pywikipathways

https://pywikipathways.readthedocs.io/en/latest/
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### 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.")
```

--------------------------------

### 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])
```

--------------------------------

### 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]
```

--------------------------------

### 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
```
```
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