### Get Help for `list_pathways` Function Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Use the `help()` function to understand the parameters, return types, and examples for the `list_pathways` function. ```python help(pwpw.list_pathways) ``` -------------------------------- ### Install pywikipathways Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Installs the pywikipathways package using pip. This is a prerequisite for using the library. ```bash !pip install pywikipathways ``` -------------------------------- ### Install pywikipathways and bridgedbpy Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-bridgedbpy.ipynb.txt Installs the necessary Python packages for interacting with WikiPathways and BridgeDb. Run this command in your terminal or notebook. ```bash !pip install pywikipathways bridgedbpy ``` -------------------------------- ### Load Pathways with Pywikipathways Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Demonstrates how to load pathways using the Pywikipathways library. Ensure the library is installed and pathways are accessible. ```python from pywikipathways import WP pathways = WP.get_pathways_by_organism("Homo sapiens") print(f"Loaded {len(pathways)} pathways for Homo sapiens") ``` -------------------------------- ### Install pywikipathways and bridgedbpy Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Install the necessary Python packages for interacting with WikiPathways and BridgeDb. This command should be run in your terminal or a compatible environment. ```bash !pip install pywikipathways bridgedbpy ``` -------------------------------- ### Install WikiPathways App Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Installs the WikiPathways app within Cytoscape, necessary for accessing the WikiPathways database directly from Cytoscape. This command is for Cytoscape 3.7.0 and above. ```bash !cyclient install wikipathways ``` -------------------------------- ### Install WikiPathways App in Cytoscape Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Installs the WikiPathways application within Cytoscape. Requires Cytoscape version 3.7.0 or higher. ```python p4c.install_app('WikiPathways') #only available in Cytoscape 3.7.0 and above ``` -------------------------------- ### Initialize py4cytoscape in Remote Environment Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Sets up py4cytoscape in a remote notebook environment like Google Colab. It fetches initialization code and starts the browser client. ```python _PY4CYTOSCAPE = 'git+https://github.com/cytoscape/py4cytoscape@0.0.10' import requests exec(requests.get("https://raw.githubusercontent.com/cytoscape/jupyter-bridge/master/client/p4c_init.py").text) IPython.display.Javascript(_PY4CYTOSCAPE_BROWSER_CLIENT_JS) # Start browser client ``` -------------------------------- ### Get Help for find_pathway_ids_by_xref Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Displays the help documentation for the `find_pathway_ids_by_xref` function. This is useful for understanding the function's parameters, return values, and usage. ```python help(pwpw.find_pathway_ids_by_xref) ``` -------------------------------- ### Get Help for find_pathway_names_by_xref Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Displays the help documentation for the `find_pathway_names_by_xref` function. This is useful for understanding the function's parameters, return values, and usage. ```python help(pwpw.find_pathway_names_by_xref) ``` -------------------------------- ### Install WikiPathways App in Cytoscape Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Installs the WikiPathways app within Cytoscape using py4cytoscape. This function is available for Cytoscape versions 3.7.0 and above. ```python p4c.install_app('WikiPathways') #only available in Cytoscape 3.7.0 and above ``` -------------------------------- ### Get Full System Name from Code Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Useful for identifying the full name of an identifier system when you only have its short system code, for example, from a pywikipathways return value. ```python brdgdbp.get_full_name('Ce') ``` -------------------------------- ### Get Pathway Information with PyWikiPathways Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Retrieve general information about a pathway using its WPID. This includes its name, species, and revision number. ```python pwpw.get_pathway_info('WP554') ``` -------------------------------- ### Get Pathway Details by ID Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Demonstrates fetching a specific pathway using its unique ID from WikiPathways. This is useful when you know the exact pathway you need. ```python from pywikipathways import WP # Example: Get the 'Metabolic pathways' pathway for Homo sapiens (ID: WP100) pathway_id = "WP100" homo_sapiens = "Homo sapiens" pathway = WP.get_pathway(pathway_id, organism=homo_sapiens) if pathway: print(f"Successfully retrieved pathway: {pathway.name}") else: print(f"Could not retrieve pathway with ID {pathway_id} for {homo_sapiens}.") ``` -------------------------------- ### Get Pathway Xrefs as Chemspider IDs Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Retrieve cross-references for a pathway WPID, mapped to Chemspider IDs for small molecules. Use the system code 'Cs'. ```python pwpw.get_xref_list('WP554', 'Cs') ``` -------------------------------- ### Get Network Data Columns Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Retrieves specified columns ('name', 'degree.layout', 'COMMON') from the current network data in Cytoscape. ```python net_data = p4c.get_table_columns(columns=['name','degree.layout','COMMON']) ``` -------------------------------- ### List Supported Organisms with PyWikiPathways Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Use `list_organisms()` to get a list of all species supported by WikiPathways. This is useful for ensuring correct organism names for subsequent queries. ```python pwpw.list_organisms() ``` -------------------------------- ### Get Pathway Xrefs as Ensembl IDs Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Retrieve cross-references for a pathway WPID, mapped to Ensembl IDs. Use the system code 'En' for Ensembl. ```python pwpw.get_xref_list('WP554', 'En') ``` -------------------------------- ### Get Pathway Xrefs as ChEBI IDs Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Obtain cross-references for a pathway WPID, mapped to ChEBI IDs for metabolites and small molecules. The system code 'Ce' is required. ```python pwpw.get_xref_list('WP554', 'Ce') ``` -------------------------------- ### Get Pathway Xrefs as HMDB IDs Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Fetch cross-references for a pathway WPID, specifically for metabolites and small molecules identified by HMDB IDs. Use the system code 'Ch'. ```python pwpw.get_xref_list('WP554', 'Ch') ``` -------------------------------- ### Get System Code for Ensembl with BridgeDbPy Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-bridgedbpy.ipynb.txt Fetches the system code for the 'Ensembl' identifier system. This code is used by BridgeDb to reference Ensembl identifiers. ```python brdgdbp.get_system_code("Ensembl") ``` -------------------------------- ### Get Pathway Information by WPID Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Fetches detailed information about a specific pathway using its WikiPathways ID (WPID). This is useful for collecting pathway metadata when the WPID is already known. ```python pwpw.get_pathway('WP554') ``` -------------------------------- ### Initialize py4cytoscape in Remote Environment Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Sets up py4cytoscape for use in remote notebook environments like Google Colab. Requires Cytoscape to be running separately. ```python _PY4CYTOSCAPE = 'git+https://github.com/cytoscape/py4cytoscape@0.0.10' import requests exec(requests.get("https://raw.githubusercontent.com/cytoscape/jupyter-bridge/master/client/p4c_init.py").text) IPython.display.Javascript(_PY4CYTOSCAPE_BROWSER_CLIENT_JS) # Start browser client ``` -------------------------------- ### Help on listing pathway URLs with PyWikiPathways Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Displays the help documentation for the `list_pathway_urls` function, outlining how to retrieve URLs for pathways. ```python help(pwpw.list_pathway_urls) ``` -------------------------------- ### Help on listing pathway names with PyWikiPathways Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Displays the help documentation for the `list_pathway_names` function, including its arguments and return values for retrieving pathway names. ```python help(pwpw.list_pathway_names) ``` -------------------------------- ### Initialize Py4cytoscape and Load Pathway Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Initializes the Py4cytoscape connection and loads the converted pathway data. This sets up the environment for visualization. ```python from py4cytoscape import py4cytoscape # Initialize py4cytoscape cy = py4cytoscape() # Load the pathway into Cytoscape cy.pathways.load_pathway(pw_pathway) ``` -------------------------------- ### Import pywikipathways Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Imports the pywikipathways library, aliasing it as pwpw for convenience in subsequent code. ```python import pywikipathways as pwpw ``` -------------------------------- ### Visualize Pathway in Cytoscape Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Illustrates how to visualize a pathway within Cytoscape using Py4cytoscape. This involves connecting to a running Cytoscape instance and loading the graph. ```python from py4cytoscape import cyrest # Connect to Cytoscape (ensure Cytoscape is running) cyrest.set_base_url('http://localhost:1234/v1') # Load the converted graph into Cytoscape if 'graph' in locals(): network_id = cyrest.network.create_network_from_json(graph) print(f"Pathway loaded into Cytoscape with network ID: {network_id}") # Apply a layout layout_task = get_cytoscape_layout('cose') cyrest.layout.apply_layout(network_id, layout_task) print("Applied 'cose' layout.") else: print("Graph not generated. Cannot visualize.") ``` -------------------------------- ### Import py4cytoscape Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Imports the py4cytoscape library, aliasing it as p4c for convenience in subsequent code. ```python import py4cytoscape as p4c ``` -------------------------------- ### Download Pathway Archive Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Downloads a ZIP archive of pathway files. By default, it downloads the latest GPML collection. Specify organism and format for specific downloads. ```python pwpw.download_pathway_archive() ``` -------------------------------- ### Get Organism Code with BridgeDbPy Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-bridgedbpy.ipynb.txt Retrieves the system code for a given organism name using BridgeDbPy. This is useful for specifying the biological context in subsequent queries. ```python brdgdbp.get_organism_code(org_names[14]) ``` -------------------------------- ### Search for Pathways Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Shows how to search for pathways based on keywords using Pywikipathways. This is helpful for discovering relevant pathways when the exact ID is unknown. ```python from pywikipathways import WP # Search for pathways related to 'diabetes' in 'Homo sapiens' search_term = "diabetes" organism = "Homo sapiens" search_results = WP.search_pathways(search_term, organism=organism) print(f"Found {len(search_results)} pathways matching '{search_term}' for {organism}:") for result in search_results: print(f"- {result.name} (ID: {result.id})") ``` -------------------------------- ### Download Pathway Archive for Specific Organism and Format Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Downloads a pathway archive for a specified organism and file format (e.g., GMT). The function returns the name of the downloaded file. ```python pwpw.download_pathway_archive(organism="Mus musculus", format="gmt") ``` -------------------------------- ### Get Shape of Pathway DataFrame Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html After retrieving pathways for an organism, you can use the `.shape` attribute on the resulting pandas DataFrame to quickly determine the number of pathways and columns. ```python hs_pathways.shape ``` -------------------------------- ### Load Pathway Data with Pywikipathways Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Loads pathway data from a specified source. Ensure the pathway ID is correct for successful loading. ```python from pywikipathways.api import get_pathway # Load a pathway by its ID pw = get_pathway('WP2870') ``` -------------------------------- ### List Pathway URLs for a Species Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Retrieve a list of pathway URLs for a specific organism. Requires the organism name as input. ```python help(pwpw.list_pathway_urls) ``` ```python list_pathway_urls('Mus musculus') ``` -------------------------------- ### Import pywikipathways Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Import the pywikipathways package into your Python script or notebook. This makes the package's functions available for use. ```python import pywikipathways as pwpw ``` -------------------------------- ### Get Ensembl Gene IDs from Pathway Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Retrieve a list of Ensembl gene identifiers associated with a given pathway ID. Uses bridgedbpy to specify the target system code. ```python pwpw.get_xref_list('WP554', brdgdbp.get_system_code('Ensembl')) ``` -------------------------------- ### Download Pathway Archive with Specific Date Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Downloads a pathway archive for a specific date, organism, and format. This ensures reproducibility by accessing a historical data release. ```python pwpw.download_pathway_archive(date="20171010", organism="Mus musculus", format="gmt") ``` -------------------------------- ### Get ChEBI Metabolite IDs from Pathway Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Retrieve a list of ChEBI metabolite identifiers associated with a given pathway ID. Uses bridgedbpy to specify the target system code. ```python pwpw.get_xref_list('WP554', brdgdbp.get_system_code('ChEBI')) ``` -------------------------------- ### Get System Code for Ensembl Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Retrieve the system code for the 'Ensembl' identifier system using bridgedbpy. This code is used to reference Ensembl identifiers within the BridgeDb framework. ```python brdgdbp.get_system_code("Ensembl") ``` -------------------------------- ### Display Cytoscape Image Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Renders the current Cytoscape visualization within a notebook environment. This command is used to display the imported pathway. ```python p4c.notebook_show_image() ``` -------------------------------- ### List Pathway Names for a Species Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Retrieve a list of pathway names for a specific organism. Requires the organism name as input. ```python help(pwpw.list_pathway_names) ``` ```python list_pathway_names('Mus musculus') ``` -------------------------------- ### Get Pathway Xrefs as Entrez Genes Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Extract all cross-references for a given pathway WPID, specifically mapped to Entrez Gene IDs. Ensure the correct system code 'L' is used. ```python pwpw.get_xref_list('WP554','L') ``` -------------------------------- ### Get System Code for Entrez Gene with BridgeDbPy Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-bridgedbpy.ipynb.txt Retrieves the system code for the 'Entrez Gene' identifier system. Note that this code is 'L' due to historical naming ('Locus Link'). ```python brdgdbp.get_system_code("Entrez Gene") ``` -------------------------------- ### List Supported Organisms with pywikipathways Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Retrieve a list of all supported organism names from WikiPathways. This list is useful for ensuring correct organism names are used in subsequent queries. ```python org_names = pwpw.list_organisms() ``` -------------------------------- ### Display Pathway Information DataFrame Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html When `list_pathways()` is called without arguments, it returns a DataFrame of all pathways. Displaying the DataFrame shows its structure and content. ```python hs_pathways ``` -------------------------------- ### Find Pathway IDs by HGNC Symbol Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Use this to find all pathway IDs that contain a specific gene, identified by its HGNC symbol. Requires bridgedbpy to get the system code for HGNC. ```python tnf_pathways = pwpw.find_pathway_ids_by_xref('TNF', brdgdbp.get_system_code('HGNC')) tnf_pathways ``` -------------------------------- ### Preview Pathway GPML Data Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Displays the first 1000 characters of the retrieved GPML data for a pathway. Useful for a quick inspection of the XML structure. ```python gpml[:1000] ``` -------------------------------- ### Get Organism Code with bridgedbpy Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Convert a full organism name to its corresponding short code used by BridgeDb and WikiPathways. This is useful when functions require the organism code instead of the full name. ```python brdgdbp.get_organism_code(org_names[14]) ``` -------------------------------- ### Get System Code for Entrez Gene Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Retrieve the system code for the 'Entrez Gene' identifier system using bridgedbpy. Note that 'Entrez Gene' maps to the code 'L' due to historical naming ('Locus Link'). ```python brdgdbp.get_system_code("Entrez Gene") ``` -------------------------------- ### Import pywikipathways and bridgedbpy Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Import the pywikipathways and bridgedbpy libraries into your Python script. These imports are necessary to use the functions provided by these packages. ```python import pywikipathways as pwpw import bridgedbpy as brdgdbp ``` -------------------------------- ### Open Cytoscape Session Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Opens a Cytoscape session. This action will overwrite the current session. ```python p4c.open_session() ``` -------------------------------- ### Display Organism List Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-bridgedbpy.html Prints the list of organism names obtained from pywikipathways.list_organisms(). This helps in verifying the available species. ```python org_names ``` -------------------------------- ### Import py4cytoscape Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Imports the py4cytoscape library for use in Python scripts. ```python import py4cytoscape as p4c ``` -------------------------------- ### Find Pathways by Text using Pywikipathways Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Searches for pathways related to a given text keyword. Returns a DataFrame containing multiple pathway results. ```python gbm_pathways = pwpw.find_pathways_by_text('Glioblastoma') # many pathways returned ``` -------------------------------- ### Convert Pathway to Cytoscape Graph Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Shows the conversion of a loaded pathway into a Cytoscape graph format using Py4cytoscape. This is a crucial step for visualization and analysis within Cytoscape. ```python from py4cytoscape.utils import get_cytoscape_layout from py4cytoscape.core import NetworkUtil # Assuming 'pathways' is a list of Pathway objects from Pywikipathways if pathways: pathway_to_convert = pathways[0] # Convert the first pathway as an example graph = NetworkUtil.to_cytoscapejs(pathway_to_convert) print("Pathway converted to Cytoscape.js format.") else: print("No pathways loaded to convert.") ``` -------------------------------- ### Retrieve Pathway in GPML Format Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Fetches a specific pathway in GPML (XML) format using its ID. The retrieved data is a string containing the XML content. ```python gpml = pwpw.get_pathway('WP554') ``` ```python gpml[:1000] ``` -------------------------------- ### Import Pathway into Cytoscape Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways-and-py4cytoscape.html Imports a specific pathway into Cytoscape using its ID. Requires py4cytoscape to be initialized and connected. ```python p4c.commands_run('wikipathways import-as-pathway id=' + human_gbm_wpids[0]) ``` -------------------------------- ### List Pathways for a Specific Organism Source: https://pywikipathways.readthedocs.io/en/latest/pywikipathways_Overview.html Retrieve a list of all available pathways for a given organism using `list_pathways()`. The result is a pandas DataFrame containing pathway IDs, URLs, names, species, and revision numbers. ```python hs_pathways = pwpw.list_pathways('Homo sapiens') ``` -------------------------------- ### Convert Pathway to Cytoscape Format Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Converts the loaded pathway data into a format compatible with Cytoscape. This step is crucial for visualization with Py4cytoscape. ```python from py4cytoscape.pathways import Pathway # Convert the pathway to a Pathway object pw_pathway = Pathway(pw) ``` -------------------------------- ### list_pathways Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Retrieves a list of pathways for a given species, including WPID, name, species, URL, and the latest revision number. Returns a pandas DataFrame. ```APIDOC ## list_pathways ### Description Retrieve list of pathways per species, including WPID, name, species, URL and latest revision number. ### Method Signature `list_pathways(organism='')` ### Parameters #### Arguments - **organism** (str) - Optional - A particular species. ### Returns - pandas.DataFrame: A dataframe of pathway information. ### Examples ```python >>> list_pathways('Mus musculus') id url \ 0 WP1 https://www.wikipathways.org/index.php/Pathway:WP1_r117947 1 WP10 https://www.wikipathways.org/index.php/Pathway:WP10_r117067 2 WP103 https://www.wikipathways.org/index.php/Pathway:WP103_r116834 3 WP108 https://www.wikipathways.org/index.php/Pathway:WP108_r117940 4 WP113 https://www.wikipathways.org/index.php/Pathway:WP113_r116497 .. ... ... 230 WP79 https://www.wikipathways.org/index.php/Pathway:WP79_r104913 231 WP85 https://www.wikipathways.org/index.php/Pathway:WP85_r116710 232 WP87 https://www.wikipathways.org/index.php/Pathway:WP87_r116529 233 WP88 https://www.wikipathways.org/index.php/Pathway:WP88_r116521 234 WP93 https://www.wikipathways.org/index.php/Pathway:WP93_r117991 name species revision 0 Statin pathway Mus musculus 117947 1 IL-9 signaling pathway Mus musculus 117067 2 Cholesterol biosynthesis Mus musculus 116834 3 Selenium metabolism / selenoproteins Mus musculus 117940 4 TGF-beta signaling pathway Mus musculus 116497 .. ... ... ... 230 Tryptophan metabolism Mus musculus 104913 231 Focal adhesion Mus musculus 116710 232 Nucleotide metabolism Mus musculus 116529 233 Toll-like receptor signaling Mus musculus 116521 234 IL-4 signaling pathway Mus musculus 117991 [235 rows x 5 columns] ``` ``` -------------------------------- ### Display Network Data Table Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Displays the retrieved network table data. This is typically used after fetching data with `get_table_columns` to inspect the results. ```python net_data ``` -------------------------------- ### Check Cytoscape Connection Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways-and-py4cytoscape.ipynb.txt Verifies the connection to a running Cytoscape instance using py4cytoscape. ```python p4c.cytoscape_ping() ``` -------------------------------- ### List Pathway IDs Source: https://pywikipathways.readthedocs.io/en/latest/_sources/pywikipathways_Overview.ipynb.txt Retrieves a list of all pathway IDs available for a given organism. If no organism is specified, it defaults to listing all available pathway IDs. ```APIDOC ## list_pathway_ids ### Description Retrieves a list of pathway IDs. ### Arguments * `organism` (str, optional): A particular species. Defaults to ''. ### Returns * `pandas.Series`: A series of pathway IDs. ### Examples ```python >>> import pywikipathways as pwpw >>> pwpw.list_pathway_ids() 0 WP10 1 WP100 2 WP101 3 WP102 4 WP103 ... 230 WP79 231 WP85 232 WP87 233 WP88 234 WP93 Name: id, Length: 235, dtype: object ``` ```