{ "cells": [ { "cell_type": "code", "execution_count": null, "metadata": { "tags": [ "remove-cell" ] }, "outputs": [], "source": [ "import subprocess\n", "import sys\n", "\n", "COLAB = \"google.colab\" in sys.modules\n", "\n", "\n", "def _install(package):\n", " if COLAB:\n", " ans = input(f\"Install { package }? [y/n]:\")\n", " if ans.lower() in [\"y\", \"yes\"]:\n", " subprocess.check_call(\n", " [sys.executable, \"-m\", \"pip\", \"install\", \"--quiet\", package]\n", " )\n", " print(f\"{ package } installed!\")\n", "\n", "\n", "def _colab_install_missing_deps(deps):\n", " import importlib\n", "\n", " for dep in deps:\n", " if importlib.util.find_spec(dep) is None:\n", " if dep == \"iris\":\n", " dep = \"scitools-iris\"\n", " _install(dep)\n", "\n", "\n", "deps = [\"palettable\"]\n", "_colab_install_missing_deps(deps)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Using r-obistools and r-obis to explore the OBIS database\n", "\n", "Created: 2018-02-20\n", "\n", "The [Ocean Biogeographic Information System (OBIS)](https://www.obis.org/) is an open-access data and information system for marine biodiversity for science, conservation and sustainable development.\n", "\n", "In this example we will use R libraries [`obistools`](https://iobis.github.io/obistools) and [`robis`](https://iobis.github.io/robis) to search data regarding marine turtles occurrence in the South Atlantic Ocean.\n", "\n", "Let's start by loading the R-to-Python extension and check the database for the 7 known species of marine turtles found in the world's oceans." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "%load_ext rpy2.ipython" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "R[write to console]: 7 names, 0 without matches, 0 with multiple matches\n", "\n" ] } ], "source": [ "%%R -o matches\n", "\n", "library(obistools)\n", "\n", "\n", "species <- c(\n", " 'Caretta caretta',\n", " 'Chelonia mydas',\n", " 'Dermochelys coriacea',\n", " 'Eretmochelys imbricata',\n", " 'Lepidochelys kempii',\n", " 'Lepidochelys olivacea',\n", " 'Natator depressa'\n", ")\n", "\n", "matches = match_taxa(species, ask=FALSE)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | scientificName | \n", "scientificNameID | \n", "match_type | \n", "
---|---|---|---|
1 | \n", "Caretta caretta | \n", "urn:lsid:marinespecies.org:taxname:137205 | \n", "exact | \n", "
2 | \n", "Chelonia mydas | \n", "urn:lsid:marinespecies.org:taxname:137206 | \n", "exact | \n", "
3 | \n", "Dermochelys coriacea | \n", "urn:lsid:marinespecies.org:taxname:137209 | \n", "exact | \n", "
4 | \n", "Eretmochelys imbricata | \n", "urn:lsid:marinespecies.org:taxname:137207 | \n", "exact | \n", "
5 | \n", "Lepidochelys kempii | \n", "urn:lsid:marinespecies.org:taxname:137208 | \n", "exact | \n", "
6 | \n", "Lepidochelys olivacea | \n", "urn:lsid:marinespecies.org:taxname:220293 | \n", "exact | \n", "
7 | \n", "Natator depressa | \n", "urn:lsid:marinespecies.org:taxname:344093 | \n", "exact | \n", "
\n", " | date_year | \n", "scientificNameID | \n", "scientificName | \n", "dynamicProperties | \n", "superfamilyid | \n", "individualCount | \n", "associatedReferences | \n", "dropped | \n", "aphiaID | \n", "decimalLatitude | \n", "... | \n", "taxonConceptID | \n", "organismQuantity | \n", "organismQuantityType | \n", "fieldNumber | \n", "eventRemarks | \n", "preparations | \n", "identifiedBy | \n", "typeStatus | \n", "otherCatalogNumbers | \n", "locationID | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | \n", "2012 | \n", "urn:lsid:marinespecies.org:taxname:137209 | \n", "Dermochelys coriacea | \n", "MachineObservation | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Robinson, ... | \n", "0 | \n", "137209 | \n", "-33.500000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
2 | \n", "1998 | \n", "urn:lsid:marinespecies.org:taxname:137206 | \n", "Chelonia mydas | \n", "None | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Luschi, P.... | \n", "0 | \n", "137206 | \n", "-7.226000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
3 | \n", "2014 | \n", "urn:lsid:marinespecies.org:taxname:137205 | \n", "Caretta caretta | \n", "MachineObservation | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. ... | \n", "0 | \n", "137205 | \n", "-29.500000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
4 | \n", "2015 | \n", "urn:lsid:marinespecies.org:taxname:220293 | \n", "Lepidochelys olivacea | \n", "MachineObservation | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. ... | \n", "0 | \n", "220293 | \n", "-14.500000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
5 | \n", "-2147483648 | \n", "urn:lsid:marinespecies.org:taxname:137206 | \n", "Chelonia mydas | \n", "None | \n", "987094 | \n", "None | \n", "None | \n", "0 | \n", "137206 | \n", "-3.883472 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
5616 | \n", "2003 | \n", "urn:lsid:marinespecies.org:taxname:137209 | \n", "Dermochelys coriacea | \n", "None | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Luschi, P.... | \n", "0 | \n", "137209 | \n", "-32.194000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
5617 | \n", "1998 | \n", "urn:lsid:marinespecies.org:taxname:137206 | \n", "Chelonia mydas | \n", "None | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Luschi, P.... | \n", "0 | \n", "137206 | \n", "-8.895000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
5618 | \n", "2003 | \n", "urn:lsid:marinespecies.org:taxname:137209 | \n", "Dermochelys coriacea | \n", "None | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Luschi, P.... | \n", "0 | \n", "137209 | \n", "-35.069000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
5619 | \n", "2006 | \n", "urn:lsid:marinespecies.org:taxname:137209 | \n", "Dermochelys coriacea | \n", "MachineObservation | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Coyne, M. ... | \n", "0 | \n", "137209 | \n", "-30.500000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
5620 | \n", "1996 | \n", "urn:lsid:marinespecies.org:taxname:137209 | \n", "Dermochelys coriacea | \n", "None | \n", "987094 | \n", "1 | \n", "[{\"crossref\":{\"citeinfo\":{\"origin\":\"Luschi, P.... | \n", "0 | \n", "137209 | \n", "-39.724000 | \n", "... | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "None | \n", "
5620 rows × 121 columns
\n", "