{
    "info": {
        "author": "Ulises Rosas",
        "author_email": "ulisesfrosasp@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3"
        ],
        "description": "[![DOI](https://zenodo.org/badge/204370467.svg)](https://zenodo.org/badge/latestdoi/204370467)\n[![pypi](https://img.shields.io/pypi/v/OBISdat.svg)](https://pypi.python.org/pypi/OBISdat)\n[![conda](https://anaconda.org/urosas/obisdat/badges/installer/conda.svg)](https://anaconda.org/urosas/obisdat)\n\n# OBISdat\n\nFeatures:\n\n- [x] get up-to-date information from [OBIS database](https://obis.org)\n- [x] Terminal-based scripts\n\nSoftware requierements:\n* Python 3\n\n#### Installation\n\nBy using `pip`:\n\n```Shell\npip install OBISdat\n```\n\nUsing `git` (Optional):\n\n```Shell\ngit clone https://github.com/Ulises-Rosas/OBISdat.git\ncd OBISdat\npython3 setup.py install\n```\n\n### Usage within the terminal\n\nThe way this executable is used match up with this structure:\n\n```Shell\nobis.py [path] [parameters]\n```\n\nPaths that [OBIS API](https://api.obis.org) accepts are stated at `[path]` position. It has been tested the following paths so far:\n\n* `country`\n* `area`\n* `institute`\n* `checklist`\n* `checklist/redlist`\n* `checklist/newest`\n* `occurrence`\n\nEach outcome from paths can be modified by adding constraining parameters at `[parameters]` position. Paramenters available are:\n\n* `--taxa` (e.g. `Elasmobranchii Reptilia`)\n* `--of` (e.g. `Peru Colombia`)\n* `--areaid` \n* `--datasetid`\n* `--instituteid`\n* `--nodeid`\n* `--startdate`\n* `--enddate`\n* `--startdepth`\n* `--enddepth`\n* `--geometry`\n\nOnly 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. \n\n#### Examples\n\nWhen we use either `country`, `institute` or `area` paths, `--of` option is coupled in order to match requested strings:\n\n```Shell\nobis.py institute --of 'Smithsonian Institution'\n```\n```\nid\tname\tparent\tchildren\trecords\n7553\tNational Museum of Natural History, Smithsonian Institution\t{'id': 17611, 'name': 'Smithsonian Institution'}\tNone\t638317\n19436\tTennenbaum Marine Observatories Network\t{'id': 17611, 'name': 'Smithsonian Institution'}\tNone\t1135\n17611\tSmithsonian Institution\tNone\t[{'id': 19436, 'name': 'Tennenbaum Marine Observatories Network'}, {'id': 7553, 'name': 'National Museum of Natural History, Smithsonian Institution'}]\t1056\n```\n```Shell\nobis.py area --of Peru Colombia\n```\n```\nid\tname\ttype\n190\tPeru\tobis\n10198\tPeru Upwelling Cores\tebsa\n10199\tPeruvianHCSUpwelling\tebsa\n41\tColombia\tobis\n127\tJoint Regime: Colombia - Jamaica\tobis\n```\n\nAbove 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:\n\n```Shell\nobis.py checklist/redlist --areaid 190 --taxa Reptilia Mammalia\n```\n```\nscientificName\tscientificNameAuthorship\ttaxonID\ttaxonRank\ttaxonomicStatus\tacceptedNameUsage\tacceptedNameUsageID\tis_marine\tkingdom\tphylum\tsubphylum\tsuperclass\tclass\torder\tsuborder\tsuperfamily\tfamily\tgenus\tspecies\tkingdomid\tphylumid\tsubphylumid\tsuperclassid\tclassid\torderid\tsuborderid\tsuperfamilyid\tfamilyid\tgenusid\tspeciesid\tcategory\trecords\nDermochelys coriacea\t(Vandelli, 1761)\t137209\tSpecies\taccepted\tDermochelys coriacea\t137209\tTrue\tAnimalia\tChordata\tVertebrata\tTetrapoda\tReptilia\tTestudines\tCryptodira\tChelonioidea\tDermochelyidae\tDermochelys\tDermochelys coriacea\t2\t1821\t146419\t1831\t1838\t2689\t148741\t987094\t137000\t137070\t137209\tVU\t48\nCaretta caretta\t(Linnaeus, 1758)\t137205\tSpecies\taccepted\tCaretta caretta\t137205\tTrue\tAnimalia\tChordata\tVertebrata\tTetrapoda\tReptilia\tTestudines\tCryptodira\tChelonioidea\tCheloniidae\tCaretta\tCaretta caretta\t2\t1821\t146419\t1831\t1838\t2689\t148741\t987094\t136999\t137066\t137205\tVU\t31\nLepidochelys olivacea\t(Eschscholtz, 1829)\t220293\tSpecies\taccepted\tLepidochelys olivacea\t220293\tTrue\tAnimalia\tChordata\tVertebrata\tTetrapoda\tReptilia\tTestudines\tCryptodira\tChelonioidea\tCheloniidae\tLepidochelys\tLepidochelys olivacea\t2\t1821\t146419\t1831\t1838\t2689\t148741\t987094\t136999\t137069\t220293\tVU\t13\nChelonia mydas\t(Linnaeus, 1758)\t137206\tSpecies\taccepted\tChelonia mydas\t137206\tTrue\tAnimalia\tChordata\tVertebrata\tTetrapoda\tReptilia\tTestudines\tCryptodira\tChelonioidea\tCheloniidae\tChelonia\tChelonia mydas\t2\t1821\t146419\t1831\t1838\t2689\t148741\t987094\t136999\t137067\t137206\tEN\t1\nEretmochelys imbricata\t(Linnaeus, 1766)\t137207\tSpecies\taccepted\tEretmochelys imbricata\t137207\tTrue\tAnimalia\tChordata\tVertebrata\tTetrapoda\tReptilia\tTestudines\tCryptodira\tChelonioidea\tCheloniidae\tEretmochelys\tEretmochelys imbricata\t2\t1821\t146419\t1831\t1838\t2689\t148741\t987094\t136999\t137068\t137207\tCR\t1\nPhyseter macrocephalus\tLinnaeus, 1758\t137119\tSpecies\taccepted\tPhyseter macrocephalus\t137119\tTrue\tAnimalia\tChordata\tVertebrata\tTetrapoda\tMammalia\tTheria\tCetartiodactyla\tCetancodonta\tCetacea\tOdontoceti\tPhyseteridae\tPhyseter\tPhyseter macrocephalus\t2\t1821\t146419\t1831\t1837\t380416\t370511\t370545\t2688\t148723\t136985\t137032\t137119\tVU\t372\nBalaenoptera musculus\t(Linnaeus, 1758)\t137090\tSpecies\taccepted\tBalaenoptera musculus\t137090\tTrue\tAnimalia\tChordata\tVertebrata\tTetrapoda\tMammalia\tTheria\tCetartiodactyla\tCetancodonta\tCetacea\tMysticeti\tBalaenopteridae\tBalaenoptera\tBalaenoptera musculus\t2\t1821\t146419\t1831\t1837\t380416\t370511\t370545\t2688\t148724\t136979\t137013\t137090\tEN\t10\n```\n\n```Shell\nobis.py occurrence --areaid 190 --taxa 'Anchoa nasus' \n```\n```\nbrackish\tscientificNameID\tscientificName\tabsence\tdropped\taphiaID\tgenusid\tdecimalLatitude\toriginalScientificName\tmarine\tminimumDepthInMeters\tfamilyid\tphylumid\tsubphylumid\tterrestrial\tbasisOfRecord\tsuperclass\tmaximumDepthInMeters\tid\tclass\torder\tsuperclassid\torderid\tdataset_id\tdecimalLongitude\tspeciesid\tkingdom\tclassid\tphylum\tspecies\tgenus\tsubphylum\tfamily\tkingdomid\tnode_id\nTrue\turn:lsid:marinespecies.org:taxname:275528\tAnchoa nasus\tFalse\tFalse\t275528\t158697\t-9.06999969482\tAnchoa nasus\tTrue\tNone\t125465\t1821\t146419\tFalse\tHumanObservation\tPisces\tNone\t5fc5547b-f0b1-43e1-a8b2-bf90f19c9a4f\tActinopterygii\tClupeiformes\t11676\t10297\t0e1d55f3-c7dc-4355-a81f-e48a96795329\t-78.5999984741\t275528\tAnimalia\t10194\tChordata\tAnchoa nasus\tAnchoa\tVertebrata\tEngraulidae\t2\t['310922b4-9d0c-4de1-92d7-9b442d34765b']\nTrue\turn:lsid:marinespecies.org:taxname:275528\tAnchoa nasus\tFalse\tFalse\t275528\t158697\t-3.63000011444\tAnchoa nasus\tTrue\tNone\t125465\t1821\t146419\tFalse\tHumanObservation\tPisces\tNone\t86decef7-ecc8-4afc-855d-846ffd74f528\tActinopterygii\tClupeiformes\t11676\t10297\t0e1d55f3-c7dc-4355-a81f-e48a96795329\t-80.5999984741\t275528\tAnimalia\t10194\tChordata\tAnchoa nasus\tAnchoa\tVertebrata\tEngraulidae\t2\t['310922b4-9d0c-4de1-92d7-9b442d34765b']\nTrue\tP\u01f8rou\turn:lsid:marinespecies.org:taxname:275528\tAnchoa nasus\tkner ,steindachner\tFalse\tFalse\t275528\t158697\t-13.0260000229\tAnchoa nasus\tTrue\tNone\t125465\t1821\t146419\t2006-1641\tFalse\tPreservedSpecimen\tMNHN\tPisces\tNone\ta34ef4db-101f-4fba-8872-cf054c2eb7e6\tbearez\tActinopterygii\tClupeiformes\t11676\t10297\t705770e5-3474-4e69-be8b-3107a0c5610a\t-76.4779968262\tIC\t275528\tpacifique\tAnimalia\t10194\tb\u01f8arez\tChordata\tAnchoa nasus\tAnchoa\tVertebrata\tEngraulidae\t2\t['310922b4-9d0c-4de1-92d7-9b442d34765b']\nPeru\t1986\turn:lsid:marinespecies.org:taxname:308324\t1986\tAnchoa nasus\tobservedindividualcount=1;\tFalse\t275528\t-6.838116\t125465\t1821\t55397\tFalse\tHumanObservation\tPisces\tNone\tc154a9d2-7da8-41be-a936-c3791099dbaa\t9\tClupeiformes\tRC86-43\t11676\tb8617377-eb1c-4db2-baa6-8788a632e810\tOff Pimentel (Station 30), Pacific Ocean\tLambayeque\t-79.937686\t521251200000\tFishes\t275528\t521251200000\t07\tAnchoa\t1986-07-09T12:00:00Z\tTrue\tFalse\t158697\tAnchoa naso\tTrue\tNone\t146419\tROM\t521251200000\tHolm, E.\tActinopterygii\t10297\tAnimalia\t10194\tReed Horse Fishermen\tChordata\tAnchoa nasus\tVertebrata\tEngraulidae\t2\t['310922b4-9d0c-4de1-92d7-9b442d34765b']\nTrue\turn:lsid:marinespecies.org:taxname:275528\tAnchoa nasus\tFalse\tFalse\t275528\t158697\t-5.07999992371\tAnchoa nasus\tTrue\tNone\t125465\t1821\t146419\tFalse\tHumanObservation\tPisces\tNone\tf5d642a5-5a30-4d26-8921-01dd0bc229ef\tActinopterygii\tClupeiformes\t11676\t10297\t0e1d55f3-c7dc-4355-a81f-e48a96795329\t-81.1200027466\t275528\tAnimalia\t10194\tChordata\tAnchoa nasus\tAnchoa\tVertebrata\tEngraulidae\t2\t['310922b4-9d0c-4de1-92d7-9b442d34765b']\nTrue\turn:lsid:marinespecies.org:taxname:275528\tAnchoa nasus\tFalse\tFalse\t275528\t158697\t-3.65000009537\tAnchoa nasus\tTrue\tNone\t125465\t1821\t146419\tFalse\tHumanObservation\tPisces\tNone\tf8e2bccc-d19e-436f-9f8e-223a6e95de57\tActinopterygii\tClupeiformes\t11676\t10297\t0e1d55f3-c7dc-4355-a81f-e48a96795329\t-80.9499969482\t275528\tAnimalia\t10194\tChordata\tAnchoa nasus\tAnchoa\tVertebrata\tEngraulidae\t2\t['310922b4-9d0c-4de1-92d7-9b442d34765b']\n```\n\nFrom 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](https://mapper.obis.org/?geometry=POLYGON%20((9.6034%201.5839,%209.3501%201.1679,%209.1873%201.4555,%209.3027%201.6134,%209.6034%201.5839))) online app in order to get species occurrence from a tiny area of Equatorial Guinea and Gabon:\n\n\n```Shell\nobis.py occurrence --geometry 'POLYGON ((9.6034 1.5839, 9.3501 1.1679, 9.1873 1.4555, 9.3027 1.6134, 9.6034 1.5839))'\n```\n```\ndate_year\tscientificNameID\tscientificName\tdynamicProperties\tsuperfamilyid\tindividualCount\tdropped\tassociatedReferences\taphiaID\tdecimalLatitude\ttype\ttaxonRemarks\tphylumid\tfamilyid\tcatalogNumber\toccurrenceStatus\tbasisOfRecord\tsuperclass\tmaximumDepthInMeters\tmodified\tid\torder\trecordNumber\tgeoreferencedDate\tsuperclassid\tverbatimEventDate\tdataset_id\tdecimalLongitude\tdate_end\tcollectionCode\tspeciesid\toccurrenceID\tsuperfamily\tsuborderid\tlicense\tdate_start\torganismID\tdateIdentified\tgenus\tbibliographicCitation\teventDate\tscientificNameAuthorship\tabsence\ttaxonRank\tgenusid\toriginalScientificName\tmarine\tminimumDepthInMeters\tsubphylumid\tvernacularName\tinstitutionCode\tdate_mid\tidentificationRemarks\tclass\tsuborder\tnomenclaturalCode\torderid\tsex\tdatasetName\ttaxonomicStatus\tgeodeticDatum\tkingdom\tspecificEpithet\tclassid\tphylum\tlifeStage\tspecies\tcoordinatePrecision\torganismRemarks\tsubphylum\tdatasetID\toccurrenceRemarks\tfamily\tcategory\tkingdomid\tnode_id\n2009\turn:lsid:marinespecies.org:taxname:137209\tDermochelys coriacea\tMachineObservation\t987094\t4\tFalse\t[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. S., and B. J. Godley\",\"pubdate\":\"2005\",\"title_html\":\"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...]\t137209\t1.5\tEvent\tTaxon recorded as \"Leatherback\" by the provider\t1821\t137000\t1454_1238197\tpresent\tMachineObservation\tTetrapoda\tNone\t2018-06-13 14:36:11\t13fe7b7d-eb09-4aea-adfb-9b845b0783c8\tTestudines\t1454_1238197\t2008-12-11T02:19:58/2009-02-19T08:34:54\t1831\t2008-12-11 02:19:58/2009-02-19 08:34:54\t5783eb41-8787-415f-beb8-178fa05684ef\t9.5\t1235001600000\t1454\t137209\t1454_1238197\tChelonioidea\t148741\thttp://creativecommons.org/licenses/by-nc/4.0/\t1228953600000\t89071a;89072a;89075a;89076a\t2008-12-11T02:19:58/2009-02-19T08:34:54\tDermochelys\t[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. S., and B. J. Godley\",\"pubdate\":\"2005\",\"title_html\":\"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...]\t2008-12-11T02:19:58/2009-02-19T08:34:54\t(Vandelli, 1761)\tFalse\tSpecies\t137070\tDermochelys coriacea\tTrue\tNone\t146419\tLeatherback\tMTRG / Seaturtle.org\t1231977600000\tIdentification Type:Telemetry\tReptilia\tCryptodira\tWoRMS LSID\t2689\tFemale\tGabon 2008-09: Mayumba & Pongara, Leatherback Turtles\tvalid\tEPSG:4326 WGS84\tAnimalia\tcoriacea\t1838\tChordata\tAdult\tDermochelys coriacea\t0.001\tTagged animal. organismID may refer to the ID of the telemetry device.\tVertebrata\t1454\tTelemetry locations aggregated per species per 1-degree cell\tDermochelyidae\tVU\t2\t573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31\n2014\turn:lsid:marinespecies.org:taxname:137206\tChelonia mydas\tMachineObservation\t987094\t3\tFalse\t;http://www.seaturtle.org/tracking/index.shtml?project_id=1001\t137206\t1.5\tEvent\tTaxon recorded as \"Green Turtle\" by the provider\t1821\t136999\t1840_585748\tpresent\tMachineObservation\tTetrapoda\tNone\t2018-06-13 14:36:11\t30390ec2-924e-47c5-9b82-b42320d4f11c\tTestudines\t1840_585748\t2014-06-17T16:59:14/2014-10-10T22:10:39\t1831\t2014-06-17 16:59:14/2014-10-10 22:10:39\t4a06a415-2954-4597-baf3-7934b07355ea\t9.5\t1412899200000\t1840\t137206\t1840_585748\tChelonioidea\t148741\thttp://creativecommons.org/licenses/by-nc/4.0/\t1402963200000\t138424;138426;138427\t2014-06-17T16:59:14/2014-10-10T22:10:39\tChelonia\tHalpin, 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. [...]\t2014-06-17T16:59:14/2014-10-10T22:10:39\t(Linnaeus, 1758)\tFalse\tSpecies\t137067\tChelonia mydas\tTrue\tNone\t146419\tGreen Sea Turtle\tWildlife Conservation Society\t1407888000000\tIdentification Type:Telemetry\tReptilia\tCryptodira\tWoRMS LSID\t2689\tMale;Unknown\tEquatorial Guinea 2014: Foraging Green Sea Turtles\tvalid\tEPSG:4326 WGS84\tAnimalia\tmydas\t1838\tChordata\tJuvenile;Subadult\tChelonia mydas\t0.001\tTagged animal. organismID may refer to the ID of the telemetry device.\tVertebrata\t1840\tTelemetry locations aggregated per species per 1-degree cell\tCheloniidae\tEN\t2\t573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31\n2009\turn:lsid:marinespecies.org:taxname:137209\tDermochelys coriacea\tMachineObservation\t987094\t1\tFalse\t[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. S., and B. J. Godley\",\"pubdate\":\"2005\",\"title_html\":\"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...]\t137209\t1.5\tEvent\tTaxon recorded as \"Leatherback\" by the provider\t1821\t137000\t1456_1057383\tpresent\tMachineObservation\tTetrapoda\tNone\t2016-12-27 06:05:08\t35f94c5c-e83e-40b5-9092-562fa2fbb460\tTestudines\t1456_1057383\t2009-12-28T07:30:36/2009-12-28T07:30:36\t1831\t2009-12-28 07:30:36/2009-12-28 07:30:36\t961a2b3e-d2f1-4fff-b5f4-af9f01d4565a\t9.5\t1261958400000\t1456\t137209\t1456_1057383\tChelonioidea\t148741\thttp://creativecommons.org/licenses/by-nc/4.0/\t1261958400000\t92581a\t2009-12-28T07:30:36/2009-12-28T07:30:36\tDermochelys\t[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. S., and B. J. Godley\",\"pubdate\":\"2005\",\"title_html\":\"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...]\t2009-12-28T07:30:36/2009-12-28T07:30:36\t(Vandelli, 1761)\tFalse\tSpecies\t137070\tDermochelys coriacea\tTrue\tNone\t146419\tLeatherback\tMarine Turtle Research Group / Seaturtle.org\t1261958400000\tIdentification Type:Telemetry\tReptilia\tCryptodira\tWoRMS LSID\t2689\tFemale\tGabon 2009-10: Pongara, Leatherback Turtles\tvalid\tEPSG:4326 WGS84\tAnimalia\tcoriacea\t1838\tChordata\tAdult\tDermochelys coriacea\t0.001\tTagged animal. organismID may refer to the ID of the telemetry device.\tVertebrata\t1456\tTelemetry locations aggregated per species per 1-degree cell\tDermochelyidae\tVU\t2\t573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31\n2011\turn:lsid:marinespecies.org:taxname:137206\tChelonia mydas\tMachineObservation\t987094\t2\tFalse\t[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. S., and B. J. Godley\",\"pubdate\":\"2005\",\"title_html\":\"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...]\t137206\t1.5\tEvent\tTaxon recorded as \"Green Turtle\" by the provider\t1821\t136999\t718_980354\tpresent\tMachineObservation\tTetrapoda\tNone\t2017-07-18 06:02:22\t468f3da1-7a1e-46e8-946e-e272b8bf4034\tTestudines\t718_980354\t2010-12-29T07:17:52/2011-05-31T14:46:06\t1831\t2010-12-29 07:17:52/2011-05-31 14:46:06\tce258d5f-3097-412a-a969-112f34f9169e\t9.5\t1306800000000\t718\t137206\t718_980354\tChelonioidea\t148741\thttp://creativecommons.org/licenses/by-nc/4.0/\t1293580800000\t68395;68395a\t2010-12-29T07:17:52/2011-05-31T14:46:06\tChelonia\tMarine Turtle Research Group\t[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. S., and B. J. Godley\",\"pubdate\":\"2005\",\"title_html\":\"Satellite Tracking and Analysis Tool (STAT): an integrated sy [...]\t2010-12-29T07:17:52/2011-05-31T14:46:06\t(Linnaeus, 1758)\tFalse\tSpecies\t137067\tChelonia mydas\tTrue\tNone\t146419\tGreen Sea Turtle\tMarine Turtle Research Group\t1300147200000\tIdentification Type:Telemetry\tReptilia\tCryptodira\tWoRMS LSID\t2689\tUnknown\tEquatorial Guinea 2011: Green Turtles\tvalid\tEPSG:4326 WGS84\tAnimalia\tmydas\t1838\tChordata\tJuvenile\tChelonia mydas\t0.001\tTagged animal. organismID may refer to the ID of the telemetry device.\tVertebrata\t718\tTelemetry locations aggregated per species per 1-degree cell\tCheloniidae\tEN\t2\t573654c1-4ce7-4ea2-b2f1-e4d42f8f9c31\n2015\turn:lsid:marinespecies.org:taxname:220293\tLepidochelys olivacea\tMachineObservation\t987094\t1\tFalse\t[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. S., and B. J. 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