',
'phylum': 'Chordata',
'phylumKey': 44,
'protocol': 'DWC_ARCHIVE',
'publishingCountry': 'US',
'publishingOrgKey': '7b8aff00-a9f8-11d8-944b-b8a03c50a862',
'recordedBy': 'K. Swagel',
'relations': [],
'rights': 'https://creativecommons.org/publicdomain/zero/1.0/',
'rightsHolder': 'The Field Museum of Natural History',
'scientificName': 'Cottus bairdii Girard, 1850',
'species': 'Cottus bairdii',
'speciesKey': 2334131,
'specificEpithet': 'bairdii',
'startDayOfYear': '16',
'stateProvince': 'Wisconsin',
'taxonKey': 2334131,
'taxonRank': 'SPECIES',
'type': 'PhysicalObject',
'year': 2015}
In [ ]:
import pandas as pd
In [53]:
df = pd.DataFrame(res1['results']) # load results in pandas dataframes
In [52]:
df.head()
Out[52]:
accessRights
associatedReferences
associatedSequences
basisOfRecord
bibliographicCitation
catalogNumber
class
classKey
collectionCode
collectionID
...
taxonRank
taxonRemarks
type
verbatimCoordinateSystem
verbatimDepth
verbatimEventDate
verbatimLocality
vernacularName
waterBody
year
0
http://fieldmuseum.org/about/copyright-informa...
NaN
NaN
PRESERVED_SPECIMEN
NaN
126264
Actinopterygii
204
Fishes
Fishes
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
NaN
NaN
NaN
2015
1
NaN
NaN
NaN
HUMAN_OBSERVATION
NaN
2021630
Actinopterygii
204
Observations
NaN
...
SPECIES
NaN
NaN
NaN
NaN
2015-09-20
Henry Hagg Lake, Scoggins Creek, Gaston OR
NaN
NaN
2015
2
http://fieldmuseum.org/about/copyright-informa...
NaN
NaN
PRESERVED_SPECIMEN
NaN
126326
Actinopterygii
204
Fishes
Fishes
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
NaN
NaN
NaN
2015
3
NaN
NaN
NaN
PRESERVED_SPECIMEN
NaN
OSUMU 573110
Actinopterygii
204
Fishes
NaN
...
SPECIES
NaN
NaN
NaN
NaN
19 February 2014
NaN
NaN
NaN
2014
4
NaN
NaN
NaN
HUMAN_OBSERVATION
NaN
623297
Actinopterygii
204
Observations
NaN
...
SPECIES
NaN
NaN
NaN
NaN
2014-04-13
Beaver Creek
NaN
NaN
2014
5 rows × 131 columns
In [113]:
df.occurrenceID # is this unique?? does the pandas index need to be explict, or can we use existing field
Out[113]:
0 58df7d71-382c-4093-abdd-b722884b0e1f
1 http://www.inaturalist.org/observations/2021630
2 15af3b5e-6d33-45d7-bbec-dc687bf473cf
3 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
4 http://www.inaturalist.org/observations/623297
5 urn:uuid:9af60498-d56b-4bef-af7e-8f90db3772fd
6 urn:uuid:0b77ca2e-76ee-4a2c-b5b4-215b8e8e5cad
7 urn:uuid:73088911-1e14-4898-83d0-3d4cfc626bc0
8 urn:uuid:f24301f2-9c15-4f65-90bf-cfc24d556a45
9 URI:catalog:ROM:Ichthyology:98303
10 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
11 URI:catalog:ROM:Ichthyology:98297
12 URI:catalog:ROM:Ichthyology:98318
13 http://arctos.database.museum/guid/CUMV:Fish:9...
14 ee201a95-e84b-4b13-89c0-522c52fc4803
15 36848ADC-9E87-4A00-B7B7-A0D47A0C5D4F
16 F5367EDF-BFDF-4C1F-83B2-2571EF442449
17 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
18 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
19 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
20 URI:catalog:ROM:Ichthyology:98525
21 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
22 URI:catalog:ROM:Ichthyology:98524
23 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
24 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
25 62e0c068-0b44-41a0-98cd-8940be12cfe3
26 55aaaac4-0459-43f7-bac7-7a5d4789a500
27 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
28 2e5b80a1-47d5-4d78-9a3c-773b3eda2c91
29 1f2f3e05-6c7e-4886-9c86-6ab8b1b6f645
...
270 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
271 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
272 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
273 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
274 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
275 http://arctos.database.museum/guid/CUMV:Fish:9...
276 http://n2t.net/ark:/65665/3f37d00b8-95a1-4891-...
277 http://n2t.net/ark:/65665/3290fc8f0-b797-4c71-...
278 http://n2t.net/ark:/65665/3feebe543-2495-46a2-...
279 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
280 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
281 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
282 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
283 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
284 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
285 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
286 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
287 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
288 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
289 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
290 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
291 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
292 URI:catalog:ROM:Ichthyology:89037
293 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
294 URI:catalog:ROM:Ichthyology:89051
295 6EAD31A8-0A88-4F22-925B-46EDFB8677FC
296 URI:catalog:ROM:Ichthyology:89050
297 http://n2t.net/ark:/65665/33f17df70-fc36-4d91-...
298 urn:lsid:biosci.ohio-state.edu:osuc_occurrence...
299 http://n2t.net/ark:/65665/328557e69-c6c2-4834-...
Name: occurrenceID, dtype: object
In [57]:
df.columns
Out[57]:
Index(['accessRights', 'associatedReferences', 'associatedSequences',
'basisOfRecord', 'bibliographicCitation', 'catalogNumber', 'class',
'classKey', 'collectionCode', 'collectionID',
...
'taxonRank', 'taxonRemarks', 'type', 'verbatimCoordinateSystem',
'verbatimDepth', 'verbatimEventDate', 'verbatimLocality',
'vernacularName', 'waterBody', 'year'],
dtype='object', length=131)
In [58]:
df.describe()
Out[58]:
classKey
coordinateAccuracy
coordinateAccuracyInMeters
day
decimalLatitude
decimalLongitude
depth
depthAccuracy
elevation
elevationAccuracy
...
genusKey
individualCount
key
kingdomKey
month
orderKey
phylumKey
speciesKey
taxonKey
year
count
300.0
4.000000
4.000000
300.000000
290.000000
290.000000
3.00000
3.000000
1.0
1.0
...
300.0
69.000000
3.000000e+02
300.0
300.000000
300.0
300.0
300.0
3.000000e+02
300.000000
mean
204.0
0.055494
6136.500000
15.483333
41.099630
-89.450159
0.45000
0.283333
176.8
0.0
...
2334066.0
4.884058
9.745440e+08
1.0
7.390000
590.0
44.0
2334131.0
2.449097e+06
2008.156667
std
0.0
0.104713
11579.151894
8.858780
5.063249
12.797101
0.31225
0.202073
NaN
NaN
...
0.0
6.680825
1.586737e+08
0.0
1.892928
0.0
0.0
0.0
6.548168e+05
3.177911
min
204.0
0.001655
183.010000
1.000000
33.944600
-123.875000
0.10000
0.100000
176.8
0.0
...
2334066.0
1.000000
1.981784e+08
1.0
1.000000
590.0
44.0
2334131.0
2.334131e+06
2003.000000
25%
204.0
0.002713
300.032500
9.000000
36.317100
-89.023700
0.32500
0.175000
176.8
0.0
...
2334066.0
1.000000
8.835901e+08
1.0
6.000000
590.0
44.0
2334131.0
2.334131e+06
2005.000000
50%
204.0
0.003884
429.495000
15.500000
40.535550
-84.466280
0.55000
0.250000
176.8
0.0
...
2334066.0
3.000000
1.024539e+09
1.0
7.000000
590.0
44.0
2334131.0
2.334131e+06
2008.000000
75%
204.0
0.056664
6265.962500
23.000000
44.783663
-82.417625
0.62500
0.375000
176.8
0.0
...
2334066.0
5.000000
1.039502e+09
1.0
9.000000
590.0
44.0
2334131.0
2.334131e+06
2011.000000
max
204.0
0.212552
23504.000000
31.000000
56.292160
-66.227250
0.70000
0.500000
176.8
0.0
...
2334066.0
39.000000
1.262187e+09
1.0
12.000000
590.0
44.0
2334131.0
6.166335e+06
2015.000000
8 rows × 21 columns
In [90]:
df_elevation = df[df.elevation.notnull()] # how many records have elevation field?
In [91]:
df_elevation
Out[91]:
accessRights
associatedReferences
associatedSequences
basisOfRecord
bibliographicCitation
catalogNumber
class
classKey
collectionCode
collectionID
...
taxonRank
taxonRemarks
type
verbatimCoordinateSystem
verbatimDepth
verbatimEventDate
verbatimLocality
vernacularName
waterBody
year
192
NaN
NaN
NaN
PRESERVED_SPECIMEN
NaN
81769
Actinopterygii
204
Ichthyology
NaN
...
SPECIES
NaN
NaN
NaN
NaN
NaN
NaN
NaN
NaN
2007
1 rows × 131 columns
In [109]:
df_latitude = df.decimalLatitude
In [110]:
df_longitude = df.decimalLongitude
In [291]:
# changed projection from 'ortho' to 'robin' to 'merc'
# Make this plot larger.
plt.figure(figsize=(16,12))
plt.title("Cyprinus_carpio occurence records from GBIF")
my_map = Basemap(projection='merc', lat_0=50, lon_0=-100,
resolution='l', area_thresh=1000.0,
llcrnrlon=llcrnrlon1,
llcrnrlat=llcrnrlat1,
urcrnrlon=urcrnrlon1,
urcrnrlat=urcrnrlat1)
df_x, df_y = my_map(df_longitude.tolist(), df_latitude.tolist())
my_map.drawcoastlines()
my_map.drawcountries()
my_map.drawmapboundary(fill_color='#649eff')
my_map.fillcontinents(color='#cc9955')
# draw latitude and longitude
my_map.drawmeridians(np.arange(0, 360, 30))
my_map.drawparallels(np.arange(-90, 90, 30))
my_map.plot(df_x, df_y, 'bo', markersize=5, color="#b01a1a")
plt.show()
In [132]:
df.columns # wow there are 131 columns??
Out[132]:
Index(['accessRights', 'associatedReferences', 'associatedSequences',
'basisOfRecord', 'bibliographicCitation', 'catalogNumber', 'class',
'classKey', 'collectionCode', 'collectionID',
...
'taxonRank', 'taxonRemarks', 'type', 'verbatimCoordinateSystem',
'verbatimDepth', 'verbatimEventDate', 'verbatimLocality',
'vernacularName', 'waterBody', 'year'],
dtype='object', length=131)
In [158]:
df1 = df.dropna(axis=0, how='any', thresh=70) # get rows which have at least 70 NON NaN values
In [159]:
df1
Out[159]:
accessRights
associatedReferences
associatedSequences
basisOfRecord
bibliographicCitation
catalogNumber
class
classKey
collectionCode
collectionID
...
taxonRank
taxonRemarks
type
verbatimCoordinateSystem
verbatimDepth
verbatimEventDate
verbatimLocality
vernacularName
waterBody
year
0
http://fieldmuseum.org/about/copyright-informa...
NaN
NaN
PRESERVED_SPECIMEN
NaN
126264
Actinopterygii
204
Fishes
Fishes
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
NaN
NaN
NaN
2015
2
http://fieldmuseum.org/about/copyright-informa...
NaN
NaN
PRESERVED_SPECIMEN
NaN
126326
Actinopterygii
204
Fishes
Fishes
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
NaN
NaN
NaN
2015
5
Open Access, http://creativecommons.org/public...
Det. by: Thomas J. Near, Ethan France
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 027067)
YPM ICH 027067
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2014
6
Open Access, http://creativecommons.org/public...
Det. by: Thomas J. Near, Ethan France
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 027045)
YPM ICH 027045
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2014
7
Open Access, http://creativecommons.org/public...
Det. by: Thomas J. Near, Logan C. Kozal
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 027063)
YPM ICH 027063
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2014
8
Open Access, http://creativecommons.org/public...
Det. by: Thomas J. Near, Logan C. Kozal
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 027059)
YPM ICH 027059
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2014
13
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
98217
Actinopterygii
204
Fish specimens
NaN
...
SPECIES
NaN
PhysicalObject
decimal degrees
NaN
18 September 2014
Catatonk Creek at Candor, downstream from brid...
NaN
NaN
2014
14
http://fieldmuseum.org/about/copyright-informa...
NaN
NaN
PRESERVED_SPECIMEN
NaN
126145
Actinopterygii
204
Fishes
Fishes
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
NaN
NaN
Mississippi
2014
15
NaN
NaN
NaN
PRESERVED_SPECIMEN
NCSM 75346 - North Carolina Museum of Natural ...
75346
Actinopterygii
204
NCSM-Fishes
NaN
...
SPECIES
NaN
Physical Object
NaN
ca. 0.4 m
NaN
DWR Station ID: KF21; Substrate = cobble, rip/...
Mottled sculpin
North Fork New R.
2013
16
NaN
NaN
NaN
PRESERVED_SPECIMEN
NCSM 75350 - North Carolina Museum of Natural ...
75350
Actinopterygii
204
NCSM-Fishes
NaN
...
SPECIES
NaN
Physical Object
NaN
ca. 0.4 m
NaN
DWR Station ID: KF20; Substrate = cobble, boul...
Mottled sculpin
South Fork New R.
2013
25
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
61572
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | North Carolina...
NaN
New River - Ohio River - Mississippi River
2013
26
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
61563
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | North Carolina...
NaN
New River - Ohio River - Mississippi River
2013
28
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
61588
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | North Carolina...
NaN
Little Tennessee River - Tennessee River - Mis...
2013
29
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
61551
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | North Carolina...
NaN
New River - Ohio River - Mississippi River
2013
30
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
61557
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | North Carolina...
NaN
New River - Ohio River - Mississippi River
2013
38
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
59973
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Montana | Powe...
NaN
Blackfoot River - Pend Oreille River - Colombi...
2012
39
http://www.vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
UW 152734
Actinopterygii
204
ADULT COLLECTION
urn:lsid:biocol.org:col:35205
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20120716
NORTH AMERICA | USA | WASHINGTON | STEVENS | K...
mottled sculpin
NaN
2012
41
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
59456
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Colorado | Arc...
NaN
Piedra River - San Juan River - Colorado River
2012
42
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
58431
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Idaho | Fremon...
NaN
Snake River - Columbia River
2012
43
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
58438
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Idaho | Oneida...
NaN
Malad River - Bear River - Great Salt Lake
2012
44
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
58553
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Montana | Beav...
NaN
Big Hole River - Missouri River - MIssissippi ...
2012
45
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
58434
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Idaho | Bear L...
NaN
Bear River - Great Salt Lake
2012
46
http://www.vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
UW 152213
Actinopterygii
204
ADULT COLLECTION
urn:lsid:biocol.org:col:35205
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20120824
NORTH AMERICA | USA | WASHINGTON | STEVENS | K...
mottled sculpin
NaN
2012
47
http://www.vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
UW 152073
Actinopterygii
204
ADULT COLLECTION
urn:lsid:biocol.org:col:35205
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20120808
NORTH AMERICA | USA | WASHINGTON | ASOTIN | NO...
mottled sculpin
NaN
2012
48
http://www.vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
UW 152074
Actinopterygii
204
ADULT COLLECTION
urn:lsid:biocol.org:col:35205
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20120814
NORTH AMERICA | USA | WASHINGTON | CHELAN | MA...
mottled sculpin
NaN
2012
50
Open Access, http://creativecommons.org/public...
Det. by: Matthew L. Niemiller
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 026305)
YPM ICH 026305
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2012
51
Open Access, http://creativecommons.org/public...
Det. by: Gregory J. Watkins-Colwell
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 026249)
YPM ICH 026249
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2011
54
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
55564
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Michigan | New...
NaN
White River - Lake Michigan
2011
55
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
55175
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Michigan | New...
NaN
Muskegon River - Lake Michigan
2011
56
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
52873
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Michigan | Cas...
NaN
St. Joseph’s River - Lake Michigan
2011
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
178
Open Access, http://creativecommons.org/public...
Det. by: Rose L. Carlson
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 016991)
YPM ICH 016991
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2007
185
Open Access, http://creativecommons.org/public...
Det. by: Jessica R. Glass
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 018534)
YPM ICH 018534
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2007
195
not-for-profit use only
NaN
NaN
PRESERVED_SPECIMEN
NaN
81769
Actinopterygii
204
Fishes
urn:lsid:biocol.org:col:35195
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20070821
North Channel Bruce Bay and vicinity, Lake Huron
NaN
NaN
2007
198
Open Access, http://creativecommons.org/public...
Det. by: Gideon S. Bradburd
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 018194)
YPM ICH 018194
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2007
202
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
52624
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Hiwassee River - Tennessee River - Mississippi...
2007
203
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
52610
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Ocoee River - Tennessee River - Ohio River - M...
2007
204
Open Access, http://creativecommons.org/public...
Det. by: Richard C. Harrington
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 015707)
YPM ICH 015707
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2006
205
Open Access, http://creativecommons.org/public...
Det. by: Gregory J. Watkins-Colwell 2015
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 027967)
YPM ICH 027967
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2006
206
Open Access, http://creativecommons.org/public...
Det. by: Gregory J. Watkins-Colwell 2015
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 027969)
YPM ICH 027969
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2006
207
Open Access, http://creativecommons.org/public...
Det. by: Kellie Heckman
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 015971)
YPM ICH 015971
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2006
208
Open Access, http://creativecommons.org/public...
Det. by: Benjamin P. Keck
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 018594)
YPM ICH 018594
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2006
209
Open Access, http://creativecommons.org/public...
Det. by: Gregory J. Watkins-Colwell 2015
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 027968)
YPM ICH 027968
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2006
210
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
46355
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Ocoee River - Tennessee River
2006
211
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
46406
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Hiwassee River - Tennessee River
2006
212
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
46418
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Hiwassee River - Tennessee River
2006
213
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
46449
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Hiwassee River - Tennessee River
2006
214
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
46372
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Mo...
NaN
Tellico River - Tennessee River
2006
215
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
46382
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Ocoee River - Tennessee River
2006
217
Open Access, http://creativecommons.org/public...
Det. by: James G. Garner
NaN
PRESERVED_SPECIMEN
Cottus bairdii (YPM ICH 016340)
YPM ICH 016340
Actinopterygii
204
VZ
NaN
...
SPECIES
Animals and Plants: Vertebrates - Fish
PhysicalObject
NaN
NaN
NaN
NaN
bullheads; sculpins; mail-cheeked fishes; ray-...
NaN
2006
218
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
90882
Actinopterygii
204
Fish specimens
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
2005-05-08
Catatonk Creek at Candor
NaN
NaN
2005
222
not-for-profit use only
NaN
NaN
PRESERVED_SPECIMEN
NaN
79887
Actinopterygii
204
Fishes
urn:lsid:biocol.org:col:35195
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20050615
Frazer Bay, Aquaculture Pen Site, Lake Huron
NaN
NaN
2005
227
not-for-profit use only
NaN
NaN
PRESERVED_SPECIMEN
NaN
80236
Actinopterygii
204
Fishes
urn:lsid:biocol.org:col:35195
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20050825
at Baie-d'Urfe, Lac Saint-Louis
NaN
NaN
2005
229
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
44311
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Hiwassee River - Tennessee River - Mississippi...
2005
230
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
53257
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Ocoee River - Tennessee River
2005
232
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
51782
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Tennessee River - Ohio River - Mississippi River
2005
233
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
44265
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Ocoee River - Tennessee River - Mississippi River
2005
234
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
44277
Actinopterygii
204
Fish
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
NaN
North America | United States | Tennessee | Po...
NaN
Hiwassee River - Tennessee River - Mississippi...
2005
243
not-for-profit use only
NaN
NaN
PRESERVED_SPECIMEN
NaN
82765
Actinopterygii
204
Fishes
urn:lsid:biocol.org:col:35195
...
SPECIES
NaN
PhysicalObject
NaN
NaN
20040617
Upstream Bay Point Sarnia Harbour, St Clair River
NaN
NaN
2004
275
http://vertnet.org/resources/norms.html
NaN
NaN
PRESERVED_SPECIMEN
NaN
90297
Actinopterygii
204
Fish specimens
NaN
...
SPECIES
NaN
PhysicalObject
NaN
NaN
2004-09-13
Catatonk Creek at Candor
NaN
NaN
2004
295
NaN
NaN
NaN
PRESERVED_SPECIMEN
NCSM 36195 - North Carolina Museum of Natural ...
36195
Actinopterygii
204
NCSM-Fishes
NaN
...
SPECIES
NaN
Physical Object
NaN
to 1 m
NaN
Add. Field #: MER-2003-04
Mottled sculpin
Cumberland R.
2003
122 rows × 131 columns
In [163]:
res1['endOfRecords'] # there should be 6,458 occurrences: http://www.gbif.org/species/2334131
Out[163]:
False
In [275]:
cottus_bairdii = name_backbone(name="Cottus_bairdii", verbose=False)
usageKey = cottus_bairdii['usageKey']
res2 = search(taxonKey=usageKey, limit=100000) # same result as above
In [276]:
full_results = copy.deepcopy(res2)
counter = 1
while res2['endOfRecords'] is False:
res2 = search(taxonKey=usageKey, offset=300*counter, limit=10000)
full_results['results'] = copy.deepcopy(full_results['results']) + copy.deepcopy(res2['results'])
#full_results.update(res2)
#full_results['count'] = res2['count']
#full_results['endOfRecords'] = res2['endOfRecords']
counter+=1
In [277]:
full_results['count'] # awesome
Out[277]:
6458
In [278]:
len(full_results['results']) # yep
Out[278]:
6458
In [279]:
df_full = pd.DataFrame(full_results['results']) # load results in pandas dataframes
In [281]:
df_full.columns
Out[281]:
Index(['accessRights', 'associatedOccurrences', 'associatedReferences',
'associatedSequences', 'basisOfRecord', 'bibliographicCitation',
'catalogNumber', 'class', 'classKey', 'collectionCode',
...
'type', 'typeStatus', 'verbatimCoordinateSystem', 'verbatimDepth',
'verbatimElevation', 'verbatimEventDate', 'verbatimLocality',
'vernacularName', 'waterBody', 'year'],
dtype='object', length=138)
In [287]:
df_elevation = df_full[df_full.elevation.notnull()] # how many records have elevation field?
df_elevation.elevation.size
Out[287]:
107
In [288]:
df_full_latitude = df_full.decimalLatitude
df_full_longitude = df_full.decimalLongitude
In [294]:
# changed projection from 'ortho' to 'robin' to 'merc'
# Make this plot larger.
plt.figure(figsize=(16,12))
plt.title("Cyprinus_carpio occurence records from GBIF")
my_map = Basemap(projection='merc', lat_0=50, lon_0=-100,
resolution='l', area_thresh=1000.0,
llcrnrlon=llcrnrlon1,
llcrnrlat=llcrnrlat1,
urcrnrlon=urcrnrlon1,
urcrnrlat=urcrnrlat1)
df_x, df_y = my_map(df_full_longitude.tolist(), df_full_latitude.tolist())
my_map.drawcoastlines()
my_map.drawcountries()
my_map.drawmapboundary(fill_color='#649eff')
my_map.fillcontinents(color='#cc9955')
# draw latitude and longitude
my_map.drawmeridians(np.arange(0, 360, 30))
my_map.drawparallels(np.arange(-90, 90, 30))
my_map.plot(df_x, df_y, 'bo', markersize=5, color="#b01a1a")
plt.show()
In [293]:
Out[293]:
2334131
In [413]:
def plot_species_occurrence(name_species):
usageKey = name_backbone(name=name_species, verbose=False)['usageKey']
first_res = search(taxonKey=usageKey, limit=100000)
full_results = copy.deepcopy(first_res)
# results are paginated so we need a loop to fetch them all
counter = 1
while first_res['endOfRecords'] is False:
first_res = search(taxonKey=usageKey, offset=300*counter, limit=10000)
full_results['results'] = copy.deepcopy(full_results['results']) + copy.deepcopy(first_res['results'])
counter+=1
print(full_results['count']) # awesome
print(len(full_results['results'])) # match?
df_full = pd.DataFrame(full_results['results']) # load results in pandas dataframes
# latitude/longitude lists
df_full_latitude = df_full.decimalLatitude
df_full_longitude = df_full.decimalLongitude
# changed projection from 'ortho' to 'robin' to 'merc' finally
# Make this plot larger.
plt.figure(figsize=(16,12))
plt.title("%s occurence records from GBIF" % name_species )
# "+5" in the corner points is on purpose, to zoom out a bit
my_map = Basemap(projection='merc', lat_0=50, lon_0=-100,
resolution='l', area_thresh=1000.0,
llcrnrlon=df_full_longitude.min()-5, # lower left corner longitude point
llcrnrlat=df_full_latitude.min()-5, # lower left corner latitude point
urcrnrlon=df_full_longitude.max()+5, # upper right longitude point
urcrnrlat=df_full_latitude.max()+5 # upper right latitude point
)
df_x, df_y = my_map(df_full_longitude.tolist(), df_full_latitude.tolist())
df_fictional_x, df_fictional_y = my_map(numpy.random.uniform(-360, 720,10000).tolist(),
numpy.random.uniform(-90, 90,10000).tolist())
my_map.drawcoastlines()
my_map.drawcountries()
my_map.drawmapboundary(fill_color='#649eff')
my_map.fillcontinents(color='#cc9955')
# draw latitude and longitude
my_map.drawmeridians(np.arange(0, 360, 30))
my_map.drawparallels(np.arange(-90, 90, 30))
my_map.plot(df_x, df_y, 'bo', markersize=5, color="#b01a1a")
my_map.plot(df_fictional_x, df_fictional_y, 'bo', markersize=5, color="#64ce33")
plt.show()
In [314]:
plot_species_occurrence(name_species = "Typhlopidae Merrem") # http://www.gbif.org/species/5021 26,122 occurrences
26122
26122
In [324]:
plot_species_occurrence("Alvarezsauridae Bonaparte")
---------------------------------------------------------------------------
KeyboardInterrupt Traceback (most recent call last)
<ipython-input-324-5a6df4e8d280> in <module>()
----> 1 plot_species_occurrence(name_species = "Crocodylia")
<ipython-input-321-a8b70380fd08> in plot_species_occurrence(name_species, usageKey)
13 while first_res['endOfRecords'] is False:
14 first_res = search(taxonKey=usageKey, offset=300*counter, limit=10000)
---> 15 full_results['results'] = copy.deepcopy(full_results['results']) + copy.deepcopy(first_res['results'])
16 counter+=1
17
/home/daniela/anaconda/envs/biodiversity/lib/python3.5/copy.py in deepcopy(x, memo, _nil)
153 copier = _deepcopy_dispatch.get(cls)
154 if copier:
--> 155 y = copier(x, memo)
156 else:
157 try:
/home/daniela/anaconda/envs/biodiversity/lib/python3.5/copy.py in _deepcopy_list(x, memo)
217 memo[id(x)] = y
218 for a in x:
--> 219 y.append(deepcopy(a, memo))
220 return y
221 d[list] = _deepcopy_list
/home/daniela/anaconda/envs/biodiversity/lib/python3.5/copy.py in deepcopy(x, memo, _nil)
153 copier = _deepcopy_dispatch.get(cls)
154 if copier:
--> 155 y = copier(x, memo)
156 else:
157 try:
/home/daniela/anaconda/envs/biodiversity/lib/python3.5/copy.py in _deepcopy_dict(x, memo)
242 memo[id(x)] = y
243 for key, value in x.items():
--> 244 y[deepcopy(key, memo)] = deepcopy(value, memo)
245 return y
246 d[dict] = _deepcopy_dict
/home/daniela/anaconda/envs/biodiversity/lib/python3.5/copy.py in deepcopy(x, memo, _nil)
149 return y
150
--> 151 cls = type(x)
152
153 copier = _deepcopy_dispatch.get(cls)
KeyboardInterrupt:
In [330]:
df_full.
Out[330]:
Index(['accessRights', 'associatedOccurrences', 'associatedReferences',
'associatedSequences', 'basisOfRecord', 'bibliographicCitation',
'catalogNumber', 'class', 'classKey', 'collectionCode',
...
'type', 'typeStatus', 'verbatimCoordinateSystem', 'verbatimDepth',
'verbatimElevation', 'verbatimEventDate', 'verbatimLocality',
'vernacularName', 'waterBody', 'year'],
dtype='object', length=138)
In [331]:
import csv
In [341]:
Ohio_dataset = "/home/daniela/Documents/NLeSC/Biodiversity/Aafke/2Daniela.xlsx"
In [340]:
import xlrd # conda install xlrd
In [343]:
book = xlrd.open_workbook(Ohio_dataset)
In [346]:
fish_selection = book.sheet_by_name('fish_selection')
In [362]:
print(fish_selection.row_slice(rowx=1, start_colx=0, end_colx=3))
[text:'Etheostoma_blennioides', number:997.0, number:1004.0]
In [356]:
number_rows = fish_selection.nrows
In [395]:
fish_explore = []
for rownum in range(fish_selection.nrows):
if fish_selection.row_values(rownum)[4]=='y':
fish_explore.append(fish_selection.row_values(rownum)[0])
In [396]:
fish_explore
Out[396]:
['Etheostoma_blennioides',
'Hypentelium_nigricans',
'Rhinichthys_obtusus',
'Etheostoma_flabellare',
'Ameiurus_natalis',
'Etheostoma_caeruleum',
'Ambloplites_rupestris',
'Micropterus_salmoides',
'Luxilus_chrysocephalus',
'Notropis_buccatus',
'Micropterus_dolomieux',
'Cyprinella_spiloptera',
'Lepomis_macrochirus',
'Moxostoma_erythrurum',
'Notropis_stramineus',
'Cyprinus_carpio',
'Lepomis_megalotis',
'Cottus_bairdii',
'Etheostoma_nigrum',
'Percina_caprodes',
'Lepomis_cyanellus',
'Etheostoma_spectabile',
'Percina_maculata',
'Etheostoma_zonale',
'Campostoma_anomalum',
'Notropis_photogenis',
'Pimephales_promelas',
'Phoxinus_erythrogaster',
'Lythrurus_fasciolaris',
'Luxilus_cornutus',
'Catostomus_commersonii',
'Dorosoma_cepedianum',
'Moxostoma_duquesnei',
'Esox_americanus',
'Semotilus_atromaculatus',
'Pimephales_notatus',
'Ictalurus_punctatus',
'Notropis_rubellus',
'Noturus_flavus',
'Lepomis_gibbosus',
'Fundulus_notatus',
'Lythrurus_umbratilis',
'Micropterus_punctulatus',
'Moxostoma_anisurum',
'Carpiodes_cyprinus',
'Notemigonus_crysoleucas',
'Clinostomus_elongatus',
'Minytrema_melanops',
'Phenacobius_mirabilis',
'Pomoxis_annularis',
'Notropis_volucellus',
'Lampetra_aepyptera',
'Nocomis_micropogon',
'Aplodinotus_grunniens',
'Labidesthes_sicculus',
'Umbra_limi',
'Lepomis_humilis',
'Notropis_atherinoides',
'Pomoxis_nigromaculatus',
'Ameiurus_melas',
'Hybopsis_amblops',
'Perca_flavescens',
'Percopsis_omiscomaycus',
'Moxostoma_breviceps',
'Lepomis_gulosus',
'Pylodictis_olivaris']
In [414]:
plot_species_occurrence(name_species = "Alvarezsauridae Bonaparte") # http://www.gbif.org/species/5021 26,122 occurrences
24
24
In [401]:
df_full.decimalLongitude
Out[401]:
0 -87.35990
1 -123.19395
2 -87.68428
3 -83.74880
4 -83.56716
5 -82.56875
6 -84.05169
7 -84.03617
8 -84.56492
9 -89.57449
10 -82.90120
11 -88.46825
12 -83.87016
13 -76.33849
14 -88.26946
15 -81.51110
16 -81.40160
17 -82.80890
18 -84.59900
19 -77.77950
20 -84.85225
21 -77.85720
22 -84.85089
23 -84.69750
24 -84.23190
25 -81.64732
26 -81.65890
27 -84.80130
28 -81.68091
29 -83.50650
...
6428 NaN
6429 -84.98000
6430 -81.44000
6431 NaN
6432 NaN
6433 -123.37000
6434 NaN
6435 NaN
6436 NaN
6437 NaN
6438 NaN
6439 NaN
6440 -83.68730
6441 -71.36000
6442 NaN
6443 NaN
6444 NaN
6445 NaN
6446 -83.32490
6447 NaN
6448 NaN
6449 NaN
6450 NaN
6451 NaN
6452 NaN
6453 NaN
6454 NaN
6455 NaN
6456 NaN
6457 NaN
Name: decimalLongitude, dtype: float64
In [403]:
import numpy.random
In [409]:
numpy.random.uniform(-360, 720,10).tolist()
Out[409]:
[98.44867501934391,
61.88207227233755,
-332.6065534659042,
677.08370032267,
710.5780343600034,
122.67532556032381,
533.3997118180291,
-227.11071362221975,
406.2995258977485,
460.28754765478095]
In [ ]:
Content source: remenska/iSDM
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