{ "cells": [ { "cell_type": "markdown", "metadata": { "id": "7gJOUxL2Bqhk" }, "source": [ "# Overview\n", "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/kozo2/pywikipathways/blob/main/docs/pywikipathways_Overview.ipynb)\n", "\n", "**by Kozo Nishida and Alexander Pico**\n", "\n", "**pywikipathways 0.0.2**\n", "\n", "*WikiPathways* is a well-known repository for biological pathways that provides unique tools to the research community for content creation, editing and utilization [1].\n", "\n", "**Python** is a powerful programming language and environment for statistical and exploratory data analysis.\n", "\n", "*pywikipathways* leverages the WikiPathways API to communicate between **Python** and WikiPathways, allowing any pathway to be queried, interrogated and downloaded in both data and image formats. Queries are typically performed based on “Xrefs”, standardized identifiers for genes, proteins and metabolites. Once you can identified a pathway, you can use the WPID (WikiPathways identifier) to make additional queries.\n", "\n", "## Prerequisites\n", "All you need is this **pywikipathways** package!\n", "To install pywikipathways, run" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "!pip install pywikipathways" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "id": "Qd_9CKFubDWI" }, "outputs": [], "source": [ "import pywikipathways as pwpw" ] }, { "cell_type": "markdown", "metadata": { "id": "ldQX1B-YC8E8" }, "source": [ "## Getting started\n", "Lets first get oriented with what WikiPathways contains. For example, here’s how you check to see which species are currently supported by WikiPathways:" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "id": "CCrccZGTbJEr" }, "outputs": [ { "data": { "text/plain": [ "['Unspecified',\n", " 'Acetobacterium woodii',\n", " 'Anopheles gambiae',\n", " 'Arabidopsis thaliana',\n", " 'Bacillus subtilis',\n", " 'Beta vulgaris',\n", " 'Bos taurus',\n", " 'Caenorhabditis elegans',\n", " 'Canis familiaris',\n", " 'Clostridium thermocellum',\n", " 'Danio rerio',\n", " 'Daphnia magna',\n", " 'Daphnia pulex',\n", " 'Drosophila melanogaster',\n", " 'Escherichia coli',\n", " 'Equus caballus',\n", " 'Gallus gallus',\n", " 'Glycine max',\n", " 'Gibberella zeae',\n", " 'Homo sapiens',\n", " 'Hordeum vulgare',\n", " 'Mus musculus',\n", " 'Mycobacterium tuberculosis',\n", " 'Oryza sativa',\n", " 'Pan troglodytes',\n", " 'Populus trichocarpa',\n", " 'Rattus norvegicus',\n", " 'Saccharomyces cerevisiae',\n", " 'Solanum lycopersicum',\n", " 'Sus scrofa',\n", " 'Vitis vinifera',\n", " 'Xenopus tropicalis',\n", " 'Zea mays',\n", " 'Plasmodium falciparum',\n", " 'Brassica napus']" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "pwpw.list_organisms()" ] }, { "cell_type": "markdown", "metadata": { "id": "n9cznBF5DGil" }, "source": [ "You should see 30 or more species listed. This list is useful for subsequent queries that take an *organism* argument, to avoid misspelling.\n", "\n", "Next, let’s see how many pathways are available for Human:" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "id": "5vVJAMrCDMs4" }, "outputs": [], "source": [ "hs_pathways = pwpw.list_pathways('Homo sapiens')" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "id": "KZb5zLfHDTuA" }, "outputs": [ { "data": { "text/html": [ "
\n", " | id | \n", "url | \n", "name | \n", "species | \n", "revision | \n", "
---|---|---|---|---|---|
0 | \n", "WP100 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Glutathione metabolism | \n", "Homo sapiens | \n", "107114 | \n", "
1 | \n", "WP106 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Alanine and aspartate metabolism | \n", "Homo sapiens | \n", "114258 | \n", "
2 | \n", "WP107 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Translation factors | \n", "Homo sapiens | \n", "117851 | \n", "
3 | \n", "WP111 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Electron transport chain: OXPHOS system in mit... | \n", "Homo sapiens | \n", "117097 | \n", "
4 | \n", "WP117 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "GPCRs, other | \n", "Homo sapiens | \n", "117743 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
1327 | \n", "WP734 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Serotonin receptor 4/6/7 and NR3C signaling | \n", "Homo sapiens | \n", "117826 | \n", "
1328 | \n", "WP75 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Toll-like receptor signaling pathway | \n", "Homo sapiens | \n", "119233 | \n", "
1329 | \n", "WP78 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "TCA cycle (aka Krebs or citric acid cycle) | \n", "Homo sapiens | \n", "119082 | \n", "
1330 | \n", "WP80 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Nucleotide GPCRs | \n", "Homo sapiens | \n", "111167 | \n", "
1331 | \n", "WP98 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Prostaglandin synthesis and regulation | \n", "Homo sapiens | \n", "117172 | \n", "
1332 rows × 5 columns
\n", "\n", " | score | \n", "id | \n", "url | \n", "name | \n", "species | \n", "revision | \n", "
---|---|---|---|---|---|---|
0 | \n", "0.38982576 | \n", "WP5071 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "PPAR-gamma pathway | \n", "Homo sapiens | \n", "116510 | \n", "
1 | \n", "0.38982576 | \n", "WP5073 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "PPAR Beta/Delta pathway | \n", "Homo sapiens | \n", "115726 | \n", "
2 | \n", "0.38982576 | \n", "WP5115 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Network map of SARS-CoV-2 signaling pathway | \n", "Homo sapiens | \n", "119638 | \n", "
3 | \n", "0.27564844 | \n", "WP176 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Folate metabolism | \n", "Homo sapiens | \n", "118404 | \n", "
4 | \n", "0.27564844 | \n", "WP2328 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Allograft Rejection | \n", "Homo sapiens | \n", "106557 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
80 | \n", "0.27564844 | \n", "WP5088 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Prostaglandin signaling | \n", "Homo sapiens | \n", "119639 | \n", "
81 | \n", "0.27564844 | \n", "WP5093 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Opioid receptor pathway annotation | \n", "Homo sapiens | \n", "119684 | \n", "
82 | \n", "0.27564844 | \n", "WP5094 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Orexin receptor pathway | \n", "Homo sapiens | \n", "119637 | \n", "
83 | \n", "0.27564844 | \n", "WP5098 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "T-cell activation SARS-CoV-2 | \n", "Homo sapiens | \n", "119538 | \n", "
84 | \n", "0.27564844 | \n", "WP2513 | \n", "https://www.wikipathways.org/index.php/Pathway... | \n", "Nanoparticle triggered regulated necrosis | \n", "Homo sapiens | \n", "119820 | \n", "
85 rows × 6 columns
\n", "