{"id":13577548,"url":"https://github.com/sckott/pytaxize","last_synced_at":"2025-04-23T20:14:54.306Z","repository":{"id":62583886,"uuid":"13102072","full_name":"sckott/pytaxize","owner":"sckott","description":"python port of taxize (taxonomy toolbelt) for R","archived":false,"fork":false,"pushed_at":"2020-09-11T01:30:45.000Z","size":11825,"stargazers_count":34,"open_issues_count":11,"forks_count":13,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-23T20:14:32.164Z","etag":null,"topics":["python","taxize","taxonomy"],"latest_commit_sha":null,"homepage":"https://sckott.github.io/pytaxize/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sckott.png","metadata":{"files":{"readme":"README.rst","changelog":"Changelog.rst","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2013-09-25T18:39:05.000Z","updated_at":"2024-03-28T16:00:47.000Z","dependencies_parsed_at":"2022-11-03T21:50:23.560Z","dependency_job_id":null,"html_url":"https://github.com/sckott/pytaxize","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fpytaxize","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fpytaxize/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fpytaxize/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sckott%2Fpytaxize/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sckott","download_url":"https://codeload.github.com/sckott/pytaxize/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250506141,"owners_count":21441723,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["python","taxize","taxonomy"],"created_at":"2024-08-01T15:01:22.405Z","updated_at":"2025-04-23T20:14:54.286Z","avatar_url":"https://github.com/sckott.png","language":"Python","funding_links":[],"categories":["Python"],"sub_categories":[],"readme":"pytaxize\n========\n\n|pypi| |travis| |coverage| |black|\n\nThis is a port of the R package `taxize \u003chttps://github.com/ropensci/taxize\u003e`__.  There is a lot going on in the R version of this library, so it will take a while to get all the same functionality over here.\n\nWhy?  A significant advantage of a Python version of `taxize` will be for those that are pythonistas at heart. Also, you could use `pytaxize` in a web app, whereas you could with `taxize` (e.g., in a Shiny app), but it wouldn't scale, be very fast, etc.\n\npython 2/3\n==========\n\npytaxize is only developed in and tested with Python 3\n\nInstallation\n============\n\nStable from pypi\n\n.. code-block:: console\n\n    pip install pytaxize\n\nDevelopment version\n\n.. code-block:: console\n\n    sudo pip install git+git://github.com/sckott/pytaxize.git#egg=pytaxize\n\n\nTaxonomic Ids\n=============\n\nI've started working on a class interface for taxonomic IDs, which will have a bunch of extension methods to do various things with taxon ids. What's available right now is just getting COL ids.\n\n.. code-block:: python\n    \n    from pytaxize import Ids\n    res = Ids('Poa annua')\n    res.ncbi()\n    res.ids\n\n.. code-block:: python\n\n    {'Poa annua': [{'id': '93036',\n       'name': 'Poa annua',\n       'rank': 'species',\n       'uri': 'https://www.ncbi.nlm.nih.gov/taxonomy/93036'}]}\n\nVascan search\n=============\n\n.. code-block:: python\n  \n    import pytaxize\n    pytaxize.vascan_search(q = [\"Helianthus annuus\"])\n\n.. code-block:: python\n\n    {u'apiVersion': u'0.1',\n     u'results': [{u'matches': [{u'canonicalName': u'Helianthus annuus',\n         u'distribution': [{u'establishmentMeans': u'introduced',\n           u'locality': u'NS',\n           u'locationID': u'ISO 3166-2:CA-NS',\n           u'occurrenceStatus': u'introduced'},\n          {u'establishmentMeans': u'',\n           u'locality': u'PE',\n           u'locationID': u'ISO 3166-2:CA-PE',\n           u'occurrenceStatus': u'excluded'},\n          {u'establishmentMeans': u'',\n           u'locality': u'NT',\n           u'locationID': u'ISO 3166-2:CA-NT',\n           u'occurrenceStatus': u'doubtful'},\n          {u'establishmentMeans': u'introduced',\n\nScrape taxonomic names\n======================\n\n.. code-block:: python\n\n    out = pytaxize.scrapenames(url = 'http://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf')\n    out['data'][0:3]\n\n.. code-block:: python\n\n    [{'verbatim': '(Hemiptera:',\n      'scientificName': 'Hemiptera',\n      'offsetStart': 222,\n      'offsetEnd': 233},\n     {'verbatim': 'Sternorrhyncha:',\n      'scientificName': 'Sternorrhyncha',\n      'offsetStart': 234,\n      'offsetEnd': 249},\n     {'verbatim': 'Coccoidea:',\n      'scientificName': 'Coccoidea',\n      'offsetStart': 250,\n      'offsetEnd': 260}]\n\nITIS low level functions\n========================\n\n.. code-block:: python\n    \n    from pytaxize import itis\n    itis.accepted_names(504239)\n\n    {'acceptedName': 'Dasiphora fruticosa',\n       'acceptedTsn': '836659',\n       'author': '(L.) Rydb.'}\n\n.. code-block:: python\n\n    itis.comment_detail(tsn=180543)\n\n    [{'commentDetail': 'Status: CITES - Appendix I as U. arctos (Mexico, Bhutan, China, and Mongolia populations) and U. a. isabellinus; otherwise Appendix II. U. S. ESA - Endangered as U. arctos pruinosus, as U. arctos in Mexico, and as U. a. arctos in Italy. Threatened as U. a. ho...',\n      'commentId': '18556',\n      'commentTimeStamp': '2007-08-20 15:06:38.0',\n      'commentator': 'Wilson \u0026 Reeder, eds. (2005)',\n      'updateDate': '2014-02-03'},\n     {'commentDetail': \"Comments: Reviewed by Erdbrink (1953), Couturier (1954), Rausch (1963a), Kurtén (1973), Hall (1984) and Pasitschniak-Arts (1993). Ognev (1931) and Allen (1938) recognized U. pruinosus as distinct; not followed by Ellerman and Morrison-Scott (1951), Gao (1987), and Stroganov (1962). Lönnberg (1923b) believed that differences between pruinosus and arctos warranted subgeneric distinction as (Mylarctos) pruinosus; however, this was not supported by Pocock's (1932b) thorough revision. Synonyms allocated a...\",\n      'commentId': '18557',\n      'commentTimeStamp': '2007-08-20 15:06:38.0',\n      'commentator': 'Wilson \u0026 Reeder, eds. (2005)',\n      'updateDate': '2014-02-03'}]\n\n.. code-block:: python\n\n    itis.hierarchy_up(tsn = 36485)\n\n    {'author': 'Raf.',\n     'parentName': 'Asteraceae',\n     'parentTsn': '35420',\n     'rankName': 'Genus',\n     'taxonName': 'Agoseris',\n     'tsn': '36485'}\n\nCatalogue of Life\n=================\n\n.. code-block:: python\n  \n    from pytaxize import col\n    x = col.children(name=[\"Apis\"])\n    x[0][0:3]\n\n.. code-block:: python\n\n    [{'id': '7a4a38c5095963949d6d6ec917d471de',\n      'name': 'Apis andreniformis',\n      'rank': 'Species'},\n     {'id': '39610a4ceff7e5244e334a3fbc5e47e5',\n      'name': 'Apis cerana',\n      'rank': 'Species'},\n     {'id': 'e1d4cbf3872c6c310b7a1c17ddd00ebc',\n      'name': 'Apis dorsata',\n      'rank': 'Species'}]\n\nParse names\n===========\n\nParse names using GBIF's parser API\n\n.. code-block:: python\n    \n    from pytaxize import gbif\n    gbif.parse(name=['Arrhenatherum elatius var. elatius',\n    \t 'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale',\n       'Vanessa atalanta (Linnaeus, 1758)'])\n\n.. code-block:: python\n\n    [{'scientificName': 'Arrhenatherum elatius var. elatius',\n      'type': 'SCIENTIFIC',\n      'genusOrAbove': 'Arrhenatherum',\n      'specificEpithet': 'elatius',\n      'infraSpecificEpithet': 'elatius',\n      'parsed': True,\n      'parsedPartially': False,\n      'canonicalName': 'Arrhenatherum elatius elatius',\n      'canonicalNameWithMarker': 'Arrhenatherum elatius var. elatius',\n      'canonicalNameComplete': 'Arrhenatherum elatius var. elatius',\n      'rankMarker': 'var.'},\n     {'scientificName': 'Secale cereale subsp. cereale',\n      'type': 'SCIENTIFIC',\n      ...\n\nContributors\n============\n\n* `Scott Chamberlain \u003chttps://github.com/sckott\u003e`__\n* `Colin Talbert \u003chttps://github.com/ColinTalbert\u003e`__\n* `akshayah3 \u003chttps://github.com/akshayah3\u003e`__\n* `panks \u003chttps://github.com/panks\u003e`__\n* `Yanghao Li \u003chttps://github.com/lyttonhao\u003e`__\n* `Ben Morris \u003chttps://github.com/bendmorris\u003e`__\n* `Bishakh Ghosh \u003chttps://github.com/ghoshbishakh\u003e`__\n* `Yoav Ram \u003chttps://github.com/yoavram\u003e`__\n\nMeta\n====\n\n* Please note that this project is released with a `Contributor Code of Conduct \u003chttps://github.com/sckott/pytaxize/blob/master/CONDUCT.md\u003e`__. By participating in this project you agree to abide by its terms.\n* License: MIT; see `LICENSE file \u003chttps://github.com/sckott/pytaxize/blob/master/LICENSE\u003e`__\n\n.. |pypi| image:: https://img.shields.io/pypi/v/pytaxize.svg\n   :target: https://pypi.python.org/pypi/pytaxize\n\n.. |travis| image:: https://travis-ci.org/sckott/pytaxize.svg?branch=master\n   :target: https://travis-ci.org/sckott/pytaxize\n\n.. |coverage| image:: https://codecov.io/gh/sckott/pytaxize/branch/master/graph/badge.svg\n   :target: https://codecov.io/gh/sckott/pytaxize\n\n.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\n   :target: https://github.com/psf/black\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsckott%2Fpytaxize","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsckott%2Fpytaxize","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsckott%2Fpytaxize/lists"}