### Install Reactome2py from Source

Source: https://github.com/reactome/reactome2py/blob/main/README.md

Install Reactome2py by cloning the repository and running the setup script. This is useful for development or when needing the latest unreleased version.

```shell
git clone repo
cd reactome2py
python setup.py install
```

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

### Install Reactome2py using pip

Source: https://github.com/reactome/reactome2py/blob/main/README.md

Install the Reactome2py library using pip. This is the recommended method for most users.

```bash
(sudo) pip install reactome2py
```

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

### Get Pathway Summary for Entities/Interactors

Source: https://context7.com/reactome/reactome2py/llms.txt

Returns found identifiers and interactors for a specific pathway within an analysis token result. Allows specifying the resource and filtering by 'all', 'entities', or 'interactors'.

```python
from reactome2py import analysis

# Get all found entities and interactors
summary = analysis.token_pathway_summary(
    token='MjAyMzA1MTUxMTM3NjdfMQ==',
    pathway='R-HSA-162582',
    resource='TOTAL',
    by='all'   # 'all', 'entities', or 'interactors'
)
print(summary['expNames'])
print(summary['found'])
```

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

### Get Participants of an Event

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves PhysicalEntities and their ReferenceEntities participating in a specified event. Use when you need to identify the components of a Reactome event.

```python
from reactome2py import content

parts = content.participants(id='5205685')
for p in parts[:3]:
    print(p['displayName'])
    print([r['identifier'] for r in p.get('refEntities', [])])
```

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

### participants

Source: https://context7.com/reactome/reactome2py/llms.txt

Get participants of an event.

```APIDOC
## participants

### Description
Returns PhysicalEntities and their ReferenceEntities that participate in a given event.

### Method
`content.participants(id: str)`

### Parameters
- **id** (str) - The stable ID of the event.

### Request Example
```python
from reactome2py import content

parts = content.participants(id='5205685')
for p in parts[:3]:
    print(p['displayName'])
    print([r['identifier'] for r in p.get('refEntities', [])])
```
```

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

### Build and Run Reactome2py Docker Image

Source: https://github.com/reactome/reactome2py/blob/main/README.md

Build a Docker image for Reactome2py and run it interactively. This provides a containerized environment for using the library.

```shell
(sudo) docker build -t <tag-name>:latest .
(sudo) docker run -it --rm <tag-name>:latest
```

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

### Generate a full pathway analysis report

Source: https://github.com/reactome/reactome2py/blob/main/demo/microbiologist-clinician.ipynb

Creates a directory if it doesn't exist and then generates a comprehensive PDF report of the pathway analysis. This report can be customized with various parameters like resource, diagram profile, and species.

```python
if not os.path.exists('full-report/'):
    os.makedirs('full-report/')
    
analysis.report(token, path='full-report/', file='report.pdf', number='25', resource='TOTAL', 
                diagram_profile='Modern', analysis_profile='Standard', fireworks_profile='Barium Lithium', 
                species='Homo sapiens', chunk_size=128)
```

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

### orthology

Source: https://context7.com/reactome/reactome2py/llms.txt

Get orthology of a human pathway in a specified species.

```APIDOC
## orthology

### Description
Get orthology of a human pathway in a specified species.

### Method
`content.orthology(id: str, species: str)`

### Parameters
- **id** (str) - The stable ID of the human pathway.
- **species** (str) - The species ID for which to find orthologs.

### Request Example
```python
from reactome2py import content

ortho = content.orthology(id='R-HSA-6799198', species='49633')
print(ortho['displayName'])
print(ortho['stId'])
```
```

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

### interactors_upload_content

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Paste file content and get a summary associated with a token.

```APIDOC
## interactors_upload_content

### Description
Paste file content and get a summary associated with a token.

### Parameters
* **name** (string) - Name which identifies the sample
* **content** (string) - Paste custom interactors file content

### Returns
Paste file content and get a summary associated with a token
```

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

### Download and Parse Reactome Pathway-to-Gene Mappings (GMT)

Source: https://context7.com/reactome/reactome2py/llms.txt

Downloads the Reactome GMT file and parses it into a list of dictionaries, mapping pathways to their associated HGNC gene symbols. Useful for pathway enrichment analysis.

```python
from reactome2py import fiviz

mappings = fiviz.gene_mappings()
# Each entry: {'name': 'Pathway Name', 'stId': 'R-HSA-XXXX', 'genes': ['GENE1', 'GENE2', ...]}
print(mappings[0])
# {'name': 'Apoptosis', 'stId': 'R-HSA-109581', 'genes': ['CASP3', 'CASP8', ...]}

# Build a lookup: pathway stId -> gene list
pathway_genes = {m['stId']: m['genes'] for m in mappings}
print(pathway_genes['R-HSA-109581'][:5])
```

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

### entities_complex

Source: https://context7.com/reactome/reactome2py/llms.txt

Get subunits of a complex. This function retrieves all subunit PhysicalEntities for a given Reactome complex, with optional recursive traversal.

```APIDOC
## entities_complex

### Description
Retrieves all subunit PhysicalEntities for a given Reactome complex, with optional recursive traversal.

### Method
`content.entities_complex(id: str, exclude_structures: bool = False) -> list`

### Parameters
* **id** (str) - Required - The Reactome ID of the complex.
* **exclude_structures** (bool) - Optional - Whether to exclude structural entities. Defaults to False.

### Response Example
```python
from reactome2py import content

subunits = content.entities_complex(
    id='R-HSA-5674003',
    exclude_structures=False
)
for s in subunits[:3]:
    print(s['displayName'], s['schemaClass'])
```
```

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

### Open Reactome analysis results in browser

Source: https://github.com/reactome/reactome2py/blob/main/demo/microbiologist-clinician.ipynb

Constructs a URL to view the analysis results directly on the Reactome website using the generated analysis token.

```python
url = 'https://reactome.org/PathwayBrowser/#/DTAB=AN&ANALYSIS=' + token
webbrowser.open(url)
```

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

### Export Pathway Diagram as Image

Source: https://context7.com/reactome/reactome2py/llms.txt

Downloads a pathway diagram in a specified image format (PNG, SVG, JPG, GIF) with optional analysis overlay. Specify file name and path for saving.

```python
from reactome2py import content

content.export_diagram(
    id='R-HSA-177929',
    ext='png',
    quality=8,
    diagram_profile='Modern',
    title=True,
    margin=15,
    file='signal_transduction',
    path='/diagrams/'
)
# Saves /diagrams/signal_transduction.png
```

```python
# With analysis overlay
content.export_diagram(
    id='R-HSA-177929',
    ext='svg',
    token='MjAyMzA1MTUxMTM3NjdfMQ==',
    analysis_profile='Standard',
    file='overlay_diagram',
    path='/diagrams/'
)
```

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

### Download Analysis Result as JSON (Python)

Source: https://context7.com/reactome/reactome2py/llms.txt

Downloads a full analysis result using a provided token. The 'reactome2py.analysis' module is required. Results can be returned as a Python dictionary or saved to a gzipped JSON file.

```python
from reactome2py import analysis

token = 'MjAyMzA1MTUxMTM3NjdfMQ=='

# Return as Python dict
result = analysis.result2json(token=token)
print(result['pathways'][0])

# Save gzipped to disk
analysis.result2json(
    token=token,
    path='/results/',
    file='egfr_result.json.gz',
    save=True,
    gzip=True
)
```

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

### Get Subunits of a Complex

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves all subunit PhysicalEntities for a given Reactome complex. Supports optional recursive traversal and exclusion of structures.

```python
from reactome2py import content

subunits = content.entities_complex(
    id='R-HSA-5674003',
    exclude_structures=False
)
for s in subunits[:3]:
    print(s['displayName'], s['schemaClass'])
```

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

### Fetch and export downstream pathway diagrams

Source: https://github.com/reactome/reactome2py/blob/main/demo/microbiologist-clinician.ipynb

Fetches downstream pathways that have diagrams, highlights reactions from the enrichment analysis token, and exports each diagram as a PNG file. This allows for detailed review and comparison of specific pathways.

```python
fetch_downstream_pathways = [content.pathways_low_diagram(id=stId, species=None, all_forms=False) for stId in pathways_stId]

downstream_pathways = [low_pathway for low_pathway in fetch_downstream_pathways if low_pathway is not None]
has_diagram = [p[0]['hasDiagram'] for p in downstream_pathways]
downstream_pathway_has_diagram = list(itertools.compress(downstream_pathways, has_diagram))
downstream_pathway_stId = [p[0]['stId'] for p in downstream_pathway_has_diagram]

if not os.path.exists('diagrams/'):
    os.makedirs('diagrams/')
    
[content.export_diagram(id=stId, ext='png', quality='5', flag_interactors=False, title=True, margin='15',
                        ehld=True, diagram_profile='Modern', resource='Total', analysis_profile='Standard', 
                        token=token, flag=None, sel=[], exp_column=None, file="-".join([stId,'report']), path='diagrams/') 
 for stId in downstream_pathway_stId]
```

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

### search_fireworks

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Performs a Solr query scoped to the fireworks widget for a given QueryObject, with options for query, species, types, start, and rows.

```APIDOC
## search_fireworks

### Description
Performs a Apache Solr query (fireworks widget scoped) for a given QueryObject.

### Parameters
* **query** (string) - Search term
* **species** (string) - Species identifier (it can be the taxonomy id, species name or dbId)
* **types** (list) - Types to filter by - python list of strings
* **start** (any) - Start row
* **rows** (any) - Number of rows to include

### Returns
Json dictionary object
```

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

### token_pathways_summary

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves summary for multiple pathways using a token.

```APIDOC
## token_pathways_summary()

### Description
Retrieves a summary for multiple pathways using a token.

### Method
`reactome2py.analysis.token_pathways_summary`

### Parameters
This function does not explicitly list parameters in the provided documentation.
```

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

### Get PSICQUIC Interactor Data for an Accession

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves protein-protein interaction data from external PSICQUIC resources for a given accession. Allows querying specific resources like MINT.

```python
from reactome2py import content

# Get available PSICQUIC resources first
resources = content.interactors_psicquic_resources()
print([r['name'] for r in resources])

# Fetch interaction details from MINT
interactions = content.interactors_psicquic_acc(
    resource='MINT',
    acc='Q13501',
    by='details'
)
print(interactions['rows'][0])
```

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

### Export fireworks visualization

Source: https://github.com/reactome/reactome2py/blob/main/demo/microbiologist-clinician.ipynb

Saves a 'fireworks' visualization of the pathways to a specified directory. This visualization helps in reviewing the overall scope of highlighted pathways.

```python
if not os.path.exists('fireworks/'):
    os.makedirs('fireworks/')
    
content.export_fireworks(species='9606', ext='png', file='fireworks_report', path='fireworks/', quality='10', 
                         flag=None, flag_interactors=False, sel=[], title=True, margin='15', resource='Total', 
                         diagram_profile='', coverage=False, token=token, exp_column=None)
```

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

### token_resources

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves available resources using a token.

```APIDOC
## token_resources()

### Description
Retrieves information about available resources using a token.

### Method
`reactome2py.analysis.token_resources`

### Parameters
This function does not explicitly list parameters in the provided documentation.
```

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

### Get Static Interactor Details for an Accession

Source: https://context7.com/reactome/reactome2py/llms.txt

Fetches curated protein-protein interaction details from Reactome's built-in data for a UniProt accession. Useful for analyzing known interactions without external queries.

```python
from reactome2py import content

interactions = content.interactors_static_acc(
    acc='Q13501',
    by='details',
    page=1,
    page_size=10
)
print(interactions['columnNames'])
for row in interactions['rows'][:3]:
    print(row['accA'], row['accB'], row['score'])
```

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

### List Pathways with SBGN Files

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves pathway stable IDs for lower-level pathways that have SBGN files, excluding EHLD pathways. Useful for accessing pathways in the SBGN format.

```python
from reactome2py import fiviz

sbgn_list = fiviz.sbgn_stids()
print(f"{len(sbgn_list)} pathways have SBGN files")
print(sbgn_list[:3])
```

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

### Get Orthology of Human Pathway in Sus scrofa

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves orthologous pathways for a given human pathway ID in Sus scrofa. Requires the pathway's Reactome ID and the species ID for Sus scrofa.

```python
ortho = content.orthology(id='R-HSA-6799198', species='49633')
print(ortho['displayName'])
print(ortho['stId'])
```

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

### Export Pathway as PDF Document

Source: https://context7.com/reactome/reactome2py/llms.txt

Exports a detailed PDF document for a pathway event, including diagram, summation, references, and edit history. Specify file name and path for saving.

```python
from reactome2py import content

content.export_document(
    id='R-HSA-177929',
    level='1',
    diagram_profile='Modern',
    file='pathway_doc',
    path='/reports/'
)
# Saves /reports/pathway_doc.pdf
```

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

### Get Targets for a Specific Drug

Source: https://context7.com/reactome/reactome2py/llms.txt

Returns all known protein targets for a given drug name from specified sources like DrugCentral or Targetome. Requires specifying the Reactome release version, drug name, and data source.

```python
from reactome2py import fiviz

targets = fiviz.drug_targets(
    release='2019',
    drug='Gefitinib',
    source='drugcentral'
)
for t in targets:
    print(t['gene'], t['interactionType'])
```

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

### Compare Species Pathways

Source: https://context7.com/reactome/reactome2py/llms.txt

Compares Homo sapiens pathways to another species using Reactome's species comparison tool. Requires a species ID and allows sorting by entities FDR with a specified order and p-value.

```python
from reactome2py import analysis

# Compare Homo sapiens vs. Mus musculus (dbId: 48892)
result = analysis.compare_species(
    species='48892',
    sort_by='ENTITIES_FDR',
    order='ASC',
    p_value=0.05
)
print(result['pathways'][0]['name'])
```

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

### discover

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Discovers content within the reactome2py content module.

```APIDOC
## discover()

### Description
Discovers content.

### Module
reactome2py.content
```

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

### Export Pathway to SBGN or SBML

Source: https://context7.com/reactome/reactome2py/llms.txt

Exports a pathway or reaction in Systems Biology Graphical Notation (SBGN) or Systems Biology Markup Language (SBML) format. Specify file name and path for saving.

```python
from reactome2py import content

content.export_event(
    id='R-HSA-177929',
    format='sbgn',
    file='pathway_network',
    path='/exports/'
)
# Saves /exports/pathway_network.sbgn
```

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

### token_pathways_reactions

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves reactions for multiple pathways using a token.

```APIDOC
## token_pathways_reactions()

### Description
Retrieves reactions for multiple pathways using a token.

### Method
`reactome2py.analysis.token_pathways_reactions`

### Parameters
This function does not explicitly list parameters in the provided documentation.
```

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

### reactome2py.content.search_diagram_instance

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Searches for diagram instances.

```APIDOC
## search_diagram_instance()

### Description
Searches for specific instances within diagrams. Specific search parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/search/diagram/instance

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### Download PDF Analysis Report

Source: https://context7.com/reactome/reactome2py/llms.txt

Downloads a formatted PDF report for an analysis token. Allows customization of the save path, filename, number of pathways, resource, diagram profile, analysis profile, and species.

```python
from reactome2py import analysis

analysis.report(
    token='MjAyMzA1MTUxMTM3NjdfMQ==',
    path='/results/',
    file='pathway_report.pdf',
    number=25,
    resource='TOTAL',
    diagram_profile='Modern',
    analysis_profile='Standard',
    species='Homo sapiens'
)
```

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

### token_pathway_summary

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves pathway summary using a token.

```APIDOC
## token_pathway_summary()

### Description
Retrieves a summary of a pathway using a token.

### Method
`reactome2py.analysis.token_pathway_summary`

### Parameters
This function does not explicitly list parameters in the provided documentation.
```

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

### List All or Main Species

Source: https://context7.com/reactome/reactome2py/llms.txt

Returns the list of all or main species available in Reactome. Useful for identifying species taxonomy IDs for other API calls.

```python
from reactome2py import content

all_species = content.species(by='all')
main_species = content.species(by='main')
for s in main_species[:5]:
    print(s['taxId'], s['displayName'])
# 9606  Homo sapiens
# 10090 Mus musculus
```

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

### search_suggest

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Retrieves a list of suggestions for a given search term.

```APIDOC
## search_suggest

### Description
This method retrieves a list of suggestions for a given search term.

### Parameters
* **query** (string) - term to search

### Returns
list of matched elements
```

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

### reactome2py.content.pathways_top_level

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves top-level pathways.

```APIDOC
## pathways_top_level()

### Description
Retrieves a list of top-level pathways. Specific parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/pathways/top_level

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### export_fireworks

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Exports a pathway overview to a specified image format.

```APIDOC
## export_fireworks

### Description
Exports a given pathway overview to the specified image format (png, jpg, jpeg, svg, gif).

### Parameters
*   **species** (string) - Optional - Species identifier (taxonomy id, species name, or dbId). Defaults to '9606'.
*   **ext** (string) - Optional - File extension defining the image format. Available extensions: png, jpg, jpeg, svg, gif. Defaults to 'png'.
*   **file** (string) - Optional - Name of the file. Defaults to 'report'.
*   **path** (string) - Optional - Absolute path to save the file. Defaults to an empty string.
*   **quality** (string) - Optional - Result image quality between 1 and 10. Defaults to '5'.
*   **flag** (string) - Optional - Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram.
*   **flag_interactors** (boolean) - Optional - Defines whether to take into account interactors for the flagging. Defaults to False.
*   **sel** (list) - Optional - Highlight element(s) selection in the diagram. Example: ['X', 'Y', 'Z']. Defaults to an empty list.
*   **title** (boolean) - Optional - Sets whether the name of the pathway is shown below. Defaults to True.
*   **margin** (string) - Optional - Defines the image margin between 0 and 20. Defaults to '15'.
*   **resource** (string) - Optional - The analysis resource for which the results will be overlaid on top of the given pathways overview. Defaults to 'Total'.
*   **diagram_profile** (string) - Optional - Diagram Color Profile. Available in: Copper, Copper plus, Barium lithium, Calcium salts.
*   **coverage** (boolean) - Optional - Set to true to overlay analysis coverage values. Defaults to False.
*   **token** (string) - Optional - The analysis token with the results to be overlaid on top of the given pathways overview.
*   **exp_column** (string) - Optional - Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay.
```

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

### token_resources

Source: https://github.com/reactome/reactome2py/blob/main/docs/analysis.html

Retrieves the resources summary associated with a given token.

```APIDOC
## token_resources

### Description
Retrieves the resources summary associated with a given token.

### Parameters
#### Path Parameters
- **token** (string) - Required - The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result

### Returns
Json list object
```

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

### reactome2py.content.search_suggest

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Provides search suggestions.

```APIDOC
## search_suggest()

### Description
Provides search suggestions based on a query. Specific parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/search/suggest

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### Retrieve Reactome Database Metadata

Source: https://context7.com/reactome/reactome2py/llms.txt

Fetches the current name and version of the Reactome database backing the Analysis Service.

```python
from reactome2py import analysis

print(analysis.db_name())     # e.g. "reactome"
print(analysis.db_version())  # e.g. "79"
```

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

### Multi-Identifier Pathway Enrichment Analysis (Python)

Source: https://context7.com/reactome/reactome2py/llms.txt

Submits a comma-separated list of identifiers for pathway enrichment analysis. The 'reactome2py.analysis' module must be imported. Results include a token for retrieving full details and a summary of pathways.

```python
from reactome2py import analysis

result = analysis.identifiers(
    ids='EGF,EGFR,BRAF,TP53',
    interactors=True,
    page_size=10,
    page=1,
    species='Homo Sapiens',
    sort_by='ENTITIES_FDR',
    order='ASC',
    p_value=0.05,
    include_disease=False,
    projection=False
)

token = result['summary']['token']
print(f"Analysis token: {token}")
for pw in result['pathways'][:3]:
    print(pw['stId'], pw['name'], pw['entities']['fdr'])
# R-HSA-162582  Signal Transduction  0.0001
# R-HSA-5633007 Regulation of TP53   0.0003
```

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

### import_form

Source: https://github.com/reactome/reactome2py/blob/main/docs/analysis.html

Imports a posted JSON file into the service. The accepted format is the same as provided by the /#/download/{token}/result.json endpoint. The submitted file can be gzipped.

```APIDOC
## import_form

### Description
Imports the posted json file into the service The accepted format is the same as provided by the method /#/download/{token}/result.json. Note: The submitted file can be gzipped.

### Parameters
#### Path Parameters
- **input_file** (file) - Required

### Returns
Json list object
```

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

### token_pathway_reactions

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves pathway reactions using a token.

```APIDOC
## token_pathway_reactions()

### Description
Retrieves reactions associated with a pathway using a token.

### Method
`reactome2py.analysis.token_pathway_reactions`

### Parameters
This function does not explicitly list parameters in the provided documentation.
```

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

### token_pathways_summary

Source: https://github.com/reactome/reactome2py/blob/main/docs/analysis.html

Queries analysis token and returns a summary of the contained identifiers and interactors for all pathways.

```APIDOC
## token_pathways_summary

### Description
Queries analysis token and returns a summary of the contained identifiers and interactors for all pathways.

### Parameters
#### Path Parameters
- **token** (string) - Required - The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
- **pathways** (string) - Required - The pathways stable identifier (stId - provided in the analysis result for each pathway)
- **resource** (string) - Optional - The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND

### Returns
Json list object
```

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

### Retrieve Found Entities as DataFrame

Source: https://context7.com/reactome/reactome2py/llms.txt

Fetches all entities from a query that were found in Reactome pathways. Requires an analysis token and specifies the resource to query.

```python
from reactome2py import analysis

token = 'MjAyMzA1MTUxMTM3NjdfMQ=='

df = analysis.found_entities(token=token, resource='TOTAL')
print(df.head())
```

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

### import_json

Source: https://github.com/reactome/reactome2py/blob/main/docs/analysis.html

Imports JSON data into the analysis service. The data should be in the format expected by the /#/download/{token}/result.json endpoint. The input file can be gzipped.

```APIDOC
## import_json

### Description
Imports the posted json into the service. The accepted format is the same as provided by the method /#/download/{token}/result.json. Note: The provided file can be gzipped.

### Parameters
#### Request Body
- **input_json** (string) - Required - Identifiers to analyse followed by their expression (when applies) in json format in string

### Returns
File or json object containing data on pathway, entities, statistics, etc. found in analysis overlap
```

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

### reactome2py.content.search_diagram_pathway_flag

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Searches for pathways with diagram flags.

```APIDOC
## search_diagram_pathway_flag()

### Description
Searches for pathways that have specific diagram flags. Specific search parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/search/diagram/pathway_flag

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### import_url

Source: https://github.com/reactome/reactome2py/blob/main/docs/analysis.html

Imports JSON data from a URL into the analysis service. The data format should match that of the /#/download/{token}/result.json endpoint. The file at the URL can be gzipped.

```APIDOC
## import_url

### Description
Imports the json file provided by the posted url into the service. The accepted format is the same as provided by the method /#/download/{token}/result.json. Note: The provided file can be gzipped.

### Parameters
#### Request Body
- **input_url** (string) - Required - A URL pointing to the json data to be analysed

### Returns
File or json object containing data on pathway, entities, statistics, etc. found in analysis overlap
```

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

### reactome2py.content.references

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves reference information.

```APIDOC
## references()

### Description
Retrieves reference information. Specific parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/references

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### discover

Source: https://context7.com/reactome/reactome2py/llms.txt

Schema.org dataset object for an event. Generates a schema.org-compliant JSON representation of a Reactome event (pathway or reaction), used primarily by search engines.

```APIDOC
## discover

### Description
Generates a schema.org-compliant JSON representation of a Reactome event (pathway or reaction), used primarily by search engines.

### Method
`content.discover(id: str) -> dict`

### Parameters
* **id** (str) - Required - The Reactome ID of the event (pathway or reaction).

### Response Example
```python
from reactome2py import content

data = content.discover(id='R-HSA-446203')
print(data['name'])        # e.g. "Innate Immune System"
print(data['@type'])       # "Dataset"
print(data['description'])
```
```

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

### Download Pathway Hits as Pandas DataFrame (Python)

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves pathway hits for a given analysis token as a pandas DataFrame or saves them to a CSV file. Requires the 'reactome2py.analysis' module and pandas. Specify the resource to use for retrieval.

```python
from reactome2py import analysis

token = 'MjAyMzA1MTUxMTM3NjdfMQ=='

df = analysis.pathway2df(token=token, resource='TOTAL')
print(df.columns.tolist())
# ['Pathway identifier', 'Pathway name', '#Entities found', '#Entities total', ...]
print(df.head())

# Save to CSV
analysis.pathway2df(token=token, path='/results/', file='pathways.csv', save=True)
```

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

### Retrieve Event Ancestor Paths

Source: https://context7.com/reactome/reactome2py/llms.txt

Fetches all paths from a given event up to the top-level pathways in the Reactome hierarchy. Returns a list of lists, where each inner list represents a path.

```python
from reactome2py import content

ancestors = content.event_ancestors(id='R-HSA-5673001')
# Returns list of lists (each list is one path to top-level)
for path in ancestors:
    print(' -> '.join([e['displayName'] for e in path]))
```

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

### reactome2py.content.pathways_low_diagram

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves pathways with low-level diagram information.

```APIDOC
## pathways_low_diagram()

### Description
Retrieves pathways that have associated low-level diagram information. Specific parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/pathways/low/diagram

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### Full-Text Search Reactome Knowledgebase

Source: https://context7.com/reactome/reactome2py/llms.txt

Performs a Solr-backed full-text search across the Reactome knowledgebase with faceting and filtering support. Allows specifying query terms, species, types, and result clustering.

```python
from reactome2py import content

results = content.search_query(
    query='Biological oxidations',
    species=['Homo sapiens'],
    types=['Pathway'],
    cluster=True,
    rows=10
)
for entry in results['results'][0]['entries'][:3]:
    print(entry['stId'], entry['name'])
```

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

### Import necessary libraries

Source: https://github.com/reactome/reactome2py/blob/main/demo/microbiologist-clinician.ipynb

Imports the required modules from the reactome2py library and other standard Python libraries for analysis and file operations.

```python
from reactome2py import content, analysis
import pprint
import webbrowser
import itertools
import os
```

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

### pathways_top_level

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Retrieves the list of all top-level pathways for a specified species.

```APIDOC
## pathways_top_level

### Description
Retrieves the list of top level pathways for the given species.

### Parameters
* **species** (string, optional) - Specifies the species by the taxonomy identifier (eg: 9606) or species name (eg: ‘Homo+sapiens’). Defaults to '9606'.

### Returns
Json list object of all Reactome top level pathways.
```

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

### Generate Schema.org Dataset Object for Event

Source: https://context7.com/reactome/reactome2py/llms.txt

Generates a schema.org-compliant JSON representation of a Reactome event (pathway or reaction). Used by search engines. Requires an event ID.

```python
from reactome2py import content

data = content.discover(id='R-HSA-446203')
print(data['name'])        # e.g. "Innate Immune System"
print(data['@type'])       # "Dataset"
print(data['description'])
```

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

### reactome2py.content.search_diagram

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Searches for diagrams.

```APIDOC
## search_diagram()

### Description
Searches for diagrams within Reactome. Specific search parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/search/diagram

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### gene_mappings

Source: https://context7.com/reactome/reactome2py/llms.txt

Reactome pathway-to-gene mappings (GMT).

```APIDOC
## gene_mappings

### Description
Downloads and parses the Reactome GMT file, returning a list of dictionaries mapping each pathway to its associated HGNC gene symbols.

### Method
`fiviz.gene_mappings()`

### Request Example
```python
from reactome2py import fiviz

mappings = fiviz.gene_mappings()
# Each entry: {'name': 'Pathway Name', 'stId': 'R-HSA-XXXX', 'genes': ['GENE1', 'GENE2', ...]}
print(mappings[0])
# {'name': 'Apoptosis', 'stId': 'R-HSA-109581', 'genes': ['CASP3', 'CASP8', ...]}`

# Build a lookup: pathway stId -> gene list
pathway_genes = {m['stId']: m['genes'] for m in mappings}
print(pathway_genes['R-HSA-109581'][:5])
```
```

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

### reactome2py.content.schema

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves schema information.

```APIDOC
## schema()

### Description
Retrieves schema information for Reactome data. Specific parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/schema

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### search_query

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Performs a Solr query on the Reactome knowledgebase, with options for pagination, filtering by species, types, compartments, keywords, and clustering.

```APIDOC
## search_query

### Description
This method performs a Solr query on the Reactome knowledgebase. Results can be provided in a paginated format.

### Parameters
* **query** (string) - term to search
* **species** (list) - list of species - python list of strings
* **types** (list) - Types to filter by - python list of strings
* **compartments** (list) - Compartments - python list of strings
* **keywords** (list) - Keywords - python list of strings
* **cluster** (boolean) - Cluster results
* **start** (any) - Start row
* **rows** (any) - number of rows to include

### Returns
Json dictionary object
```

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

### URL-Based Pathway Enrichment Analysis (Python)

Source: https://context7.com/reactome/reactome2py/llms.txt

Submits identifiers from a URL for pathway enrichment analysis using the 'reactome2py.analysis' module. Requires the 'reactome2py.analysis' module. Specify the external URL containing the identifiers.

```python
from reactome2py import analysis

result = analysis.identifiers_url(
    external_url='https://example.com/my_gene_list.txt',
    interactors=False,
    species='Homo Sapiens',
    p_value=0.05
)
print(result['summary']['token'])
```

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

### export_event

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Exports a given pathway or reaction to SBGN or SBML format.

```APIDOC
## export_event

### Description
Exports a given pathway or reaction to the format requested (SBGN or SBML).

### Parameters
*   **id** (string) - Required - DbId or StId of the requested pathway or reaction.
*   **format** (string) - Required - 'sbgn' or 'sbml'.
*   **file** (string) - Optional - Name of the file. Defaults to 'report'.
*   **path** (string) - Optional - Absolute path to save the file. Defaults to an empty string.
```

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

### reactome2py.content.references

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Retrieves a list of all reference entities for a given identifier.

```APIDOC
## reactome2py.content.references

### Description
Retrieves a list containing all the reference entities for a given identifier.

### Parameters
*   **id** (string) - Identifier for a given entity

### Returns
Json list object of all ReferenceEntities for a given identifier
```

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

### export_diagram

Source: https://context7.com/reactome/reactome2py/llms.txt

Export pathway diagram as image. Downloads a pathway diagram in a specified image format (PNG, SVG, JPG, GIF) with optional analysis overlay.

```APIDOC
## export_diagram

### Description
Export pathway diagram as image. Downloads a pathway diagram in a specified image format (PNG, SVG, JPG, GIF) with optional analysis overlay.

### Method
```python
content.export_diagram(
    id: str,
    ext: str,
    quality: int = None,
    diagram_profile: str = None,
    title: bool = None,
    margin: int = None,
    file: str = None,
    path: str = None,
    token: str = None,
    analysis_profile: str = None
)
```

### Parameters
#### Path Parameters
- **id** (str) - Required - The stable ID of the pathway.
- **ext** (str) - Required - The image format (e.g., 'png', 'svg', 'jpg', 'gif').

#### Query Parameters
- **quality** (int) - Optional - The quality of the image (1-10).
- **diagram_profile** (str) - Optional - The diagram profile to use.
- **title** (bool) - Optional - Whether to include the title.
- **margin** (int) - Optional - The margin around the diagram.
- **file** (str) - Optional - The base filename for the exported image.
- **path** (str) - Optional - The directory to save the image in.
- **token** (str) - Optional - An analysis token for overlaying analysis results.
- **analysis_profile** (str) - Optional - The analysis profile to use for overlay.

### Request Example
```python
content.export_diagram(
    id='R-HSA-177929',
    ext='png',
    quality=8,
    diagram_profile='Modern',
    title=True,
    margin=15,
    file='signal_transduction',
    path='/diagrams/'
)
```

### Response
This function saves a file and does not return a value.
```

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

### reactome2py.content.discover

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Generates a JSON representation of a Reactome event (reaction or pathway) as a schema.org dataset object, useful for search engine indexing.

```APIDOC
## discover

### Description
Generates a JSON representation of a Reactome event (reaction or pathway) as a schema.org dataset object, useful for search engine indexing.

### Parameters
* **id** (string) - Optional - An event identifier, such as a pathway stable identifier (stId). Defaults to 'R-HSA-446203'.

### Returns
Json dictionary object conforming to schema.org for an Event in Reactome knowledgebase.
```

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

### File-Based Pathway Enrichment Analysis (Python)

Source: https://context7.com/reactome/reactome2py/llms.txt

Reads identifiers from a local text file for pathway enrichment analysis. Requires the 'reactome2py.analysis' module. Supports projection to map non-human identifiers to Homo sapiens.

```python
from reactome2py import analysis

# identifiers.txt contains one identifier per line, or expression values:
# EGFR  1.5
# BRAF  -2.3
# TP53  0.8
result = analysis.identifiers_form(
    path='/data/identifiers.txt',
    interactors=False,
    species='Homo Sapiens',
    sort_by='ENTITIES_FDR',
    p_value=0.05,
    projection=True   # project non-human identifiers to Homo sapiens
)
print(result['summary']['token'])
```

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

### reactome2py.content.mapping

Source: https://github.com/reactome/reactome2py/blob/main/docs/content.html

Retrieves pathways or reactions for a given identifier.

```APIDOC
## reactome2py.content.mapping

### Description
Retrieves pathways or reactions associated with a given identifier. It can map identifiers to the pathways they participate in or the reactions they are involved in.

### Parameters
*   **id** (string) - The identifier to be mapped.
*   **resource** (string) - The resource name for which the identifier is submitted (e.g., 'UniProt').
*   **species** (string) - Species for which the result is filtered. Accepts taxonomy id, species name, or dbId. Defaults to '9606' (Homo sapiens) if the identifier points to a chemical and species is not provided.
*   **by** (string) - Specifies the mapping type: 'pathways' or 'reactions'.

### Returns
*   Json list object containing the mapped pathways or reactions.
```

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

### List Pathways with Enhanced High-Level Diagrams (EHLDs)

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves a list of top-level pathway stable IDs that have Enhanced High Level Diagrams (EHLDs) available. Useful for identifying pathways with detailed visual representations.

```python
from reactome2py import fiviz

ehld_list = fiviz.ehld_stids()
print(f"{len(ehld_list)} pathways have EHLDs")
print(ehld_list[:5])
# ['R-HSA-1430728', 'R-HSA-162582', ...]
```

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

### List Top-Level Pathways for a Species

Source: https://context7.com/reactome/reactome2py/llms.txt

Retrieves all top-level pathways for a given species taxonomy ID. Useful for exploring the main branches of the Reactome hierarchy for a specific organism.

```python
from reactome2py import content

pathways = content.pathways_top_level(species='9606')  # Homo sapiens
for pw in pathways:
    print(pw['stId'], pw['displayName'])
# R-HSA-1430728  Metabolism
# R-HSA-162582   Signal Transduction
# ...
```

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

### reactome2py.analysis.token

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Handles token-based analysis.

```APIDOC
## token()

### Description
Handles token-based analysis operations. Specific parameters and return types are not detailed in the source.

### Method
POST

### Endpoint
/analysis/token

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### report

Source: https://context7.com/reactome/reactome2py/llms.txt

Download a PDF analysis report. This function downloads a formatted PDF report for an analysis token, covering the top pathways with diagrams and statistics.

```APIDOC
## report

### Description
Downloads a formatted PDF report for an analysis token, covering the top pathways with diagrams and statistics.

### Method
`analysis.report(token: str, path: str, file: str, number: int = 25, resource: str = 'TOTAL', diagram_profile: str = 'Modern', analysis_profile: str = 'Standard', species: str = 'Homo sapiens')`

### Parameters
* **token** (str) - Required - Analysis token.
* **path** (str) - Required - Directory to save the report.
* **file** (str) - Required - Filename for the report.
* **number** (int) - Optional - Number of top pathways to include. Defaults to 25.
* **resource** (str) - Optional - Resource to use for analysis. Defaults to 'TOTAL'.
* **diagram_profile** (str) - Optional - Profile for diagram generation. Defaults to 'Modern'.
* **analysis_profile** (str) - Optional - Profile for analysis. Defaults to 'Standard'.
* **species** (str) - Optional - Species for the report. Defaults to 'Homo sapiens'.

### Response Example
```python
from reactome2py import analysis

analysis.report(
    token='MjAyMzA1MTUxMTM3NjdfMQ==',
    path='/results/',
    file='pathway_report.pdf',
    number=25,
    resource='TOTAL',
    diagram_profile='Modern',
    analysis_profile='Standard',
    species='Homo sapiens'
)
```
```

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

### compare_species

Source: https://github.com/reactome/reactome2py/blob/main/docs/analysis.html

Compares Homo sapiens to a specified species to identify pathway over-representation. Allows customization of sorting, filtering, and pagination.

```APIDOC
## compare_species

### Description
Compares Homo sapiens to the specified species to identify pathway over-representation.

### Parameters
* **species** (string) - The reactome dbId string of the species to compare to. Defaults to '48892' (Mus musculus).
* **page_size** (string) - Page size. Defaults to '1'.
* **page** (string) - Number of pages. Defaults to '1'.
* **sort_by** (string) - How to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO. Defaults to 'ENTITIES_FDR'.
* **order** (string) - Order ASC or DESC. Defaults to 'ASC'.
* **resource** (string) - The resource to sort. Available options: TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND. Defaults to 'TOTAL'.
* **p_value** (string) - Defines the pValue threshold. Only hit pathways with pValue equal to or below the threshold will be returned. Defaults to '1'.

### Returns
Json dictionary object.
```

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

### db_version

Source: https://github.com/reactome/reactome2py/blob/main/docs/analysis.html

Retrieves the version number of the current Reactome database.

```APIDOC
## db_version

### Description
Returns the version number of the current database.

### Returns
String of the version number of current database.
```

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

### reactome2py.content.search_query

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Performs a general search query.

```APIDOC
## search_query()

### Description
Performs a general search query across Reactome data. Specific search parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/search/query

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```

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

### reactome2py.content.species

Source: https://github.com/reactome/reactome2py/blob/main/docs/genindex.html

Retrieves information about species.

```APIDOC
## species()

### Description
Retrieves information about different species available in Reactome. Specific parameters and return types are not detailed in the source.

### Method
GET

### Endpoint
/species

### Parameters
None specified in source.

### Request Example
None specified in source.

### Response
#### Success Response (200)
Details not specified in source.
```