{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "![title](https://rs.gbif.org/style/logo.svg)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#
" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Latinoamérica dispone de un gran riqueza en biodiversidad, razón por la cual es oportuna la ocasión de realizar un ejercicio práctico para contar una historia; en este caso de las Especies protegidas bajo la Convención sobre el Comercio Internacional de Especies Amenazadas de Fauna y Flora Silvestres [CITES](https://es.wikipedia.org/wiki/CITES) (3) utilizando como referencia el listado de Especies asociado a Venezuela, el cual puede consultaremos usando el API de [SPECIES+/CITES CHECKLIST API](http://checklist.cites.org/#/en) (4)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "![title](https://www.roqueleal.me/images/cites.jpg)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Venezuela además del petróleo, ocupa el séptimo lugar dentro de los países con mayor biodiversidad del mundo [(5)](https://es.wikipedia.org/wiki/Biodiversidad_de_Venezuela) por lo que analizar la distribución de sus Especies protegidas nos puede dar un vistazo más definido sobre la magnitud de la biodiversidad venezolana además de su distribución espacial utilizando estas dos valiosas fuentes de datos, basado en el script de consulta Python desarrollado por [Marie Grosjean](https://github.com/ManonGros/Small-scripts-using-GBIF-API/blob/master/query_species_list/functions_query_from_species_list.py) (6) " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Fuente de los Datos\n", "\n", "Se necesitarán las siguientes fuentes de datos para extraer y generar la información requerida:\n", "\n", "1.- Consultar el GBIF API utilizando nuestras credenciales. (1)\n", "\n", "2.- Lista de Especies protegidas bajo el Convenio CITES para Venezuela. (4)\n", "\n", "3.- Script de Funciones para la consulta del GBIF API de consulta Python. (6)\n", "\n", "Los datos se utilizarán en los siguientes procesos:\n", "\n", "**1- Para descubrir la distribución espacial y datos de observación de las especies.**\n", "\n", "**2- Para identificar las Especies CITES en Venezuela.**\n", "\n", "**3- Para crear los query's de consultas.**" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Librerias" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "#Libreria de pandas\n", "import pandas as pd\n", "#Libreria de kepler-gl\n", "from keplergl import KeplerGl\n", "# Scripts de funciones https://github.com/ManonGros/Small-scripts-using-GBIF-API/blob/master/query_species_list/functions_query_from_species_list.py\n", "from functions_query_from_species_list import *" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Constantes" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "# Credenciales para el API de GBIF\n", "GBIF_USER_NAME = \"xxx\"\n", "GBIF_PASSWORD = \"xxx\"\n", "GBIF_NOTIFICATION_ADDRESSES = \"xxx\"\n", "GBIF_DOWNLOAD_FORMAT = \"SIMPLE_CSV\"\n", "\n", "# Directorio de entrada \n", "INPUT_DIR = \"C:/Users/xxx/\"\n", "\n", "# Archivo CSV de entrada con lista de especies a procesar tomado de la Lista de Especies protegidas bajo el Convenio CITES para Venezuela. (4)\n", "INPUT_CHECKLIST = INPUT_DIR + \"cites_vzla.csv\"\n", "# Columna con el nombre científico de la especie\n", "INPUT_SCINAME_COL = \"full_name\"\n", "\n", "# Directorio de salida\n", "OUTPUT_DIR = \"C:/Users/xxx/\"\n", "\n", "# Archivo CSV con especies del archivo de entrada que se procesan\n", "INPUT_CHECKLIST_PROCESSED_SPECIES = OUTPUT_DIR + \"especies-procesadas.csv\"\n", "\n", "# Archivo CSV con especies del archivo de entrada que no se procesan\n", "INPUT_CHECKLIST_NON_PROCESSED_SPECIES = OUTPUT_DIR + \"especies-no-procesadas.csv\"\n", "\n", "# Archivo CSV de salida con los registros de presencia de todas las especies\n", "OCCURRENCES_CSV = INPUT_DIR + \"especies-procesadas.csv\"\n", "\n", "# Número máximo de registros a desplegar en los dataframes de Pandas\n", "pd.options.display.max_rows = 5" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Carga de datos" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "The schema in GBIF Colombia 🇨🇴 (pic.twitter.com/xTGRxbqjRb
— Dairo Escobar (@daiesco) March 5, 2020
\n", " | id | \n", "kingdom_name | \n", "phylum_name | \n", "class_name | \n", "order_name | \n", "family_name | \n", "genus_name | \n", "species_name | \n", "subspecies_name | \n", "full_name | \n", "... | \n", "synonyms_with_authors | \n", "english_names | \n", "spanish_names | \n", "french_names | \n", "countries_iso_codes | \n", "countries_full_names | \n", "current_listing | \n", "current_parties_iso_codes | \n", "current_parties_full_names | \n", "current_listing_changes | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "82867 | \n", "Plantae | \n", "NaN | \n", "NaN | \n", "Orchidales | \n", "Orchidaceae | \n", "Epidendrum | \n", "agathosmicum | \n", "NaN | \n", "Epidendrum agathosmicum | \n", "... | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "II | \n", "[List] | \n", "[List] | \n", "[List] | \n", "
1 | \n", "81567 | \n", "Plantae | \n", "NaN | \n", "NaN | \n", "Orchidales | \n", "Orchidaceae | \n", "Epidendrum | \n", "alpicola | \n", "NaN | \n", "Epidendrum alpicola | \n", "... | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "II | \n", "[List] | \n", "[List] | \n", "[List] | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
1744 | \n", "4281 | \n", "Animalia | \n", "Chordata | \n", "Aves | \n", "Apodiformes | \n", "Trochilidae | \n", "Topaza | \n", "pella | \n", "NaN | \n", "Topaza pella | \n", "... | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "II | \n", "[List] | \n", "[List] | \n", "[List] | \n", "
1745 | \n", "5338 | \n", "Animalia | \n", "Chordata | \n", "Aves | \n", "Apodiformes | \n", "Trochilidae | \n", "Topaza | \n", "pyra | \n", "NaN | \n", "Topaza pyra | \n", "... | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "[List] | \n", "II | \n", "[List] | \n", "[List] | \n", "[List] | \n", "
1746 rows × 23 columns
\n", "\n", " | canonicalName | \n", "class | \n", "classKey | \n", "confidence | \n", "family | \n", "familyKey | \n", "genus | \n", "genusKey | \n", "inputName | \n", "kingdom | \n", "... | \n", "orderKey | \n", "phylum | \n", "phylumKey | \n", "rank | \n", "scientificName | \n", "species | \n", "speciesKey | \n", "status | \n", "synonym | \n", "usageKey | \n", "
---|
0 rows × 24 columns
\n", "\n", " | gbifID | \n", "datasetKey | \n", "occurrenceID | \n", "kingdom | \n", "phylum | \n", "class | \n", "order | \n", "family | \n", "genus | \n", "species | \n", "... | \n", "identifiedBy | \n", "dateIdentified | \n", "license | \n", "rightsHolder | \n", "recordedBy | \n", "typeStatus | \n", "establishmentMeans | \n", "lastInterpreted | \n", "mediaType | \n", "issue | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "1211815285 | \n", "c5c4a23e-2035-4416-ab64-032d6df52ddb | \n", "URI:catalog:ROM:Mammals:107836 | \n", "Animalia | \n", "Chordata | \n", "Mammalia | \n", "Carnivora | \n", "Canidae | \n", "Cerdocyon | \n", "Cerdocyon thous | \n", "... | \n", "NaN | \n", "NaN | \n", "CC_BY_NC_4_0 | \n", "Royal Ontario Museum; ROM | \n", "Lim, BK; Lee, Te, Jr; Hanson, Jd | \n", "NaN | \n", "NaN | \n", "2020-02-10T20:50:01.515Z | \n", "NaN | \n", "COORDINATE_ROUNDED;GEODETIC_DATUM_ASSUMED_WGS84 | \n", "
1 | \n", "1453241628 | \n", "50c9509d-22c7-4a22-a47d-8c48425ef4a7 | \n", "http://www.inaturalist.org/observations/4634444 | \n", "Animalia | \n", "Chordata | \n", "Reptilia | \n", "Squamata | \n", "Boidae | \n", "Eunectes | \n", "Eunectes murinus | \n", "... | \n", "NaN | \n", "2016-11-25T13:09:39Z | \n", "CC_BY_NC_4_0 | \n", "Brad Walker | \n", "Brad Walker | \n", "NaN | \n", "NaN | \n", "2020-02-19T16:22:29.228Z | \n", "StillImage;StillImage;StillImage;StillImage | \n", "GEODETIC_DATUM_ASSUMED_WGS84 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
139875 | \n", "1317757887 | \n", "821cc27a-e3bb-4bc5-ac34-89ada245069d | \n", "http://n2t.net/ark:/65665/3188edd67-eb6a-4a72-... | \n", "Animalia | \n", "Chordata | \n", "Mammalia | \n", "Rodentia | \n", "Cuniculidae | \n", "Cuniculus | \n", "Cuniculus paca | \n", "... | \n", "NaN | \n", "NaN | \n", "CC0_1_0 | \n", "NaN | \n", "Smithsonian Venezuelan Project | \n", "NaN | \n", "NaN | \n", "2020-02-13T22:08:24.058Z | \n", "NaN | \n", "GEODETIC_DATUM_ASSUMED_WGS84 | \n", "
139876 | \n", "1998558297 | \n", "861e6afe-f762-11e1-a439-00145eb45e9a | \n", "39f2b678-cec7-4e16-b3e6-ba9a8c310879 | \n", "Plantae | \n", "Tracheophyta | \n", "Liliopsida | \n", "Asparagales | \n", "Orchidaceae | \n", "Epidendrum | \n", "Epidendrum alsum | \n", "... | \n", "Dunsterville | \n", "NaN | \n", "CC_BY_4_0 | \n", "President and Fellows of Harvard College | \n", "J. A. Steyermark & C. Brewer-Carias | \n", "NaN | \n", "NaN | \n", "2020-02-11T00:11:35.141Z | \n", "NaN | \n", "GEODETIC_DATUM_ASSUMED_WGS84;GEODETIC_DATUM_IN... | \n", "
139877 rows × 50 columns
\n", "