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match_names_gnrd.ipynb
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| { | |
| "nbformat": 4, | |
| "nbformat_minor": 0, | |
| "metadata": { | |
| "colab": { | |
| "name": "match_names_gnrd.ipynb", | |
| "provenance": [], | |
| "collapsed_sections": [], | |
| "include_colab_link": true | |
| }, | |
| "kernelspec": { | |
| "name": "python3", | |
| "display_name": "Python 3" | |
| }, | |
| "language_info": { | |
| "name": "python" | |
| } | |
| }, | |
| "cells": [ | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "id": "view-in-github", | |
| "colab_type": "text" | |
| }, | |
| "source": [ | |
| "<a href=\"https://colab.research.google.com/gist/adyork/5983a1ed9763ffb37fb7cd15df24e895/match_names_gnrd.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>" | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "id": "rit8245jUGye" | |
| }, | |
| "source": [ | |
| "# Match taxonomic names using the global names resolver\n", | |
| "\n", | |
| "Takes a data file and matches a column of taxanomic names to data sources using the Global Names Resover. http://resolver.globalnames.org/api\n", | |
| "\n", | |
| "Outputs supplied name, and match results for each data source (e.g. EOL, COL, GBIF,ITIS, WoRMS)." | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "cJ2Q-B-rGpnv" | |
| }, | |
| "source": [ | |
| "import pandas as pd\n", | |
| "import json\n", | |
| "import os,re\n", | |
| "import requests\n", | |
| "from requests.exceptions import HTTPError" | |
| ], | |
| "execution_count": null, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "vD28JT9QHY3_", | |
| "outputId": "61a9b94a-07f9-4c4d-be80-461aeebe5b4e" | |
| }, | |
| "source": [ | |
| "# First, let's go through an example using two names and look at the \n", | |
| "# data struccture returned.\n", | |
| "\n", | |
| "names=['Gadus morhua','Acomys cahirinus']\n", | |
| "\n", | |
| "# datasource ids\n", | |
| "# http://resolver.globalnames.org/data_sources\n", | |
| "# sources = {'EOL':12,'ITIS':3,'WoRMS':9,'OBIS':149,'NCBI':4,'GBIF':11}\n", | |
| "\n", | |
| "\n", | |
| "response = requests.get(\n", | |
| " 'http://resolver.globalnames.org/name_resolvers.json',\n", | |
| " params={'names': '|'.join(names),\n", | |
| " \"data_source_ids\": '9',\n", | |
| " \"best_match_only\": \"true\",\n", | |
| " \"with_context\": \"true\"\n", | |
| " },\n", | |
| " )\n", | |
| "response.status_code" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "200" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 78 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "PAKCiDYKM_BP", | |
| "outputId": "b2fcab67-5ac5-4640-d109-a0b30db2d006" | |
| }, | |
| "source": [ | |
| "#Wrapping the request to catch errors\n", | |
| "\n", | |
| "try:\n", | |
| " response = requests.get(\n", | |
| " 'http://resolver.globalnames.org/name_resolvers.json',\n", | |
| " params={'names': '|'.join(names),\n", | |
| " \"data_source_ids\": '9',\n", | |
| " \"best_match_only\": \"true\",\n", | |
| " \"with_context\": \"true\"\n", | |
| " },\n", | |
| " )\n", | |
| "\n", | |
| " # If the response was successful, no Exception will be raised\n", | |
| " response.raise_for_status()\n", | |
| "except HTTPError as http_err:\n", | |
| " (f'HTTP error occurred: {http_err}') \n", | |
| "except Exception as err:\n", | |
| " print(f'Other error occurred: {err}') \n", | |
| "else:\n", | |
| " print('200: Success!')\n" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "200: Success!\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "Hr4zowhYH4xF", | |
| "outputId": "91f5849b-f490-4a87-a0e7-426858566a4b" | |
| }, | |
| "source": [ | |
| "results = response.json()\n", | |
| "results" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "{'context': [{'context_clade': 'Gadus morhua', 'context_data_source_id': 9}],\n", | |
| " 'data': [{'data_sources_number': 1,\n", | |
| " 'in_curated_sources': False,\n", | |
| " 'is_known_name': True,\n", | |
| " 'results': [{'canonical_form': 'Gadus morhua',\n", | |
| " 'classification_path': 'Biota|Animalia|Chordata|Vertebrata|Gnathostomata|Pisces|Actinopterygii|Gadiformes|Gadidae|Gadus|Gadus morhua',\n", | |
| " 'classification_path_ids': 'urn:lsid:marinespecies.org:taxname:1|urn:lsid:marinespecies.org:taxname:2|urn:lsid:marinespecies.org:taxname:1821|urn:lsid:marinespecies.org:taxname:146419|urn:lsid:marinespecies.org:taxname:1828|urn:lsid:marinespecies.org:taxname:11676|urn:lsid:marinespecies.org:taxname:10194|urn:lsid:marinespecies.org:taxname:10313|urn:lsid:marinespecies.org:taxname:125469|urn:lsid:marinespecies.org:taxname:125732|urn:lsid:marinespecies.org:taxname:126436',\n", | |
| " 'classification_path_ranks': '|Kingdom|Phylum|Subphylum|Infraphylum|Superclass|Class|Order|Family|Genus|Species',\n", | |
| " 'data_source_id': 9,\n", | |
| " 'data_source_title': 'World Register of Marine Species',\n", | |
| " 'edit_distance': 0,\n", | |
| " 'gni_uuid': '5128ca17-9b42-5b3b-a280-b6121ffff53b',\n", | |
| " 'imported_at': '2021-06-23T14:03:10Z',\n", | |
| " 'match_type': 2,\n", | |
| " 'match_value': 'Exact match by canonical form',\n", | |
| " 'name_string': 'Gadus morhua Linnaeus, 1758',\n", | |
| " 'prescore': '3|0|0',\n", | |
| " 'score': 0.988,\n", | |
| " 'taxon_id': 'urn:lsid:marinespecies.org:taxname:126436'}],\n", | |
| " 'supplied_name_string': 'Gadus morhua'},\n", | |
| " {'is_known_name': False, 'supplied_name_string': 'Acomys cahirinus'}],\n", | |
| " 'data_sources': [{'id': 9, 'title': 'World Register of Marine Species'}],\n", | |
| " 'id': 'bolp00bdidle',\n", | |
| " 'message': 'Success',\n", | |
| " 'parameters': {'best_match_only': True,\n", | |
| " 'data_sources': [9],\n", | |
| " 'header_only': False,\n", | |
| " 'preferred_data_sources': [],\n", | |
| " 'resolve_once': False,\n", | |
| " 'with_canonical_ranks': False,\n", | |
| " 'with_context': True,\n", | |
| " 'with_vernaculars': False},\n", | |
| " 'status': 'success',\n", | |
| " 'url': 'http://resolver.globalnames.org/name_resolvers/bolp00bdidle.json'}" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 80 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "9qLkamPGOv5T", | |
| "outputId": "6bb14bda-36c2-4099-ed49-191e2274f162" | |
| }, | |
| "source": [ | |
| "#looking at the first data source results at index [0] since python starts at 0.\n", | |
| "results['data'][0]" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "{'data_sources_number': 1,\n", | |
| " 'in_curated_sources': False,\n", | |
| " 'is_known_name': True,\n", | |
| " 'results': [{'canonical_form': 'Gadus morhua',\n", | |
| " 'classification_path': 'Biota|Animalia|Chordata|Vertebrata|Gnathostomata|Pisces|Actinopterygii|Gadiformes|Gadidae|Gadus|Gadus morhua',\n", | |
| " 'classification_path_ids': 'urn:lsid:marinespecies.org:taxname:1|urn:lsid:marinespecies.org:taxname:2|urn:lsid:marinespecies.org:taxname:1821|urn:lsid:marinespecies.org:taxname:146419|urn:lsid:marinespecies.org:taxname:1828|urn:lsid:marinespecies.org:taxname:11676|urn:lsid:marinespecies.org:taxname:10194|urn:lsid:marinespecies.org:taxname:10313|urn:lsid:marinespecies.org:taxname:125469|urn:lsid:marinespecies.org:taxname:125732|urn:lsid:marinespecies.org:taxname:126436',\n", | |
| " 'classification_path_ranks': '|Kingdom|Phylum|Subphylum|Infraphylum|Superclass|Class|Order|Family|Genus|Species',\n", | |
| " 'data_source_id': 9,\n", | |
| " 'data_source_title': 'World Register of Marine Species',\n", | |
| " 'edit_distance': 0,\n", | |
| " 'gni_uuid': '5128ca17-9b42-5b3b-a280-b6121ffff53b',\n", | |
| " 'imported_at': '2021-06-23T14:03:10Z',\n", | |
| " 'match_type': 2,\n", | |
| " 'match_value': 'Exact match by canonical form',\n", | |
| " 'name_string': 'Gadus morhua Linnaeus, 1758',\n", | |
| " 'prescore': '3|0|0',\n", | |
| " 'score': 0.988,\n", | |
| " 'taxon_id': 'urn:lsid:marinespecies.org:taxname:126436'}],\n", | |
| " 'supplied_name_string': 'Gadus morhua'}" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 81 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "id": "UlvoBFL5PS-V" | |
| }, | |
| "source": [ | |
| "## Match types\n", | |
| "* take a closer look at any name that isn't an exact match. It could indicate formatting or spelling errors.\n", | |
| "* from global names resolver documentation:\n", | |
| " 1 - Exact match\n", | |
| " 2 - Exact match by canonical form of a name\n", | |
| " 3 - Fuzzy match by canonical form\n", | |
| " 4 - Partial exact match by species part of canonical form\n", | |
| " 5 - Partial fuzzy match by species part of canonical form\n", | |
| " 6 - Exact match by genus part of a canonical form" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "DhxRhmkYF9P1", | |
| "outputId": "8e19f8e1-0dfe-4526-c78d-1af704bcb4e2" | |
| }, | |
| "source": [ | |
| "# To get down to the level with the name match results you have to drill down into\n", | |
| "# the json heirarchy.\n", | |
| "# For example, to get the first name match result from the first data source:\n", | |
| "results['data'][0]['results'][0]" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/plain": [ | |
| "{'canonical_form': 'Gadus morhua',\n", | |
| " 'classification_path': 'Biota|Animalia|Chordata|Vertebrata|Gnathostomata|Pisces|Actinopterygii|Gadiformes|Gadidae|Gadus|Gadus morhua',\n", | |
| " 'classification_path_ids': 'urn:lsid:marinespecies.org:taxname:1|urn:lsid:marinespecies.org:taxname:2|urn:lsid:marinespecies.org:taxname:1821|urn:lsid:marinespecies.org:taxname:146419|urn:lsid:marinespecies.org:taxname:1828|urn:lsid:marinespecies.org:taxname:11676|urn:lsid:marinespecies.org:taxname:10194|urn:lsid:marinespecies.org:taxname:10313|urn:lsid:marinespecies.org:taxname:125469|urn:lsid:marinespecies.org:taxname:125732|urn:lsid:marinespecies.org:taxname:126436',\n", | |
| " 'classification_path_ranks': '|Kingdom|Phylum|Subphylum|Infraphylum|Superclass|Class|Order|Family|Genus|Species',\n", | |
| " 'data_source_id': 9,\n", | |
| " 'data_source_title': 'World Register of Marine Species',\n", | |
| " 'edit_distance': 0,\n", | |
| " 'gni_uuid': '5128ca17-9b42-5b3b-a280-b6121ffff53b',\n", | |
| " 'imported_at': '2021-06-23T14:03:10Z',\n", | |
| " 'match_type': 2,\n", | |
| " 'match_value': 'Exact match by canonical form',\n", | |
| " 'name_string': 'Gadus morhua Linnaeus, 1758',\n", | |
| " 'prescore': '3|0|0',\n", | |
| " 'score': 0.988,\n", | |
| " 'taxon_id': 'urn:lsid:marinespecies.org:taxname:126436'}" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 82 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "EObs6cuJP7SE", | |
| "outputId": "091886fd-7a51-402a-f432-b5f91d897793", | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 35 | |
| } | |
| }, | |
| "source": [ | |
| "# And to get the taxon_id from that name match:\n", | |
| "results['data'][0]['results'][0]['taxon_id']\n", | |
| "\n", | |
| "# * more about the taxon_id variability between data sources at the end of this notebook...." | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "application/vnd.google.colaboratory.intrinsic+json": { | |
| "type": "string" | |
| }, | |
| "text/plain": [ | |
| "'urn:lsid:marinespecies.org:taxname:126436'" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 83 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "sMP73lO_hEqO" | |
| }, | |
| "source": [ | |
| "#get_name_matches takes a list of species names and one data source and \n", | |
| "# returns a data frame with match information for each name\n", | |
| "def get_name_matches(names=['Gadus morhua','Acomys cahirinus'],datasource_id=3):\n", | |
| "\n", | |
| " #uses global name resolver, see http://resolver.globalnames.org/api\n", | |
| " \n", | |
| " # .e.g.\n", | |
| " # http://resolver.globalnames.org/name_resolvers.xml?names=Plantago+major|Monohamus+galloprovincialis|Felis+concolor&data_source_ids=1|12\n", | |
| "\n", | |
| " try:\n", | |
| " response = requests.get(\n", | |
| " 'http://resolver.globalnames.org/name_resolvers.json',\n", | |
| " params={'names': '|'.join(names),\n", | |
| " \"data_source_ids\": datasource_id,\n", | |
| " \"best_match_only\": \"true\",\n", | |
| " \"with_context\": \"true\"\n", | |
| " },\n", | |
| " )\n", | |
| "\n", | |
| " # If the response was successful, no Exception will be raised\n", | |
| " response.raise_for_status()\n", | |
| " except HTTPError as http_err:\n", | |
| " (f'HTTP error occurred: {http_err}') \n", | |
| " except Exception as err:\n", | |
| " print(f'Other error occurred: {err}') \n", | |
| " else:\n", | |
| " results = response.json()\n", | |
| "\n", | |
| "\n", | |
| " #transform the results data from json to a dataframe. \n", | |
| " # Also fill in dummy values when name not matched\n", | |
| "\n", | |
| " ''' \n", | |
| " If not a known name won't have a \"results\" under data so this doesn't work\n", | |
| " because ignore only allows keyerrors for meta not \"record_path\"\n", | |
| " \n", | |
| " '''\n", | |
| "\n", | |
| " #Before I json_normalize below, I need to add an empty results key in the dict so the normalize\n", | |
| " # won't get a key error. It can handle the metas being missing but not the \"record paths.\"\n", | |
| " for i, v in enumerate(results['data']):\n", | |
| " if not 'results' in v:\n", | |
| " print('\\t\\t No match for: ' +str(v))\n", | |
| " #add results list with first item a dict\n", | |
| " results['data'][i]['results'] = [{'match_value': 'No match found'}]\n", | |
| "\n", | |
| " df = pd.json_normalize(results['data'], errors='ignore',\n", | |
| " meta=['is_known_name', 'supplied_name_string'],\n", | |
| " record_path='results' # I want cols from all keys under this\n", | |
| " )\n", | |
| " return df" | |
| ], | |
| "execution_count": null, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 235 | |
| }, | |
| "id": "q8AjfGGeS0D4", | |
| "outputId": "bfe0b946-b96d-406d-df21-6d231dc32f59" | |
| }, | |
| "source": [ | |
| "get_name_matches(names=['Gadus morha','Acomys cahirinus'],datasource_id=3)\n", | |
| "# the above name is spelled wrong, it should be Gadus morhua" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>data_source_id</th>\n", | |
| " <th>data_source_title</th>\n", | |
| " <th>gni_uuid</th>\n", | |
| " <th>name_string</th>\n", | |
| " <th>canonical_form</th>\n", | |
| " <th>classification_path</th>\n", | |
| " <th>classification_path_ranks</th>\n", | |
| " <th>classification_path_ids</th>\n", | |
| " <th>taxon_id</th>\n", | |
| " <th>edit_distance</th>\n", | |
| " <th>imported_at</th>\n", | |
| " <th>match_type</th>\n", | |
| " <th>match_value</th>\n", | |
| " <th>prescore</th>\n", | |
| " <th>score</th>\n", | |
| " <th>current_taxon_id</th>\n", | |
| " <th>current_name_string</th>\n", | |
| " <th>is_known_name</th>\n", | |
| " <th>supplied_name_string</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>5128ca17-9b42-5b3b-a280-b6121ffff53b</td>\n", | |
| " <td>Gadus morhua Linnaeus, 1758</td>\n", | |
| " <td>Gadus morhua</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|1610...</td>\n", | |
| " <td>164712</td>\n", | |
| " <td>1</td>\n", | |
| " <td>2021-06-23T03:49:29Z</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Gadus morha</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>261f2ff8-be59-5a09-b7fe-77fd219a14c6</td>\n", | |
| " <td>Acomys cahirinus (Desmarest, 1819)</td>\n", | |
| " <td>Acomys cahirinus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>585099</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:53:12Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>970754</td>\n", | |
| " <td>Acomys cahirinus (É. Geoffroy, 1803)</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Acomys cahirinus</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " data_source_id ... supplied_name_string\n", | |
| "0 3 ... Gadus morha\n", | |
| "1 3 ... Acomys cahirinus\n", | |
| "\n", | |
| "[2 rows x 19 columns]" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 85 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 219 | |
| }, | |
| "id": "NURs3WXBS5jQ", | |
| "outputId": "b08828b8-27c5-4f09-8b74-4c376d5c3674" | |
| }, | |
| "source": [ | |
| "#note that it still returns the row for unmatched names\n", | |
| "get_name_matches(names=['Gadus morha','Acomys cahirinus'],datasource_id=9)\n", | |
| "# the above name is spelled wrong, it should be Gadus morhua\n", | |
| "# And I changed the data source from ITIS to WoRMS" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "\t\t No match for: {'supplied_name_string': 'Acomys cahirinus', 'is_known_name': False}\n" | |
| ] | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>data_source_id</th>\n", | |
| " <th>data_source_title</th>\n", | |
| " <th>gni_uuid</th>\n", | |
| " <th>name_string</th>\n", | |
| " <th>canonical_form</th>\n", | |
| " <th>classification_path</th>\n", | |
| " <th>classification_path_ranks</th>\n", | |
| " <th>classification_path_ids</th>\n", | |
| " <th>taxon_id</th>\n", | |
| " <th>edit_distance</th>\n", | |
| " <th>imported_at</th>\n", | |
| " <th>match_type</th>\n", | |
| " <th>match_value</th>\n", | |
| " <th>prescore</th>\n", | |
| " <th>score</th>\n", | |
| " <th>is_known_name</th>\n", | |
| " <th>supplied_name_string</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>5128ca17-9b42-5b3b-a280-b6121ffff53b</td>\n", | |
| " <td>Gadus morhua Linnaeus, 1758</td>\n", | |
| " <td>Gadus morhua</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:126436</td>\n", | |
| " <td>1.0</td>\n", | |
| " <td>2021-06-23T14:03:10Z</td>\n", | |
| " <td>3.0</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.75</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Gadus morha</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>No match found</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Acomys cahirinus</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " data_source_id ... supplied_name_string\n", | |
| "0 9.0 ... Gadus morha\n", | |
| "1 NaN ... Acomys cahirinus\n", | |
| "\n", | |
| "[2 rows x 17 columns]" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 86 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "id": "yR25EVeEHMgV" | |
| }, | |
| "source": [ | |
| "'''\n", | |
| "Takes a data frame (df_orig) and matches the column with taxonomic name (taxa_col) \n", | |
| " then calls get_match_names() to add match information to the dataset data frame.\n", | |
| "''' \n", | |
| "\n", | |
| "def match_df(df_orig=None,taxa_col = 'Species',sources = {'GBIF': 11, 'WoRMS': 9}):\n", | |
| "\n", | |
| " df_results = df_orig.copy()\n", | |
| " df_results_all = df_orig.copy()\n", | |
| "\n", | |
| "\n", | |
| " for source,source_id in sources.items():\n", | |
| " print('Matching names with GNRD source '+str(source_id)+': ' + source)\n", | |
| " df_matches = get_name_matches(names=df_orig[taxa_col],datasource_id=source_id)\n", | |
| " df_matches = df_matches.add_prefix(source+'_') #add prefix EOL_ etc to each col\n", | |
| "\n", | |
| " #add columns for this data source to results df\n", | |
| " df_results_all = pd.concat([df_results_all, df_matches], axis=1, sort=False)\n", | |
| "\n", | |
| " df_matches[source+'_matched_name'] = df_matches[source+'_canonical_form']\n", | |
| "\n", | |
| " #get just the critical columns\n", | |
| " df_results = pd.concat(\n", | |
| " [\n", | |
| " df_results,\n", | |
| " df_matches[[\n", | |
| " source + '_match_value',\n", | |
| " source+'_matched_name',\n", | |
| " source+'_taxon_id',\n", | |
| " #source + '_is_known_name'\n", | |
| " ]]\n", | |
| " ],\n", | |
| " axis=1,\n", | |
| " sort=False\n", | |
| " )\n", | |
| "\n", | |
| " df_results.to_csv('match_results.csv',index=False)\n", | |
| " df_results_all.to_csv('match_results_all.csv', index=False)\n", | |
| "\n", | |
| " print('done')\n", | |
| " return df_results_all" | |
| ], | |
| "execution_count": null, | |
| "outputs": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "ouPNrpp-QpUY", | |
| "outputId": "c7371e02-c674-4be3-a92a-4aa4e5a9e0be" | |
| }, | |
| "source": [ | |
| "'''\n", | |
| "Run it all! Specify sources, get a data table with species names, and return \n", | |
| " added columns with match information to the data table from each source using \n", | |
| " the above function we just defined.\n", | |
| "\n", | |
| "* Keep in mind which sources are domain-specific! Note that terrestrial species\n", | |
| " like Chamaea fasciata (a bird) are not known names in \n", | |
| " the World Register of Marine Species (WoRMS). \n", | |
| "'''\n", | |
| "\n", | |
| "sources = {'EOL':12,'WoRMS':9,'NCBI':4,'GBIF':11,'ITIS':3}\n", | |
| "\n", | |
| "df_orig = pd.read_csv('https://datadocs.bco-dmo.org/data/305/CC_Fishery_Adaptations/752795/1/data/animal_mobility.csv')\n", | |
| "\n", | |
| "#limiting for demo purposes\n", | |
| "df_orig = df_orig.head(100)\n", | |
| "\n", | |
| "print(df_orig)\n", | |
| "\n", | |
| "df = match_df(df_orig,'Species',sources)" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| " System Group Species BM HR Refs\n", | |
| "0 M B Sterna forsteri 149 58.000 (150)\n", | |
| "1 M B Ptychoramphus aleuticus 164 3008.000 (151|152)\n", | |
| "2 M B Brachyramphus marmoratus 220 127.000 (153)\n", | |
| "3 M B Calonectris diomedea 535 485776.000 (154)\n", | |
| "4 M B Alca torda 600 2201.000 (155)\n", | |
| ".. ... ... ... ... ... ...\n", | |
| "95 T B Habia rubica 33 0.049 (221)\n", | |
| "96 T B Habia fuscicauda 38 0.061 (221)\n", | |
| "97 T B Dasyornis brachypterus 42 0.100 (222);(223)\n", | |
| "98 T B Lanius ludovicianus 48 0.073 (221|224–227) \n", | |
| "99 T B Laniuis ludovicianus 48 0.076 (221)\n", | |
| "\n", | |
| "[100 rows x 6 columns]\n", | |
| "Matching names with GNRD source 12: EOL\n", | |
| "Matching names with GNRD source 9: WoRMS\n", | |
| "\t\t No match for: {'supplied_name_string': 'Chamaea fasciata', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Laniuis collurio', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Habia rubica', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Habia fuscicauda', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dasyornis brachypterus', 'is_known_name': False}\n", | |
| "Matching names with GNRD source 4: NCBI\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica magnolia', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica virens', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica pensylvanica', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica fusca', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica kirtlandi', 'is_known_name': False}\n", | |
| "Matching names with GNRD source 11: GBIF\n", | |
| "Matching names with GNRD source 3: ITIS\n", | |
| "done\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 839 | |
| }, | |
| "id": "JwXSKS9-iWyQ", | |
| "outputId": "d9186634-da4f-4976-c694-5f99dc42f443" | |
| }, | |
| "source": [ | |
| "df" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>System</th>\n", | |
| " <th>Group</th>\n", | |
| " <th>Species</th>\n", | |
| " <th>BM</th>\n", | |
| " <th>HR</th>\n", | |
| " <th>Refs</th>\n", | |
| " <th>EOL_data_source_id</th>\n", | |
| " <th>EOL_data_source_title</th>\n", | |
| " <th>EOL_gni_uuid</th>\n", | |
| " <th>EOL_name_string</th>\n", | |
| " <th>EOL_canonical_form</th>\n", | |
| " <th>EOL_classification_path</th>\n", | |
| " <th>EOL_classification_path_ranks</th>\n", | |
| " <th>EOL_classification_path_ids</th>\n", | |
| " <th>EOL_taxon_id</th>\n", | |
| " <th>EOL_local_id</th>\n", | |
| " <th>EOL_edit_distance</th>\n", | |
| " <th>EOL_imported_at</th>\n", | |
| " <th>EOL_match_type</th>\n", | |
| " <th>EOL_match_value</th>\n", | |
| " <th>EOL_prescore</th>\n", | |
| " <th>EOL_score</th>\n", | |
| " <th>EOL_is_known_name</th>\n", | |
| " <th>EOL_supplied_name_string</th>\n", | |
| " <th>WoRMS_data_source_id</th>\n", | |
| " <th>WoRMS_data_source_title</th>\n", | |
| " <th>WoRMS_gni_uuid</th>\n", | |
| " <th>WoRMS_name_string</th>\n", | |
| " <th>WoRMS_canonical_form</th>\n", | |
| " <th>WoRMS_classification_path</th>\n", | |
| " <th>WoRMS_classification_path_ranks</th>\n", | |
| " <th>WoRMS_classification_path_ids</th>\n", | |
| " <th>WoRMS_taxon_id</th>\n", | |
| " <th>WoRMS_edit_distance</th>\n", | |
| " <th>WoRMS_imported_at</th>\n", | |
| " <th>WoRMS_match_type</th>\n", | |
| " <th>WoRMS_match_value</th>\n", | |
| " <th>WoRMS_prescore</th>\n", | |
| " <th>WoRMS_score</th>\n", | |
| " <th>WoRMS_current_taxon_id</th>\n", | |
| " <th>...</th>\n", | |
| " <th>NCBI_is_known_name</th>\n", | |
| " <th>NCBI_supplied_name_string</th>\n", | |
| " <th>GBIF_data_source_id</th>\n", | |
| " <th>GBIF_data_source_title</th>\n", | |
| " <th>GBIF_gni_uuid</th>\n", | |
| " <th>GBIF_name_string</th>\n", | |
| " <th>GBIF_canonical_form</th>\n", | |
| " <th>GBIF_classification_path</th>\n", | |
| " <th>GBIF_classification_path_ranks</th>\n", | |
| " <th>GBIF_classification_path_ids</th>\n", | |
| " <th>GBIF_taxon_id</th>\n", | |
| " <th>GBIF_edit_distance</th>\n", | |
| " <th>GBIF_imported_at</th>\n", | |
| " <th>GBIF_match_type</th>\n", | |
| " <th>GBIF_match_value</th>\n", | |
| " <th>GBIF_prescore</th>\n", | |
| " <th>GBIF_score</th>\n", | |
| " <th>GBIF_current_taxon_id</th>\n", | |
| " <th>GBIF_current_name_string</th>\n", | |
| " <th>GBIF_is_known_name</th>\n", | |
| " <th>GBIF_supplied_name_string</th>\n", | |
| " <th>ITIS_data_source_id</th>\n", | |
| " <th>ITIS_data_source_title</th>\n", | |
| " <th>ITIS_gni_uuid</th>\n", | |
| " <th>ITIS_name_string</th>\n", | |
| " <th>ITIS_canonical_form</th>\n", | |
| " <th>ITIS_classification_path</th>\n", | |
| " <th>ITIS_classification_path_ranks</th>\n", | |
| " <th>ITIS_classification_path_ids</th>\n", | |
| " <th>ITIS_taxon_id</th>\n", | |
| " <th>ITIS_edit_distance</th>\n", | |
| " <th>ITIS_imported_at</th>\n", | |
| " <th>ITIS_match_type</th>\n", | |
| " <th>ITIS_match_value</th>\n", | |
| " <th>ITIS_prescore</th>\n", | |
| " <th>ITIS_score</th>\n", | |
| " <th>ITIS_current_taxon_id</th>\n", | |
| " <th>ITIS_current_name_string</th>\n", | |
| " <th>ITIS_is_known_name</th>\n", | |
| " <th>ITIS_supplied_name_string</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>149</td>\n", | |
| " <td>58.000</td>\n", | |
| " <td>(150)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>75cd7ab7-b950-5609-85e6-352d56155f2b</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509329</td>\n", | |
| " <td>45509329</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>540b124d-66e3-5a21-8c74-d70906cb1a5a</td>\n", | |
| " <td>Sterna forsteri Nuttall, 1834</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:159057</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:05:19Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>540b124d-66e3-5a21-8c74-d70906cb1a5a</td>\n", | |
| " <td>Sterna forsteri Nuttall, 1834</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Laridae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|9316|2481227|5229247</td>\n", | |
| " <td>5229247</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:19:59Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>540b124d-66e3-5a21-8c74-d70906cb1a5a</td>\n", | |
| " <td>Sterna forsteri Nuttall, 1834</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>176887</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>164</td>\n", | |
| " <td>3008.000</td>\n", | |
| " <td>(151|152)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>7884810e-fb20-5c52-a78f-c84ccaa8ad46</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509361</td>\n", | |
| " <td>45509361</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>449fb8f0-b255-5506-b7a9-f94fce8a0ff2</td>\n", | |
| " <td>Ptychoramphus aleuticus (Pallas, 1811)</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:344115</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:11:37Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>449fb8f0-b255-5506-b7a9-f94fce8a0ff2</td>\n", | |
| " <td>Ptychoramphus aleuticus (Pallas, 1811)</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Alcidae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|2985|2481301|2481302</td>\n", | |
| " <td>2481302</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T23:59:22Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>449fb8f0-b255-5506-b7a9-f94fce8a0ff2</td>\n", | |
| " <td>Ptychoramphus aleuticus (Pallas, 1811)</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>177013</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>2</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>220</td>\n", | |
| " <td>127.000</td>\n", | |
| " <td>(153)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>1a704327-c41c-5fa5-9a5a-4a745ca8c5a5</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509352</td>\n", | |
| " <td>45509352</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>5c6c9cc6-e3ea-5654-97bc-f98a0ff18455</td>\n", | |
| " <td>Brachyramphus marmoratus (Gmelin, 1789)</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:254308</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:08:53Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>5c6c9cc6-e3ea-5654-97bc-f98a0ff18455</td>\n", | |
| " <td>Brachyramphus marmoratus (Gmelin, 1789)</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Alcidae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|2985|2481326|5229281</td>\n", | |
| " <td>5229281</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T01:34:45Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>5c6c9cc6-e3ea-5654-97bc-f98a0ff18455</td>\n", | |
| " <td>Brachyramphus marmoratus (Gmelin, 1789)</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>176996</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>3</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>535</td>\n", | |
| " <td>485776.000</td>\n", | |
| " <td>(154)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>d1c5f3ee-b763-5bf4-be74-de78125d2a43</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>51900544</td>\n", | |
| " <td>51900544</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:22:56Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>2c4fe23c-30fb-5e01-9894-b4f72766bc8f</td>\n", | |
| " <td>Calonectris diomedea (Scopoli, 1769)</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:137194</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:04:04Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>2c4fe23c-30fb-5e01-9894-b4f72766bc8f</td>\n", | |
| " <td>Calonectris diomedea (Scopoli, 1769)</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Animalia|Chordata|Aves|Procellariiformes|Proce...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192755|9339|2481517|2481521</td>\n", | |
| " <td>2481521</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T23:59:23Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>2c4fe23c-30fb-5e01-9894-b4f72766bc8f</td>\n", | |
| " <td>Calonectris diomedea (Scopoli, 1769)</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>203446</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:49:58Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>4</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>600</td>\n", | |
| " <td>2201.000</td>\n", | |
| " <td>(155)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>5d7c4673-7f5b-5b74-ac0c-cfeb677ce2b1</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509345</td>\n", | |
| " <td>45509345</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>4ff6d04a-7e9a-5925-9ce3-3b6f11fa296a</td>\n", | |
| " <td>Alca torda Linnaeus, 1758</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:137128</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:04:03Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4ff6d04a-7e9a-5925-9ce3-3b6f11fa296a</td>\n", | |
| " <td>Alca torda Linnaeus, 1758</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Alcidae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|2985|2481308|8277073</td>\n", | |
| " <td>8277073</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T03:34:18Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4ff6d04a-7e9a-5925-9ce3-3b6f11fa296a</td>\n", | |
| " <td>Alca torda Linnaeus, 1758</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>176971</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>...</th>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>95</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>33</td>\n", | |
| " <td>0.049</td>\n", | |
| " <td>(221)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>734a7ff9-6ac2-54b4-a211-45481c1a084d</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>921778</td>\n", | |
| " <td>921778</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:16:44Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>No match found</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4b5708dc-817b-53b9-8721-e2e949ccbf9d</td>\n", | |
| " <td>Habia rubica (Vieillot, 1817)</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Cardinali...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9285|5230696|5230705</td>\n", | |
| " <td>5230705</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:20:25Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4b5708dc-817b-53b9-8721-e2e949ccbf9d</td>\n", | |
| " <td>Habia rubica (Vieillot, 1817)</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>560348</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:52:19Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>96</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>38</td>\n", | |
| " <td>0.061</td>\n", | |
| " <td>(221)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>d01ecfc5-69be-5797-a414-8831f8a0cc69</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>921776</td>\n", | |
| " <td>921776</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:16:44Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>No match found</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>f1dd20fe-6493-5129-a552-a423c50a1c66</td>\n", | |
| " <td>Habia fuscicauda (Cabanis, 1861)</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Cardinali...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9285|5230696|5230697</td>\n", | |
| " <td>5230697</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:20:25Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>f1dd20fe-6493-5129-a552-a423c50a1c66</td>\n", | |
| " <td>Habia fuscicauda (Cabanis, 1861)</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>560346</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:52:19Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>97</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>42</td>\n", | |
| " <td>0.100</td>\n", | |
| " <td>(222);(223)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>2b2e6e76-5c5d-5d86-ad3a-5c2b74613c30</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45518088</td>\n", | |
| " <td>45518088</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:12:38Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>No match found</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>46dc4c95-fff7-5463-89bd-8b19182f074f</td>\n", | |
| " <td>Dasyornis brachypterus (Latham, 1802)</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Dasyornit...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|5788774|5230412|5230413</td>\n", | |
| " <td>5230413</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:20:23Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>46dc4c95-fff7-5463-89bd-8b19182f074f</td>\n", | |
| " <td>Dasyornis brachypterus (Latham, 1802)</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>559685</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:52:18Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>98</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>48</td>\n", | |
| " <td>0.073</td>\n", | |
| " <td>(221|224–227)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>1332f6b2-0911-5802-b6d5-7a4aa2666dc1</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:16:33Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1484469</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:39:12Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Laniidae|...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9315|2483315|2492870</td>\n", | |
| " <td>2492870</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T00:02:08Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>178515</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:09Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>99</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>48</td>\n", | |
| " <td>0.076</td>\n", | |
| " <td>(221)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>1332f6b2-0911-5802-b6d5-7a4aa2666dc1</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>1</td>\n", | |
| " <td>2021-06-24T16:16:33Z</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1484469</td>\n", | |
| " <td>1.0</td>\n", | |
| " <td>2021-06-23T14:39:12Z</td>\n", | |
| " <td>3.0</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Laniidae|...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9315|2483315|2492870</td>\n", | |
| " <td>2492870</td>\n", | |
| " <td>1</td>\n", | |
| " <td>2021-06-24T00:02:08Z</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>178515</td>\n", | |
| " <td>1</td>\n", | |
| " <td>2021-06-23T03:50:09Z</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "<p>100 rows × 98 columns</p>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " System Group ... ITIS_is_known_name ITIS_supplied_name_string\n", | |
| "0 M B ... True Sterna forsteri\n", | |
| "1 M B ... True Ptychoramphus aleuticus\n", | |
| "2 M B ... True Brachyramphus marmoratus\n", | |
| "3 M B ... True Calonectris diomedea\n", | |
| "4 M B ... True Alca torda\n", | |
| ".. ... ... ... ... ...\n", | |
| "95 T B ... True Habia rubica\n", | |
| "96 T B ... True Habia fuscicauda\n", | |
| "97 T B ... True Dasyornis brachypterus\n", | |
| "98 T B ... True Lanius ludovicianus\n", | |
| "99 T B ... False Laniuis ludovicianus\n", | |
| "\n", | |
| "[100 rows x 98 columns]" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 89 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/" | |
| }, | |
| "id": "5n_36WvobjRN", | |
| "outputId": "280ab8da-06e2-4758-c8be-69508823094a" | |
| }, | |
| "source": [ | |
| "# Let's do another match after pulling data from BCO-DMO's ERDDAP endpoint\n", | |
| "\n", | |
| "url = \"https://erddap.bco-dmo.org/erddap/tabledap/bcodmo_dataset_752795.json\"\n", | |
| "\n", | |
| "response = requests.get(url)\n", | |
| "print(response.status_code)" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "200\n" | |
| ] | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 675 | |
| }, | |
| "id": "o6Bf13M6bsfW", | |
| "outputId": "74f80dc3-2391-4a15-9cb2-bc519846e274" | |
| }, | |
| "source": [ | |
| "j = response.json()\n", | |
| "\n", | |
| "# Let's get this in a data frame\n", | |
| "\n", | |
| "df = pd.DataFrame(data=j['table']['rows'][0:20],columns=j['table']['columnNames'])\n", | |
| "\n", | |
| "# Print the dataframe\n", | |
| "df" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>System</th>\n", | |
| " <th>Group</th>\n", | |
| " <th>Species</th>\n", | |
| " <th>BM</th>\n", | |
| " <th>HR</th>\n", | |
| " <th>Refs</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>149</td>\n", | |
| " <td>5.800000e+01</td>\n", | |
| " <td>(150)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>164</td>\n", | |
| " <td>3.008000e+03</td>\n", | |
| " <td>(151|152)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>2</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>220</td>\n", | |
| " <td>1.270000e+02</td>\n", | |
| " <td>(153)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>3</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>535</td>\n", | |
| " <td>4.857760e+05</td>\n", | |
| " <td>(154)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>4</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>600</td>\n", | |
| " <td>2.201000e+03</td>\n", | |
| " <td>(155)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>5</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Uria aalge</td>\n", | |
| " <td>907</td>\n", | |
| " <td>8.150000e+02</td>\n", | |
| " <td>(155|156)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>6</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Sula sula</td>\n", | |
| " <td>956</td>\n", | |
| " <td>5.454000e+03</td>\n", | |
| " <td>(157)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>7</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Melanitta nigra</td>\n", | |
| " <td>1052</td>\n", | |
| " <td>1.298000e+03</td>\n", | |
| " <td>(158)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>8</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Procellaria aequinoctialis</td>\n", | |
| " <td>1213</td>\n", | |
| " <td>6.830000e+05</td>\n", | |
| " <td>(159)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>9</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Procellaria conspicillata</td>\n", | |
| " <td>1278</td>\n", | |
| " <td>5.965460e+05</td>\n", | |
| " <td>(160)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>10</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Papasula abbotti</td>\n", | |
| " <td>1572</td>\n", | |
| " <td>1.085030e+05</td>\n", | |
| " <td>(161)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>11</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Somateria mollissima</td>\n", | |
| " <td>2067</td>\n", | |
| " <td>6.800000e+01</td>\n", | |
| " <td>(162)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>12</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Eudyptes filholi</td>\n", | |
| " <td>2330</td>\n", | |
| " <td>2.605360e+06</td>\n", | |
| " <td>(163)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>13</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Thalassarche chrysostoma</td>\n", | |
| " <td>3508</td>\n", | |
| " <td>6.400000e+05</td>\n", | |
| " <td>(164)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>14</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Thalassarche melanophrys</td>\n", | |
| " <td>3564</td>\n", | |
| " <td>4.440000e+05</td>\n", | |
| " <td>(164)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>15</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Pygoscelis antarctica</td>\n", | |
| " <td>3800</td>\n", | |
| " <td>3.270000e+02</td>\n", | |
| " <td>(165)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>16</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Gaviia immer</td>\n", | |
| " <td>5186</td>\n", | |
| " <td>5.470000e+02</td>\n", | |
| " <td>(166)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>17</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Pygoscelis papua</td>\n", | |
| " <td>5190</td>\n", | |
| " <td>1.260000e+02</td>\n", | |
| " <td>(165)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>18</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Eudyptes chrysolophus</td>\n", | |
| " <td>21700</td>\n", | |
| " <td>1.760000e+06</td>\n", | |
| " <td>(167)</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>19</th>\n", | |
| " <td>M</td>\n", | |
| " <td>F</td>\n", | |
| " <td>Ctenochaetus striatus</td>\n", | |
| " <td>57</td>\n", | |
| " <td>1.200000e-05</td>\n", | |
| " <td>(168);(169)</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " System Group Species BM HR Refs\n", | |
| "0 M B Sterna forsteri 149 5.800000e+01 (150)\n", | |
| "1 M B Ptychoramphus aleuticus 164 3.008000e+03 (151|152)\n", | |
| "2 M B Brachyramphus marmoratus 220 1.270000e+02 (153)\n", | |
| "3 M B Calonectris diomedea 535 4.857760e+05 (154)\n", | |
| "4 M B Alca torda 600 2.201000e+03 (155)\n", | |
| "5 M B Uria aalge 907 8.150000e+02 (155|156)\n", | |
| "6 M B Sula sula 956 5.454000e+03 (157)\n", | |
| "7 M B Melanitta nigra 1052 1.298000e+03 (158)\n", | |
| "8 M B Procellaria aequinoctialis 1213 6.830000e+05 (159)\n", | |
| "9 M B Procellaria conspicillata 1278 5.965460e+05 (160)\n", | |
| "10 M B Papasula abbotti 1572 1.085030e+05 (161)\n", | |
| "11 M B Somateria mollissima 2067 6.800000e+01 (162)\n", | |
| "12 M B Eudyptes filholi 2330 2.605360e+06 (163)\n", | |
| "13 M B Thalassarche chrysostoma 3508 6.400000e+05 (164)\n", | |
| "14 M B Thalassarche melanophrys 3564 4.440000e+05 (164)\n", | |
| "15 M B Pygoscelis antarctica 3800 3.270000e+02 (165)\n", | |
| "16 M B Gaviia immer 5186 5.470000e+02 (166)\n", | |
| "17 M B Pygoscelis papua 5190 1.260000e+02 (165)\n", | |
| "18 M B Eudyptes chrysolophus 21700 1.760000e+06 (167)\n", | |
| "19 M F Ctenochaetus striatus 57 1.200000e-05 (168);(169)" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 91 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "metadata": { | |
| "colab": { | |
| "base_uri": "https://localhost:8080/", | |
| "height": 1000 | |
| }, | |
| "id": "MdPW_TqKd08v", | |
| "outputId": "0695befd-454f-4420-ec79-6a0c8521c35c" | |
| }, | |
| "source": [ | |
| "# Add the match info to the data frame\n", | |
| "df_matches = match_df(df_orig,'Species',sources)\n", | |
| "df_matches\n" | |
| ], | |
| "execution_count": null, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "name": "stdout", | |
| "text": [ | |
| "Matching names with GNRD source 12: EOL\n", | |
| "Matching names with GNRD source 9: WoRMS\n", | |
| "\t\t No match for: {'supplied_name_string': 'Chamaea fasciata', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Laniuis collurio', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Habia rubica', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Habia fuscicauda', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dasyornis brachypterus', 'is_known_name': False}\n", | |
| "Matching names with GNRD source 4: NCBI\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica magnolia', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica virens', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica pensylvanica', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica fusca', 'is_known_name': False}\n", | |
| "\t\t No match for: {'supplied_name_string': 'Dendroica kirtlandi', 'is_known_name': False}\n", | |
| "Matching names with GNRD source 11: GBIF\n", | |
| "Matching names with GNRD source 3: ITIS\n", | |
| "done\n" | |
| ] | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "data": { | |
| "text/html": [ | |
| "<div>\n", | |
| "<style scoped>\n", | |
| " .dataframe tbody tr th:only-of-type {\n", | |
| " vertical-align: middle;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe tbody tr th {\n", | |
| " vertical-align: top;\n", | |
| " }\n", | |
| "\n", | |
| " .dataframe thead th {\n", | |
| " text-align: right;\n", | |
| " }\n", | |
| "</style>\n", | |
| "<table border=\"1\" class=\"dataframe\">\n", | |
| " <thead>\n", | |
| " <tr style=\"text-align: right;\">\n", | |
| " <th></th>\n", | |
| " <th>System</th>\n", | |
| " <th>Group</th>\n", | |
| " <th>Species</th>\n", | |
| " <th>BM</th>\n", | |
| " <th>HR</th>\n", | |
| " <th>Refs</th>\n", | |
| " <th>EOL_data_source_id</th>\n", | |
| " <th>EOL_data_source_title</th>\n", | |
| " <th>EOL_gni_uuid</th>\n", | |
| " <th>EOL_name_string</th>\n", | |
| " <th>EOL_canonical_form</th>\n", | |
| " <th>EOL_classification_path</th>\n", | |
| " <th>EOL_classification_path_ranks</th>\n", | |
| " <th>EOL_classification_path_ids</th>\n", | |
| " <th>EOL_taxon_id</th>\n", | |
| " <th>EOL_local_id</th>\n", | |
| " <th>EOL_edit_distance</th>\n", | |
| " <th>EOL_imported_at</th>\n", | |
| " <th>EOL_match_type</th>\n", | |
| " <th>EOL_match_value</th>\n", | |
| " <th>EOL_prescore</th>\n", | |
| " <th>EOL_score</th>\n", | |
| " <th>EOL_is_known_name</th>\n", | |
| " <th>EOL_supplied_name_string</th>\n", | |
| " <th>WoRMS_data_source_id</th>\n", | |
| " <th>WoRMS_data_source_title</th>\n", | |
| " <th>WoRMS_gni_uuid</th>\n", | |
| " <th>WoRMS_name_string</th>\n", | |
| " <th>WoRMS_canonical_form</th>\n", | |
| " <th>WoRMS_classification_path</th>\n", | |
| " <th>WoRMS_classification_path_ranks</th>\n", | |
| " <th>WoRMS_classification_path_ids</th>\n", | |
| " <th>WoRMS_taxon_id</th>\n", | |
| " <th>WoRMS_edit_distance</th>\n", | |
| " <th>WoRMS_imported_at</th>\n", | |
| " <th>WoRMS_match_type</th>\n", | |
| " <th>WoRMS_match_value</th>\n", | |
| " <th>WoRMS_prescore</th>\n", | |
| " <th>WoRMS_score</th>\n", | |
| " <th>WoRMS_current_taxon_id</th>\n", | |
| " <th>...</th>\n", | |
| " <th>NCBI_is_known_name</th>\n", | |
| " <th>NCBI_supplied_name_string</th>\n", | |
| " <th>GBIF_data_source_id</th>\n", | |
| " <th>GBIF_data_source_title</th>\n", | |
| " <th>GBIF_gni_uuid</th>\n", | |
| " <th>GBIF_name_string</th>\n", | |
| " <th>GBIF_canonical_form</th>\n", | |
| " <th>GBIF_classification_path</th>\n", | |
| " <th>GBIF_classification_path_ranks</th>\n", | |
| " <th>GBIF_classification_path_ids</th>\n", | |
| " <th>GBIF_taxon_id</th>\n", | |
| " <th>GBIF_edit_distance</th>\n", | |
| " <th>GBIF_imported_at</th>\n", | |
| " <th>GBIF_match_type</th>\n", | |
| " <th>GBIF_match_value</th>\n", | |
| " <th>GBIF_prescore</th>\n", | |
| " <th>GBIF_score</th>\n", | |
| " <th>GBIF_current_taxon_id</th>\n", | |
| " <th>GBIF_current_name_string</th>\n", | |
| " <th>GBIF_is_known_name</th>\n", | |
| " <th>GBIF_supplied_name_string</th>\n", | |
| " <th>ITIS_data_source_id</th>\n", | |
| " <th>ITIS_data_source_title</th>\n", | |
| " <th>ITIS_gni_uuid</th>\n", | |
| " <th>ITIS_name_string</th>\n", | |
| " <th>ITIS_canonical_form</th>\n", | |
| " <th>ITIS_classification_path</th>\n", | |
| " <th>ITIS_classification_path_ranks</th>\n", | |
| " <th>ITIS_classification_path_ids</th>\n", | |
| " <th>ITIS_taxon_id</th>\n", | |
| " <th>ITIS_edit_distance</th>\n", | |
| " <th>ITIS_imported_at</th>\n", | |
| " <th>ITIS_match_type</th>\n", | |
| " <th>ITIS_match_value</th>\n", | |
| " <th>ITIS_prescore</th>\n", | |
| " <th>ITIS_score</th>\n", | |
| " <th>ITIS_current_taxon_id</th>\n", | |
| " <th>ITIS_current_name_string</th>\n", | |
| " <th>ITIS_is_known_name</th>\n", | |
| " <th>ITIS_supplied_name_string</th>\n", | |
| " </tr>\n", | |
| " </thead>\n", | |
| " <tbody>\n", | |
| " <tr>\n", | |
| " <th>0</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>149</td>\n", | |
| " <td>58.000</td>\n", | |
| " <td>(150)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>75cd7ab7-b950-5609-85e6-352d56155f2b</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509329</td>\n", | |
| " <td>45509329</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>540b124d-66e3-5a21-8c74-d70906cb1a5a</td>\n", | |
| " <td>Sterna forsteri Nuttall, 1834</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:159057</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:05:19Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>540b124d-66e3-5a21-8c74-d70906cb1a5a</td>\n", | |
| " <td>Sterna forsteri Nuttall, 1834</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Laridae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|9316|2481227|5229247</td>\n", | |
| " <td>5229247</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:19:59Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>540b124d-66e3-5a21-8c74-d70906cb1a5a</td>\n", | |
| " <td>Sterna forsteri Nuttall, 1834</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>176887</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Sterna forsteri</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>1</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>164</td>\n", | |
| " <td>3008.000</td>\n", | |
| " <td>(151|152)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>7884810e-fb20-5c52-a78f-c84ccaa8ad46</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509361</td>\n", | |
| " <td>45509361</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>449fb8f0-b255-5506-b7a9-f94fce8a0ff2</td>\n", | |
| " <td>Ptychoramphus aleuticus (Pallas, 1811)</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:344115</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:11:37Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>449fb8f0-b255-5506-b7a9-f94fce8a0ff2</td>\n", | |
| " <td>Ptychoramphus aleuticus (Pallas, 1811)</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Alcidae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|2985|2481301|2481302</td>\n", | |
| " <td>2481302</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T23:59:22Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>449fb8f0-b255-5506-b7a9-f94fce8a0ff2</td>\n", | |
| " <td>Ptychoramphus aleuticus (Pallas, 1811)</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>177013</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Ptychoramphus aleuticus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>2</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>220</td>\n", | |
| " <td>127.000</td>\n", | |
| " <td>(153)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>1a704327-c41c-5fa5-9a5a-4a745ca8c5a5</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509352</td>\n", | |
| " <td>45509352</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>5c6c9cc6-e3ea-5654-97bc-f98a0ff18455</td>\n", | |
| " <td>Brachyramphus marmoratus (Gmelin, 1789)</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:254308</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:08:53Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>5c6c9cc6-e3ea-5654-97bc-f98a0ff18455</td>\n", | |
| " <td>Brachyramphus marmoratus (Gmelin, 1789)</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Alcidae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|2985|2481326|5229281</td>\n", | |
| " <td>5229281</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T01:34:45Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>5c6c9cc6-e3ea-5654-97bc-f98a0ff18455</td>\n", | |
| " <td>Brachyramphus marmoratus (Gmelin, 1789)</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>176996</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Brachyramphus marmoratus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>3</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>535</td>\n", | |
| " <td>485776.000</td>\n", | |
| " <td>(154)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>d1c5f3ee-b763-5bf4-be74-de78125d2a43</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>51900544</td>\n", | |
| " <td>51900544</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:22:56Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>2c4fe23c-30fb-5e01-9894-b4f72766bc8f</td>\n", | |
| " <td>Calonectris diomedea (Scopoli, 1769)</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:137194</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:04:04Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>2c4fe23c-30fb-5e01-9894-b4f72766bc8f</td>\n", | |
| " <td>Calonectris diomedea (Scopoli, 1769)</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Animalia|Chordata|Aves|Procellariiformes|Proce...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192755|9339|2481517|2481521</td>\n", | |
| " <td>2481521</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T23:59:23Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>2c4fe23c-30fb-5e01-9894-b4f72766bc8f</td>\n", | |
| " <td>Calonectris diomedea (Scopoli, 1769)</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>203446</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:49:58Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Calonectris diomedea</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>4</th>\n", | |
| " <td>M</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>600</td>\n", | |
| " <td>2201.000</td>\n", | |
| " <td>(155)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>5d7c4673-7f5b-5b74-ac0c-cfeb677ce2b1</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45509345</td>\n", | |
| " <td>45509345</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T17:14:03Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>4ff6d04a-7e9a-5925-9ce3-3b6f11fa296a</td>\n", | |
| " <td>Alca torda Linnaeus, 1758</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:137128</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:04:03Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4ff6d04a-7e9a-5925-9ce3-3b6f11fa296a</td>\n", | |
| " <td>Alca torda Linnaeus, 1758</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Animalia|Chordata|Aves|Charadriiformes|Alcidae...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|7192402|2985|2481308|8277073</td>\n", | |
| " <td>8277073</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T03:34:18Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4ff6d04a-7e9a-5925-9ce3-3b6f11fa296a</td>\n", | |
| " <td>Alca torda Linnaeus, 1758</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>176971</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:03Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Alca torda</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>...</th>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " <td>...</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>95</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>33</td>\n", | |
| " <td>0.049</td>\n", | |
| " <td>(221)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>734a7ff9-6ac2-54b4-a211-45481c1a084d</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>921778</td>\n", | |
| " <td>921778</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:16:44Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>No match found</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4b5708dc-817b-53b9-8721-e2e949ccbf9d</td>\n", | |
| " <td>Habia rubica (Vieillot, 1817)</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Cardinali...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9285|5230696|5230705</td>\n", | |
| " <td>5230705</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:20:25Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4b5708dc-817b-53b9-8721-e2e949ccbf9d</td>\n", | |
| " <td>Habia rubica (Vieillot, 1817)</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>560348</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:52:19Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia rubica</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>96</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>38</td>\n", | |
| " <td>0.061</td>\n", | |
| " <td>(221)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>d01ecfc5-69be-5797-a414-8831f8a0cc69</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>921776</td>\n", | |
| " <td>921776</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:16:44Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>No match found</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>f1dd20fe-6493-5129-a552-a423c50a1c66</td>\n", | |
| " <td>Habia fuscicauda (Cabanis, 1861)</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Cardinali...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9285|5230696|5230697</td>\n", | |
| " <td>5230697</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:20:25Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>f1dd20fe-6493-5129-a552-a423c50a1c66</td>\n", | |
| " <td>Habia fuscicauda (Cabanis, 1861)</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>560346</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:52:19Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Habia fuscicauda</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>97</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>42</td>\n", | |
| " <td>0.100</td>\n", | |
| " <td>(222);(223)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>2b2e6e76-5c5d-5d86-ad3a-5c2b74613c30</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45518088</td>\n", | |
| " <td>45518088</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:12:38Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>No match found</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>46dc4c95-fff7-5463-89bd-8b19182f074f</td>\n", | |
| " <td>Dasyornis brachypterus (Latham, 1802)</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Dasyornit...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|5788774|5230412|5230413</td>\n", | |
| " <td>5230413</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T02:20:23Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>46dc4c95-fff7-5463-89bd-8b19182f074f</td>\n", | |
| " <td>Dasyornis brachypterus (Latham, 1802)</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>559685</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:52:18Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Dasyornis brachypterus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>98</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>48</td>\n", | |
| " <td>0.073</td>\n", | |
| " <td>(221|224–227)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>1332f6b2-0911-5802-b6d5-7a4aa2666dc1</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T16:16:33Z</td>\n", | |
| " <td>1</td>\n", | |
| " <td>Exact string match</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1484469</td>\n", | |
| " <td>0.0</td>\n", | |
| " <td>2021-06-23T14:39:12Z</td>\n", | |
| " <td>2.0</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Laniidae|...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9315|2483315|2492870</td>\n", | |
| " <td>2492870</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-24T00:02:08Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>178515</td>\n", | |
| " <td>0</td>\n", | |
| " <td>2021-06-23T03:50:09Z</td>\n", | |
| " <td>2</td>\n", | |
| " <td>Exact match by canonical form</td>\n", | |
| " <td>3|0|0</td>\n", | |
| " <td>0.988</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>True</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " </tr>\n", | |
| " <tr>\n", | |
| " <th>99</th>\n", | |
| " <td>T</td>\n", | |
| " <td>B</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>48</td>\n", | |
| " <td>0.076</td>\n", | |
| " <td>(221)</td>\n", | |
| " <td>12</td>\n", | |
| " <td>Encyclopedia of Life</td>\n", | |
| " <td>1332f6b2-0911-5802-b6d5-7a4aa2666dc1</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td></td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>45510944</td>\n", | |
| " <td>1</td>\n", | |
| " <td>2021-06-24T16:16:33Z</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>9.0</td>\n", | |
| " <td>World Register of Marine Species</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Biota|Animalia|Chordata|Vertebrata|Gnathostoma...</td>\n", | |
| " <td>|Kingdom|Phylum|Subphylum|Infraphylum|Supercla...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1|urn:lsid:...</td>\n", | |
| " <td>urn:lsid:marinespecies.org:taxname:1484469</td>\n", | |
| " <td>1.0</td>\n", | |
| " <td>2021-06-23T14:39:12Z</td>\n", | |
| " <td>3.0</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>...</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>11</td>\n", | |
| " <td>GBIF Backbone Taxonomy</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Chordata|Aves|Passeriformes|Laniidae|...</td>\n", | |
| " <td>kingdom|phylum|class|order|family|genus|species</td>\n", | |
| " <td>1|44|212|729|9315|2483315|2492870</td>\n", | |
| " <td>2492870</td>\n", | |
| " <td>1</td>\n", | |
| " <td>2021-06-24T00:02:08Z</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Integrated Taxonomic Information SystemITIS</td>\n", | |
| " <td>4aa2abb8-7617-5996-bed3-ca66116ba2d4</td>\n", | |
| " <td>Lanius ludovicianus Linnaeus, 1766</td>\n", | |
| " <td>Lanius ludovicianus</td>\n", | |
| " <td>Animalia|Bilateria|Deuterostomia|Chordata|Vert...</td>\n", | |
| " <td>Kingdom|Subkingdom|Infrakingdom|Phylum|Subphyl...</td>\n", | |
| " <td>202423|914154|914156|158852|331030|914179|9141...</td>\n", | |
| " <td>178515</td>\n", | |
| " <td>1</td>\n", | |
| " <td>2021-06-23T03:50:09Z</td>\n", | |
| " <td>3</td>\n", | |
| " <td>Fuzzy match by canonical form</td>\n", | |
| " <td>1|0|0</td>\n", | |
| " <td>0.750</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>NaN</td>\n", | |
| " <td>False</td>\n", | |
| " <td>Laniuis ludovicianus</td>\n", | |
| " </tr>\n", | |
| " </tbody>\n", | |
| "</table>\n", | |
| "<p>100 rows × 98 columns</p>\n", | |
| "</div>" | |
| ], | |
| "text/plain": [ | |
| " System Group ... ITIS_is_known_name ITIS_supplied_name_string\n", | |
| "0 M B ... True Sterna forsteri\n", | |
| "1 M B ... True Ptychoramphus aleuticus\n", | |
| "2 M B ... True Brachyramphus marmoratus\n", | |
| "3 M B ... True Calonectris diomedea\n", | |
| "4 M B ... True Alca torda\n", | |
| ".. ... ... ... ... ...\n", | |
| "95 T B ... True Habia rubica\n", | |
| "96 T B ... True Habia fuscicauda\n", | |
| "97 T B ... True Dasyornis brachypterus\n", | |
| "98 T B ... True Lanius ludovicianus\n", | |
| "99 T B ... False Laniuis ludovicianus\n", | |
| "\n", | |
| "[100 rows x 98 columns]" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "execution_count": 92 | |
| } | |
| ] | |
| }, | |
| { | |
| "cell_type": "markdown", | |
| "metadata": { | |
| "id": "vwfGe3d5OPU4" | |
| }, | |
| "source": [ | |
| "# Looking at \"taxon_id\" variation\n", | |
| "\n", | |
| "Keep in mind that type of id returned in \"taxon_id\" vary amongst the returned results from different sources. Many are specific to that source and not globally unique. \n", | |
| "\n", | |
| "For some sources the taxon_id is a globally unique identifier, [Life Science identifier (LSID](http://www.lsid.info/)), but for others it is an identifier specific just to that source. \n", | |
| "\n", | |
| "For example, the taxon_id in the results from WoRMS \"WoRMS_taxon_id\" is the global LSID (e.g. `urn:lsid:marinespecies.org:taxname:159057`). \n", | |
| "\n", | |
| "In the ITIS results \"ITIS_taxon_id\" is the TSN identifier (e.g. `176887`) which is not globaly unique on its own. It would need be be prepended with \"urn:lsid:itis.gov:itis_tsn:\" to become an LSID.\n", | |
| "\n", | |
| "---\n", | |
| "\n", | |
| "> If you use the [DarwinCore](https://dwc.tdwg.org/) standard, the LSID is what you would include in the [scientificNameID](https://dwc.tdwg.org/terms/#dwc:scientificNameID).\" \n", | |
| "> * e.g. WoRMS LSID `urn:lsid:marinespecies.org:taxname:159057`\n", | |
| "\n" | |
| ] | |
| } | |
| ] | |
| } |
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