Features:
- get up-to-date information from OBIS database
- Terminal-based scripts
Software requierements:
- Python 3
By using pip:
pip install OBISdatUsing git (Optional):
git clone https://github.com/Ulises-Rosas/OBISdat.git
cd OBISdat
python3 setup.py installThe way this executable is used match up with this structure:
obis.py [path] [parameters]Paths that OBIS API accepts are stated at [path] position. It has been tested the following paths so far:
countryareainstitutechecklistchecklist/redlistchecklist/newestoccurrence
Each outcome from paths can be modified by adding constraining parameters at [parameters] position. Paramenters available are:
--taxa(e.g.Elasmobranchii Reptilia)--of(e.g.Peru Colombia)--areaid--datasetid--instituteid--nodeid--startdate--enddate--startdepth--enddepth--geometry
Only both --taxa and --of options accept more than one value. While whole output filenames are named in function to the path used, these can also be defined with --out option.
When we use either country, institute or area paths, --of option is coupled in order to match requested strings:
obis.py institute --of 'Smithsonian Institution'id name parent children records
7553 National Museum of Natural History, Smithsonian Institution {'id': 17611, 'name': 'Smithsonian Institution'} None 638317
19436 Tennenbaum Marine Observatories Network {'id': 17611, 'name': 'Smithsonian Institution'} None 1135
17611 Smithsonian Institution None [{'id': 19436, 'name': 'Tennenbaum Marine Observatories Network'}, {'id': 7553, 'name': 'National Museum of Natural History, Smithsonian Institution'}] 1056
obis.py area --of Peru Colombiaid name type
190 Peru obis
10198 Peru Upwelling Cores ebsa
10199 PeruvianHCSUpwelling ebsa
41 Colombia obis
127 Joint Regime: Colombia - Jamaica obis
Above examples output were named obis_institute.tsv and obis_area.tsv correspondingly. We can also retrieve data by using any geographical id from above results. On the following example, the Peruvian areaid (i.e. 190) is used to look for taxa within both checklist/redlist and occurrence paths:
obis.py checklist/redlist --areaid 190 --taxa Reptilia MammaliascientificName scientificNameAuthorship taxonID taxonRank taxonomicStatus acceptedNameUsage acceptedNameUsageID is_marine kingdom phylum subphylum superclass class order suborder superfamily family genus species kingdomid phylumid subphylumid superclassid classid orderid suborderid superfamilyid familyid genusid speciesid category records
Dermochelys coriacea (Vandelli, 1761) 137209 Species accepted Dermochelys coriacea 137209 True Animalia Chordata Vertebrata Tetrapoda Reptilia Testudines Cryptodira Chelonioidea Dermochelyidae Dermochelys Dermochelys coriacea 2 1821 146419 1831 1838 2689 148741 987094 137000 137070 137209 VU 48
Caretta caretta (Linnaeus, 1758) 137205 Species accepted Caretta caretta 137205 True Animalia Chordata Vertebrata Tetrapoda Reptilia Testudines Cryptodira Chelonioidea Cheloniidae Caretta Caretta caretta 2 1821 146419 1831 1838 2689 148741 987094 136999 137066 137205 VU 31
Lepidochelys olivacea (Eschscholtz, 1829) 220293 Species accepted Lepidochelys olivacea 220293 True Animalia Chordata Vertebrata Tetrapoda Reptilia Testudines Cryptodira Chelonioidea Cheloniidae Lepidochelys Lepidochelys olivacea 2 1821 146419 1831 1838 2689 148741 987094 136999 137069 220293 VU 13
Chelonia mydas (Linnaeus, 1758) 137206 Species accepted Chelonia mydas 137206 True Animalia Chordata Vertebrata Tetrapoda Reptilia Testudines Cryptodira Chelonioidea Cheloniidae Chelonia Chelonia mydas 2 1821 146419 1831 1838 2689 148741 987094 136999 137067 137206 EN 1
Eretmochelys imbricata (Linnaeus, 1766) 137207 Species accepted Eretmochelys imbricata 137207 True Animalia Chordata Vertebrata Tetrapoda Reptilia Testudines Cryptodira Chelonioidea Cheloniidae Eretmochelys Eretmochelys imbricata 2 1821 146419 1831 1838 2689 148741 987094 136999 137068 137207 CR 1
Physeter macrocephalus Linnaeus, 1758 137119 Species accepted Physeter macrocephalus 137119 True Animalia Chordata Vertebrata Tetrapoda Mammalia Theria Cetartiodactyla Cetancodonta Cetacea Odontoceti Physeteridae Physeter Physeter macrocephalus 2 1821 146419 1831 1837 380416 370511 370545 2688 148723 136985 137032 137119 VU 372
Balaenoptera musculus (Linnaeus, 1758) 137090 Species accepted Balaenoptera musculus 137090 True Animalia Chordata Vertebrata Tetrapoda Mammalia Theria Cetartiodactyla Cetancodonta Cetacea Mysticeti Balaenopteridae Balaenoptera Balaenoptera musculus 2 1821 146419 1831 1837 380416 370511 370545 2688 148724 136979 137013 137090 EN 10
obis.py occurrence --areaid 190 --taxa 'Anchoa nasus' brackish scientificNameID scientificName absence dropped aphiaID genusid decimalLatitude originalScientificName marine minimumDepthInMeters familyid phylumid subphylumid terrestrial basisOfRecord superclass maximumDepthInMeters id class order superclassid orderid dataset_id decimalLongitude speciesid kingdom classid phylum species genus subphylum family kingdomid node_id
True urn:lsid:marinespecies.org:taxname:275528 Anchoa nasus False False 275528 158697 -9.06999969482 Anchoa nasus True None 125465 1821 146419 False HumanObservation Pisces None 5fc5547b-f0b1-43e1-a8b2-bf90f19c9a4f Actinopterygii Clupeiformes 11676 10297 0e1d55f3-c7dc-4355-a81f-e48a96795329 -78.5999984741 275528 Animalia 10194 Chordata Anchoa nasus Anchoa Vertebrata Engraulidae 2 ['310922b4-9d0c-4de1-92d7-9b442d34765b']
True urn:lsid:marinespecies.org:taxname:275528 Anchoa nasus False False 275528 158697 -3.63000011444 Anchoa nasus True None 125465 1821 146419 False HumanObservation Pisces None 86decef7-ecc8-4afc-855d-846ffd74f528 Actinopterygii Clupeiformes 11676 10297 0e1d55f3-c7dc-4355-a81f-e48a96795329 -80.5999984741 275528 Animalia 10194 Chordata Anchoa nasus Anchoa Vertebrata Engraulidae 2 ['310922b4-9d0c-4de1-92d7-9b442d34765b']
True PǸrou urn:lsid:marinespecies.org:taxname:275528 Anchoa nasus kner ,steindachner False False 275528 158697 -13.0260000229 Anchoa nasus True None 125465 1821 146419 2006-1641 False PreservedSpecimen MNHN Pisces None a34ef4db-101f-4fba-8872-cf054c2eb7e6 bearez Actinopterygii Clupeiformes 11676 10297 705770e5-3474-4e69-be8b-3107a0c5610a -76.4779968262 IC 275528 pacifique Animalia 10194 bǸarez Chordata Anchoa nasus Anchoa Vertebrata Engraulidae 2 ['310922b4-9d0c-4de1-92d7-9b442d34765b']
Peru 1986 urn:lsid:marinespecies.org:taxname:308324 1986 Anchoa nasus observedindividualcount=1; False 275528 -6.838116 125465 1821 55397 False HumanObservation Pisces None c154a9d2-7da8-41be-a936-c3791099dbaa 9 Clupeiformes RC86-43 11676 b8617377-eb1c-4db2-baa6-8788a632e810 Off Pimentel (Station 30), Pacific Ocean Lambayeque -79.937686 521251200000 Fishes 275528 521251200000 07 Anchoa 1986-07-09T12:00:00Z True False 158697 Anchoa naso True None 146419 ROM 521251200000 Holm, E. Actinopterygii 10297 Animalia 10194 Reed Horse Fishermen Chordata Anchoa nasus Vertebrata Engraulidae 2 ['310922b4-9d0c-4de1-92d7-9b442d34765b']
True urn:lsid:marinespecies.org:taxname:275528 Anchoa nasus False False 275528 158697 -5.07999992371 Anchoa nasus True None 125465 1821 146419 False HumanObservation Pisces None f5d642a5-5a30-4d26-8921-01dd0bc229ef Actinopterygii Clupeiformes 11676 10297 0e1d55f3-c7dc-4355-a81f-e48a96795329 -81.1200027466 275528 Animalia 10194 Chordata Anchoa nasus Anchoa Vertebrata Engraulidae 2 ['310922b4-9d0c-4de1-92d7-9b442d34765b']
True urn:lsid:marinespecies.org:taxname:275528 Anchoa nasus False False 275528 158697 -3.65000009537 Anchoa nasus True None 125465 1821 146419 False HumanObservation Pisces None f8e2bccc-d19e-436f-9f8e-223a6e95de57 Actinopterygii Clupeiformes 11676 10297 0e1d55f3-c7dc-4355-a81f-e48a96795329 -80.9499969482 275528 Animalia 10194 Chordata Anchoa nasus Anchoa Vertebrata Engraulidae 2 ['310922b4-9d0c-4de1-92d7-9b442d34765b']
From above examples both would be named equal (i.e. obis_area.tsv). For that reason, --out option might be handy on these cases. Specific geographic area can be introduced in WKT format by using --geometry option. In the following example, we will use coordenates obtained from the OBIS Mapper online app in order to get species occurrence from a tiny area of Equatorial Guinea and Gabon:
obis.py occurrence --geometry 'POLYGON ((9.6034 1.5839, 9.3501 1.1679, 9.1873 1.4555, 9.3027 1.6134, 9.6034 1.5839))'date_year scientificNameID scientificName dynamicProperties superfamilyid individualCount dropped associatedReferences aphiaID decimalLatitude type taxonRemarks phylumid familyid catalogNumber occurrenceStatus basisOfRecord superclass maximumDepthInMeters modified id order recordNumber georeferencedDate superclassid verbatimEventDate dataset_id decimalLongitude date_end collectionCode speciesid occurrenceID superfamily suborderid license date_start organismID dateIdentified genus bibliographicCitation eventDate scientificNameAuthorship absence taxonRank genusid originalScientificName marine minimumDepthInMeters subphylumid vernacularName institutionCode date_mid identificationRemarks class suborder nomenclaturalCode orderid sex datasetName taxonomicStatus geodeticDatum kingdom specificEpithet classid phylum lifeStage species coordinatePrecision organismRemarks subphylum datasetID occurrenceRemarks family category kingdomid node_id
2009 urn:lsid:marinespecies.org:taxname:137209 Dermochelys coriacea MachineObservation 987094 4 False [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 137209 1.5 Event Taxon recorded as "Leatherback" by the provider 1821 137000 1454_1238197 present MachineObservation Tetrapoda None 2018-06-13 14:36:11 13fe7b7d-eb09-4aea-adfb-9b845b0783c8 Testudines 1454_1238197 2008-12-11T02:19:58/2009-02-19T08:34:54 1831 2008-12-11 02:19:58/2009-02-19 08:34:54 5783eb41-8787-415f-beb8-178fa05684ef 9.5 1235001600000 1454 137209 1454_1238197 Chelonioidea 148741 http://creativecommons.org/licenses/by-nc/4.0/ 1228953600000 89071a;89072a;89075a;89076a 2008-12-11T02:19:58/2009-02-19T08:34:54 Dermochelys [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 2008-12-11T02:19:58/2009-02-19T08:34:54 (Vandelli, 1761) False Species 137070 Dermochelys coriacea True None 146419 Leatherback MTRG / Seaturtle.org 1231977600000 Identification Type:Telemetry Reptilia Cryptodira WoRMS LSID 2689 Female Gabon 2008-09: Mayumba & Pongara, Leatherback Turtles valid EPSG:4326 WGS84 Animalia coriacea 1838 Chordata Adult Dermochelys coriacea 0.001 Tagged animal. organismID may refer to the ID of the telemetry device. Vertebrata 1454 Telemetry locations aggregated per species per 1-degree cell Dermochelyidae VU 2 573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31
2014 urn:lsid:marinespecies.org:taxname:137206 Chelonia mydas MachineObservation 987094 3 False ;http://www.seaturtle.org/tracking/index.shtml?project_id=1001 137206 1.5 Event Taxon recorded as "Green Turtle" by the provider 1821 136999 1840_585748 present MachineObservation Tetrapoda None 2018-06-13 14:36:11 30390ec2-924e-47c5-9b82-b42320d4f11c Testudines 1840_585748 2014-06-17T16:59:14/2014-10-10T22:10:39 1831 2014-06-17 16:59:14/2014-10-10 22:10:39 4a06a415-2954-4597-baf3-7934b07355ea 9.5 1412899200000 1840 137206 1840_585748 Chelonioidea 148741 http://creativecommons.org/licenses/by-nc/4.0/ 1402963200000 138424;138426;138427 2014-06-17T16:59:14/2014-10-10T22:10:39 Chelonia Halpin, P.N., A.J. Read, E. Fujioka, B.D. Best, B. Donnelly, L.J. Hazen, C. Kot, K. Urian, E. LaBrecque, A. Dimatteo, J. Cleary, C. Good, L.B. Crowder, and K.D. [...] 2014-06-17T16:59:14/2014-10-10T22:10:39 (Linnaeus, 1758) False Species 137067 Chelonia mydas True None 146419 Green Sea Turtle Wildlife Conservation Society 1407888000000 Identification Type:Telemetry Reptilia Cryptodira WoRMS LSID 2689 Male;Unknown Equatorial Guinea 2014: Foraging Green Sea Turtles valid EPSG:4326 WGS84 Animalia mydas 1838 Chordata Juvenile;Subadult Chelonia mydas 0.001 Tagged animal. organismID may refer to the ID of the telemetry device. Vertebrata 1840 Telemetry locations aggregated per species per 1-degree cell Cheloniidae EN 2 573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31
2009 urn:lsid:marinespecies.org:taxname:137209 Dermochelys coriacea MachineObservation 987094 1 False [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 137209 1.5 Event Taxon recorded as "Leatherback" by the provider 1821 137000 1456_1057383 present MachineObservation Tetrapoda None 2016-12-27 06:05:08 35f94c5c-e83e-40b5-9092-562fa2fbb460 Testudines 1456_1057383 2009-12-28T07:30:36/2009-12-28T07:30:36 1831 2009-12-28 07:30:36/2009-12-28 07:30:36 961a2b3e-d2f1-4fff-b5f4-af9f01d4565a 9.5 1261958400000 1456 137209 1456_1057383 Chelonioidea 148741 http://creativecommons.org/licenses/by-nc/4.0/ 1261958400000 92581a 2009-12-28T07:30:36/2009-12-28T07:30:36 Dermochelys [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 2009-12-28T07:30:36/2009-12-28T07:30:36 (Vandelli, 1761) False Species 137070 Dermochelys coriacea True None 146419 Leatherback Marine Turtle Research Group / Seaturtle.org 1261958400000 Identification Type:Telemetry Reptilia Cryptodira WoRMS LSID 2689 Female Gabon 2009-10: Pongara, Leatherback Turtles valid EPSG:4326 WGS84 Animalia coriacea 1838 Chordata Adult Dermochelys coriacea 0.001 Tagged animal. organismID may refer to the ID of the telemetry device. Vertebrata 1456 Telemetry locations aggregated per species per 1-degree cell Dermochelyidae VU 2 573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31
2011 urn:lsid:marinespecies.org:taxname:137206 Chelonia mydas MachineObservation 987094 2 False [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 137206 1.5 Event Taxon recorded as "Green Turtle" by the provider 1821 136999 718_980354 present MachineObservation Tetrapoda None 2017-07-18 06:02:22 468f3da1-7a1e-46e8-946e-e272b8bf4034 Testudines 718_980354 2010-12-29T07:17:52/2011-05-31T14:46:06 1831 2010-12-29 07:17:52/2011-05-31 14:46:06 ce258d5f-3097-412a-a969-112f34f9169e 9.5 1306800000000 718 137206 718_980354 Chelonioidea 148741 http://creativecommons.org/licenses/by-nc/4.0/ 1293580800000 68395;68395a 2010-12-29T07:17:52/2011-05-31T14:46:06 Chelonia Marine Turtle Research Group [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 2010-12-29T07:17:52/2011-05-31T14:46:06 (Linnaeus, 1758) False Species 137067 Chelonia mydas True None 146419 Green Sea Turtle Marine Turtle Research Group 1300147200000 Identification Type:Telemetry Reptilia Cryptodira WoRMS LSID 2689 Unknown Equatorial Guinea 2011: Green Turtles valid EPSG:4326 WGS84 Animalia mydas 1838 Chordata Juvenile Chelonia mydas 0.001 Tagged animal. organismID may refer to the ID of the telemetry device. Vertebrata 718 Telemetry locations aggregated per species per 1-degree cell Cheloniidae EN 2 573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31
2015 urn:lsid:marinespecies.org:taxname:220293 Lepidochelys olivacea MachineObservation 987094 1 False [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 220293 1.5 Event Taxon recorded as "Olive Ridley" by the provider 1821 136999 1328_627560 present MachineObservation Tetrapoda None 2016-09-20 05:56:52 b65e791e-4f51-4d69-8e25-58569844e2af Testudines 1328_627560 2015-11-26T05:10:58/2015-11-29T14:28:43 1831 2015-11-26 05:10:58/2015-11-29 14:28:43 f282147d-5689-4da7-a8aa-6aa54c5bb5be 9.5 1448755200000 1328 220293 1328_627560 Chelonioidea 148741 http://creativecommons.org/licenses/by-nc/4.0/ 1448496000000 152857 2015-11-26T05:10:58/2015-11-29T14:28:43 Lepidochelys [{"crossref":{"citeinfo":{"origin":"Coyne, M. S., and B. J. Godley","pubdate":"2005","title_html":"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...] 2015-11-26T05:10:58/2015-11-29T14:28:43 (Eschscholtz, 1829) False Species 137069 Lepidochelys olivacea True None 146419 Olive Ridley Old Dominion Univ/Univ of Exeter/Wildlife Conservation Society 1448582400000 Identification Type:Telemetry Reptilia Cryptodira WoRMS LSID 2689 Female Gabon Olive Ridley Tracking Project: Pongara National Park 2015 valid EPSG:4326 WGS84 Animalia olivacea 1838 Chordata Adult Lepidochelys olivacea 0.001 Tagged animal. organismID may refer to the ID of the telemetry device. Vertebrata 1328 Telemetry locations aggregated per species per 1-degree cell Cheloniidae VU 2 573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31
2007 urn:lsid:marinespecies.org:taxname:137165 Sterna paradisaea MachineObservation 2 False [{"crossref":{"citeinfo":{"origin":"Egevang, C., I.J. Stenhouse, R.A. Phillips, A. Petersen, J.W. Fox and J.R.D. Silk","pubdate":"2010","title_html":"Tracking o [...] 137165 1.5 Event Taxon recorded as "Arctic tern" by the provider 148764 1821 705_2186 present MachineObservation Tetrapoda None 2011-02-24 13:46:04 d9405451-f8cf-4ee4-9e08-13b84cca5962 Charadriiformes 705_2186 2007-10-11T00:10:00/2007-10-13T12:07:00 1831 2007-10-11 00:10:00/2007-10-13 12:07:00 b7939ba9-6d4c-4359-b92b-136cf591e072 9.5 1192233600000 705 137165 705_2186 http://creativecommons.org/licenses/by-nc/4.0/ 1192060800000 ARTE_376;ARTE_395 2007-10-11T00:10:00/2007-10-13T12:07:00 Sterna Greenland Institute of Natural Resources [{"crossref":{"citeinfo":{"origin":"Egevang, C., I.J. Stenhouse, R.A. Phillips, A. Petersen, J.W. Fox and J.R.D. Silk","pubdate":"2010","title_html":"Tracking o [...] 2007-10-11T00:10:00/2007-10-13T12:07:00 Pontoppidan, 1763 False Species 137047 Sterna paradisaea True None 146419 Arctic Tern Greenland Institute of Natural Resources 1192147200000 Identification Type:Telemetry Aves WoRMS LSID 2682 Tracking of Arctic tern migrations 2007-2008 valid EPSG:4326 WGS84 Greenland,high-Arctic,Antarctica,Weddell Sea Animalia paradisaea 1836 Chordata Sterna paradisaea 0.000001 Tagged animal. organismID may refer to the ID of the telemetry device. Vertebrata 705 Telemetry locations aggregated per species per 1-degree cell Sternidae 2 573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31
2012 urn:lsid:marinespecies.org:taxname:137209 Dermochelys coriacea MachineObservation 987094 4 False ;http://www.seaturtle.org/tracking/index.shtml?project_id=776 137209 1.5 Event Taxon recorded as "Leatherback" by the provider 1821 137000 1836_393151 present MachineObservation Tetrapoda None 2018-06-13 14:36:11 f3ee062e-2671-4d32-a813-acd517c8dcc8 Testudines 1836_393151 2012-11-03T08:40:01/2012-12-25T18:02:31 1831 2012-11-03 08:40:01/2012-12-25 18:02:31 768d9e0b-a4d8-4e02-8c50-74f0adf4cf52 9.5 1356393600000 1836 137209 1836_393151 Chelonioidea 148741 http://creativecommons.org/licenses/by-nc/4.0/ 1351900800000 122426a;122428a;122433a;122434a 2012-11-03T08:40:01/2012-12-25T18:02:31 Dermochelys Halpin, P.N., A.J. Read, E. Fujioka, B.D. Best, B. Donnelly, L.J. Hazen, C. Kot, K. Urian, E. LaBrecque, A. Dimatteo, J. Cleary, C. Good, L.B. Crowder, and K.D. [...] 2012-11-03T08:40:01/2012-12-25T18:02:31 (Vandelli, 1761) False Species 137070 Dermochelys coriacea True None 146419 Leatherback University of Exeter 1354147200000 Identification Type:Telemetry Reptilia Cryptodira WoRMS LSID 2689 Female Gabon 2012: Pongara, Leatherback Turtles valid EPSG:4326 WGS84 Animalia coriacea 1838 Chordata Adult Dermochelys coriacea 0.001 Tagged animal. organismID may refer to the ID of the telemetry device. Vertebrata 1836 Telemetry locations aggregated per species per 1-degree cell Dermochelyidae VU 2 573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31
The way it is used inside python3 is pretty the same from the console:
# import class
from OBISdat.core_obis import Obis
# set parameters as a dict
query = {
'scientificname': ['Reptilia', 'Mammalia'],
'areaid': '190',
'size': 5000
}
# get results in a list
Obis(path = 'checklist', opts = query).dataRetriever()
# get results from paths such as country, area or institute
Obis(path = 'area').geographics(of = ['Peru'])