### Get Species List

Source: https://reactome.github.io/reactome2py/content.html

Retrieves a list of main species in Reactome. The 'by' parameter can be set to 'all' or 'main'. Returns a JSON list object.

```APIDOC
## GET /content/species

### Description
Retrieves a list of main species in Reactome.

### Parameters
#### Query Parameters
- **by** (string) - Optional - Specifies whether to return 'all' or 'main' species.

### Response
#### Success Response (200)
- **species_list** (json) - A JSON object containing a list of species.
```

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

### interactors_upload_content

Source: https://reactome.github.io/reactome2py/content.html

Upload custom interactor 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.

### Method
reactome2py.content.interactors_upload_content(name, content)

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

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

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

### interactors_url

Source: https://reactome.github.io/reactome2py/content.html

Send interactor file content via URL and get a summary associated with a token.

```APIDOC
## interactors_url

### Description
Send file via URL and get a summary associated with a token.

### Method
reactome2py.content.interactors_url(name, interactors_url)

### Parameters
#### Path Parameters
- **name** (string) - Required - Name which identifies the sample
- **interactors_url** (string) - Required - A URL pointing to the Interactors file

### Returns

```

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

### reactome2py.analysis.report

Source: https://reactome.github.io/reactome2py/analysis.html

Downloads a report for a given pathway analysis result and saves it as a PDF file.

```APIDOC
## reactome2py.analysis.report

### Description
Downloads a report for a given pathway analysis result.

### Parameters
- **token** (string) - Required - The token associated with the data result.
- **path** (string) - Required - Absolute path to save the report pdf file to.
- **file** (string) - Optional - Pdf file name to save the analysis report to - default set to report.pdf.
- **number** (string) - Optional - Number of pathways reported (max 50).
- **resource** (string) - Optional - The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND.
- **diagram_profile** (string) - Optional - Diagram Color Profile - as string.
- **analysis_profile** (string) - Optional - Analysis Color Profile - as string.
- **fireworks_profile** (string) - Optional - Diagram Color Profile - as string.
- **species** (string) - Optional - The species for which results will be reported.
- **chunk_size** (integer) - Optional - Python generator iter_content() chunk size - default set to 128.

### Returns
Saves a reactome analysis pdf report to the indicated path and file name.
```

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

### import_form

Source: https://reactome.github.io/reactome2py/analysis.html

Imports a posted JSON file into the service for analysis. The file format should match the output of the /#/download/{token}/result.json endpoint. Supports gzipped files.

```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 - A json file with the data to be analysed.
```

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

### search_suggest

Source: https://reactome.github.io/reactome2py/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) - Required - term to search

### Returns
list of matched elements
```

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

### token_resources

Source: https://reactome.github.io/reactome2py/analysis.html

Retrieves the resources summary associated with a given token.

```APIDOC
## token_resources

### Description
Returns the resources summary associated with the token.

### Parameters
* **token** (string) - Required - The token associated with the data result.

### Returns
Json list object
```

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

### token_pathways_summary

Source: https://reactome.github.io/reactome2py/analysis.html

Queries the analysis token and returns a summary of 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
* **token** (string) - Required - The token associated with the data result.
* **pathways** (string) - Required - The pathways stable identifier (stId).
* **resource** (string) - Optional - The resource to sort (e.g., TOTAL, UNIPORT, ENSEMBLE).

### Returns
Json list object
```

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

### import_url

Source: https://reactome.github.io/reactome2py/analysis.html

Imports JSON data from a posted URL into the service for analysis. The data format should match the output of the /#/download/{token}/result.json endpoint. Supports gzipped files.

```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
#### Path Parameters
- **input_url** (string) - Required - A URL pointing to the json data to be analysed.
```

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

### schema

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves schema information from the reactome2py.content module.

```APIDOC
## schema()

### Description
Retrieves schema information.

### Module
reactome2py.content
```

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

### discover

Source: https://reactome.github.io/reactome2py/genindex.html

Discovers data within the reactome2py.content module.

```APIDOC
## discover()

### Description
Discovers data.

### Module
reactome2py.content
```

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

### discover

Source: https://reactome.github.io/reactome2py/content.html

Generates a JSON representation of a dataset object for a given event (reaction or pathway), conforming to schema.org standards. Primarily used for search engine indexing.

```APIDOC
## discover

### Description
Generates a JSON representation of a dataset object for a given event (reaction or pathway), conforming to schema.org standards. Primarily used for search engine indexing.

### Parameters
* **id** (string) - Required - An event identifier (e.g., pathway stable identifier (stId) of pathway).

### Returns
Json dictionary object of the schema.org for an Event in Reactome knowledgebase.
```

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

### import_json

Source: https://reactome.github.io/reactome2py/analysis.html

Imports posted JSON data into the service for analysis. The data format should match the output of the /#/download/{token}/result.json endpoint. Supports gzipped data.

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

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

### pathways_top_level

Source: https://reactome.github.io/reactome2py/content.html

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

```APIDOC
## pathways_top_level

### Description
This method retrieves the list of top level pathways for the given species.

### Parameters
* **species** (string) - Specifies the species by the taxonomy identifier (eg: 9606) or species name (eg: ‘Homo+sapiens’)

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

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

### compare_species

Source: https://reactome.github.io/reactome2py/analysis.html

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

```APIDOC
## compare_species

### Description
Compares Homo sapiens to the specified species to identify pathway differences. Allows customization of sorting, filtering, and pagination.

### Method
`reactome2py.analysis.compare_species`

### Parameters
#### Path Parameters
- **species** (string) - Optional - The reactome dbId string of the species to compare to. Defaults to '48892'.
- **page_size** (string) - Optional - Page size. Defaults to '1'.
- **page** (string) - Optional - Number of pages. Defaults to '1'.
- **sort_by** (string) - Optional - 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) - Optional - Order ASC or DESC. Defaults to 'ASC'.
- **resource** (string) - Optional - The resource to sort. Available options: TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND. Defaults to 'TOTAL'.
- **p_value** (string) - Optional - 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
```

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

### export_fireworks

Source: https://reactome.github.io/reactome2py/content.html

Exports a given pathway overview to the specified image format.

```APIDOC
## export_fireworks

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

### Method Signature
`reactome2py.content.export_fireworks(_species ='9606'_, _ext ='png'_, _file ='report'_, _path =''_, _quality ='5'_, _flag =None_, _flag_interactors =False_, _sel =[]_, _title =True_, _margin ='15'_, _resource ='Total'_, _diagram_profile =''_, _coverage =False_, _token =None_, _exp_column =None_)`

### Parameters
#### Path Parameters
- **species** (string) - Required - Species identifier (it can be the taxonomy id, species name or dbId)

#### Query Parameters
- **ext** (string) - Optional - File extension (defines the image format) available extensions: png, jpg, jpeg, svg, gif
- **file** (string) - Optional - Name of file default is set to report
- **path** (string) - Optional - Absolute path to save the file
- **quality** (string) - Optional - Result image quality between [1 - 10]. It defines the quality of the final image (Default 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 default set to False
- **sel** (list) - Optional - Highlight element(s) selection in the diagram. CSV line. comma seperate python list ex ['X', 'Y', 'Z']
- **title** (boolean) - Optional - Sets whether the name of the pathway is shown as title
- **margin** (string) - Optional - Defines the image margin between [0 - 20] (Default 15)
- **resource** (string) - Optional - The analysis resource for which the results will be overlaid on top of the given pathways overview
- **diagram_profile** (string) - Optional - Diagram Color Profile: Modern or Standard
- **coverage** (boolean) - Optional - Defines whether textbook-like illustration are taken into account
- **token** (string) - Optional - The analysis token with the results to be overlaid on top of the given diagram
- **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

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

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

### pathways_top_level

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves top-level pathways from the reactome2py.content module.

```APIDOC
## pathways_top_level()

### Description
Retrieves top-level pathways.

### Module
reactome2py.content
```

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

### references

Source: https://reactome.github.io/reactome2py/content.html

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

```APIDOC
## 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
```

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

### pathways_low_diagram

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves pathways with low-level diagrams from the reactome2py.content module.

```APIDOC
## pathways_low_diagram()

### Description
Retrieves pathways with low-level diagrams.

### Module
reactome2py.content
```

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

### search_suggest

Source: https://reactome.github.io/reactome2py/genindex.html

Provides search suggestions within the reactome2py.content module.

```APIDOC
## search_suggest()

### Description
Provides search suggestions.

### Module
reactome2py.content
```

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

### report

Source: https://reactome.github.io/reactome2py/genindex.html

Generates a report from the reactome2py.analysis module.

```APIDOC
## report()

### Description
Generates a report.

### Module
reactome2py.analysis
```

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

### search_query

Source: https://reactome.github.io/reactome2py/content.html

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

```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) - Required - term to search
- **species** (list) - Optional - list of species - python list of strings
- **types** (list) - Optional - Types to filter by - python list of strings
- **compartments** (list) - Optional - Compartments - python list of strings
- **keywords** (list) - Optional - Keywords - python list of strings
- **cluster** (boolean) - Optional - Cluster results
- **start** (integer) - Optional - Start row
- **rows** (integer) - Optional - number of rows to include

### Returns
Json dictionary object
```

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

### db_version

Source: https://reactome.github.io/reactome2py/analysis.html

Retrieves the version number of the current Reactome database.

```APIDOC
## db_version

### Description
Retrieves the version number of the current Reactome database.

### Method
`reactome2py.analysis.db_version`

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

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

### export_event

Source: https://reactome.github.io/reactome2py/content.html

Exports a given pathway or reaction to the specified format (SBGN or SBML).

```APIDOC
## export_event

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

### Method Signature
`reactome2py.content.export_event(_id ='R-HSA-177929'_, _format ='sbgn'_, _file ='report'_, _path =''_)`

### Parameters
#### Path Parameters
- **id** (string) - Required - DbId or StId of the requested pathway or reaction

#### Query Parameters
- **format** (string) - Optional - sbgn or sbml
- **file** (string) - Optional - Name of file default is set to report
- **path** (string) - Optional - Absolute path to save the file

### Returns
Exports a given pathway or reaction to SBGN or SBML.
```

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

### export_reaction

Source: https://reactome.github.io/reactome2py/content.html

Exports a given reaction to the specified image format (png, jpg, jpeg, svg, gif).

```APIDOC
## export_reaction

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

### Parameters
#### Path Parameters
- **id** (string) - Required - Reaction identifier
- **ext** (string) - Required - File extension (defines the image format) available extensions: png, jpg, jpeg, svg, gif
- **file** (string) - Optional - Name of file default is set to report
- **path** (string) - Optional - Absolute path to save the file
- **quality** (integer) - Optional - Result image quality between [1 - 10]. It defines the quality of the final image (Default 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
- **sel** (list) - Optional - Highlight element(s) selection in the diagram. CSV line. comma seperate python list ex ['X', 'Y', 'Z']
- **title** (boolean) - Optional - Sets whether the name of the pathway is shown below
- **margin** (integer) - Optional - Defines the image margin between [0 - 20] (Default 15)
- **resource** (string) - Optional - The analysis resource for which the results will be overlaid on top of the given pathways overview
- **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 default is set 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

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

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

### db_version

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves the database version from the reactome2py.analysis module.

```APIDOC
## db_version()

### Description
Retrieves the database version.

### Module
reactome2py.analysis
```

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

### references

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves references from the reactome2py.content module.

```APIDOC
## references()

### Description
Retrieves references.

### Module
reactome2py.content
```

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

### token_pathway_summary

Source: https://reactome.github.io/reactome2py/analysis.html

Queries the analysis token and returns a summary of contained identifiers and interactors for a given pathway.

```APIDOC
## token_pathway_summary

### Description
Queries analysis token and returns a summary of
1. by='all': all the contained identifiers and interactors
2. by='entities': the found curated identifiers
3. by='interactors': the found interactors (may return null or none)
for a given pathway and token.

### Method
`reactome2py.analysis.token_pathway_summary`

### Parameters
* **token** (string) - Required - The token associated with the data result.
* **pathway** (string) - Required - The pathway stable identifier (stId).
* **resource** (string) - Optional - The resource to sort. Defaults to 'TOTAL'.
* **page** (string) - Optional - Page number. Defaults to '1'.
* **page_size** (string) - Optional - Page size. Defaults to '1'.
* **by** (string) - Optional - Filter found cases by: all, entities, interactors. Defaults to 'all'.

### Returns
Json dictionary object
```

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

### schema

Source: https://reactome.github.io/reactome2py/content.html

Retrieves entries from Reactome belonging to a specified schema class, with options for counting, simplified entries, or filtering by species and pagination.

```APIDOC
## schema

### Description
This method retrieves the list of entries in Reactome that belong to the specified schema class. Please take into account that if species is specified to filter the results, schema class needs to be an instance of Event or PhysicalEntity. Additionally, paging is required, while a maximum of 25 entries can be returned per request. If by is count, it counts the total number of entries. If by is min, it returns a list of simplified entries. If by is reference, it retrieves reference entities.

### Parameters
* **name** (string) - Schema class name (e.g., 'Pathway')
* **by** (string, optional) - Operation to perform: 'count', 'min', or 'reference'
* **species** (string, optional) - Species identifier (e.g., '9606')
* **page** (string, optional) - Page number for pagination, default is '-1'
* **offset** (string, optional) - Offset for pagination, default is '20000'

### Returns
Json list object or count of entries based on the 'by' parameter.
```

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

### search_diagram_instance

Source: https://reactome.github.io/reactome2py/genindex.html

Searches for diagram instances within the reactome2py.content module.

```APIDOC
## search_diagram_instance()

### Description
Searches for diagram instances.

### Module
reactome2py.content
```

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

### pathway2df

Source: https://reactome.github.io/reactome2py/analysis.html

Creates a DataFrame of the analysis results for all pathway hits and optionally saves it to a CSV file.

```APIDOC
## pathway2df

### Description
Create a Data frame of the analysis result for all the pathway hits - save to csv file (comma separated).

### 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.
- **path** (string) - Optional - Absolute path to save the file containing analysis results to.
- **resource** (string) - Optional - The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND. Defaults to 'TOTAL'.
- **file** (string) - Optional - Defaults to 'result.csv'.
- **save** (boolean) - Optional.
- **chunk_size** (integer) - Optional - Defaults to 128.
```

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

### person_name

Source: https://reactome.github.io/reactome2py/content.html

Retrieves a list of people in Reactome whose first or last name partly or exactly matches the given name.

```APIDOC
## person_name

### Description
Retrieves a list of people in Reactome with either their first or last name partly matching the given name. If exact is set to true, retrieves a list of people with matching first or last name exactly.

### Parameters
* **name** (string) - Person’s first or last name
* **exact** (boolean, optional) - If set to true, retrieves a list of people with matching first or last name exactly.

### Returns
Json list object of people with first or last name partly or exactly matching a given name (string)
```

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

### db_name

Source: https://reactome.github.io/reactome2py/analysis.html

Retrieves the name of the current Reactome database.

```APIDOC
## db_name

### Description
Retrieves the name of the current Reactome database.

### Method
`reactome2py.analysis.db_name`

### Returns
String of the name of current database.
```

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

### export_document

Source: https://reactome.github.io/reactome2py/content.html

Exports a given pathway diagram to the specified image format or generates a PDF document with event details.

```APIDOC
## export_document

### Description
Exports a given pathway diagram to the specified image format (png, jpg, jpeg, svg, gif) or generates a PDF document with event details.

### Method Signature
`reactome2py.content.export_document(_id ='R-HSA-177929'_, _level ='1'_, _diagram_profile ='Modern'_, _resource ='Total'_, _analysis_profile ='Standard'_, _token =None_, _exp_column =None_, _file ='report'_, _path =''_)`

### Parameters
#### Path Parameters
- **id** (string) - Required - Event identifier (it can be a pathway with diagram, a subpathway or a reaction)

#### Query Parameters
- **level** (string) - Optional - Number of levels to explore down in the pathways hierarchy [0 - 1]
- **diagram_profile** (string) - Optional - Diagram Color Profile: Modern or Standard
- **resource** (string) - Optional - The analysis resource for which the results will be overlaid on top of the given pathways overview
- **analysis_profile** (string) - Optional - Analysis Color Profile: Standard, Strosobar, Copper Plus
- **token** (string) - Optional - The analysis token with the results to be overlaid on top of the given diagram
- **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
- **file** (string) - Optional - Name of file default is 'report'
- **path** (string) - Optional - Absolute path to save the file to

### Returns
Exports a given pathway diagram to the specified image format (png, jpg, jpeg, svg, gif) or a PDF document with event details.
```

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

### drug_data_source

Source: https://reactome.github.io/reactome2py/utils.html

Query a list of drug-target interactions from targetome or drugcentral.

```APIDOC
## drug_data_source

### Description
Query a list of drug-target interactions from targetome or drugcentral.

### Parameters
* **release** (string) - Optional - release year for Functional Interactions (FI) data. Defaults to '2019'.
* **source** (string) - Optional - drugcentral or targetome. Defaults to 'drugcentral'.
```

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

### event_ancestors

Source: https://reactome.github.io/reactome2py/content.html

Retrieves a list of all possible paths from a given event to its top-level pathway(s). Events include pathways and reactions.

```APIDOC
## event_ancestors

### Description
Retrieves a list of all possible paths from a given event to its top-level pathway(s). Events include pathways and reactions.

### Parameters
* **id** (string) - Required - The event for which the ancestors are requested.

### Returns
Json list object of the ancestors of a given event.
```

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

### search_query

Source: https://reactome.github.io/reactome2py/genindex.html

Performs a general search query within the reactome2py.content module.

```APIDOC
## search_query()

### Description
Performs a general search query.

### Module
reactome2py.content
```

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

### compare_species

Source: https://reactome.github.io/reactome2py/genindex.html

Compares species data within the reactome2py.analysis module.

```APIDOC
## compare_species()

### Description
Compares species data.

### Module
reactome2py.analysis
```

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

### token_pathways_binned

Source: https://reactome.github.io/reactome2py/analysis.html

Returns a list of binned hit pathway sizes associated with the token.

```APIDOC
## token_pathways_binned

### Description
Returns a list of binned hit pathway sizes associated with the token.

### Method
`reactome2py.analysis.token_pathways_binned`

### Parameters
* **token** (string) - Required - The token associated with the data result.
* **resource** (string) - Optional - The resource to sort. Defaults to 'TOTAL'.
* **bin_size** (string) - Optional - Defines the size of each bin for the classification (min: 100). Defaults to '100'.
* **p_value** (string) - Optional - Defines the pValue threshold. Defaults to '1'.
* **include_disease** (boolean) - Optional - Set to ‘false’ to exclude disease pathways. Defaults to True.

### Returns
list
```

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

### export_diagram

Source: https://reactome.github.io/reactome2py/genindex.html

Exports a diagram from the reactome2py.content module.

```APIDOC
## export_diagram()

### Description
Exports a diagram.

### Module
reactome2py.content
```

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

### interactors_form

Source: https://reactome.github.io/reactome2py/content.html

Parse file and retrieve a summary associated with a token.

```APIDOC
## interactors_form

### Description
Parse file and retrieve a summary associated with a token.

### Parameters
#### Path Parameters
- **path** (string) - Required - Absolute path to file to be read with custom interactor
- **name** (string) - Required - Name which identifies the sample

### Returns

```

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

### pathway_boolean_network

Source: https://reactome.github.io/reactome2py/utils.html

Fetch Pathway as a boolean network.

```APIDOC
## pathway_boolean_network

### Description
Fetch Pathway as a boolean network.

### Parameters
* **release** (string) - Optional - release year for Functional Interactions (FI) data. Defaults to '2019'.
* **stId** (string) - Optional - stable Identifier (stID) of a pathway. Defaults to 'R-HSA-177929'.
* **pattern** (string) - Optional - reactome's stable Identifier (stID) string tag for Human "R-HSA-". Defaults to 'R-HSA-'.
```

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

### drug_data_source

Source: https://reactome.github.io/reactome2py/genindex.html

Accesses drug data sources within the reactome2py.utils module.

```APIDOC
## drug_data_source()

### Description
Accesses drug data sources.

### Module
reactome2py.utils
```

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

### search_diagram_pathway_flag

Source: https://reactome.github.io/reactome2py/genindex.html

Searches for diagrams with a pathway flag from the reactome2py.content module.

```APIDOC
## search_diagram_pathway_flag()

### Description
Searches for diagrams with a pathway flag.

### Module
reactome2py.content
```

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

### unfound_entities

Source: https://reactome.github.io/reactome2py/analysis.html

Lists unfound entities in the Reactome database for a given token, with options to save to a file.

```APIDOC
## unfound_entities

### Description
Lists unfound entities in the Reactome database.

### Parameters
* **token** (string) - Required - The token associated with the data result.
* **path** (string) - Optional - Absolute path to save the CSV file to, default is ''.
* **file** (string) - Optional - File name, default is 'result.csv'.
* **save** (boolean) - Optional - If true, saves the result data frame as a CSV file; otherwise, returns the data frame, default is False.
* **chunk_size** (integer) - Optional - Python generator iter_content() chunk size, default set to 128.

### Returns
Pandas data frame with genes or entities not found in pathway enrichment analysis overlap.
```

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

### event_species

Source: https://reactome.github.io/reactome2py/content.html

Retrieves the full event hierarchy for a given species, organized as a list of tree structures. Each event includes its stable identifier, name, species, URL, type, and diagram.

```APIDOC
## event_species

### Description
Retrieves the full event hierarchy for a given species, organized as a list of tree structures. Each event includes its stable identifier, name, species, URL, type, and diagram.

### Parameters
* **species** (string) - Optional - Species name (e.g., Homo sapiens) or species taxId (e.g., 9606).

### Returns
Json list object of the full event hierarchy for a given species.
```

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

### reactome2py.analysis.identifiers_form

Source: https://reactome.github.io/reactome2py/analysis.html

Performs Reactome pathway enrichment analysis using a file path containing a list of identifiers.

```APIDOC
## reactome2py.analysis.identifiers_form

### Description
Given a file path with a list of identifiers conducts reactome pathway enrichment analysis

### Parameters
- **path** (string) - Required - absolute path to the the txt file with identifier symbols to be analysed - refer to https://reactome.org/dev/analysis for format.
- **interactors** (boolean) - Optional - boolean value if set to false, your query will consider only manually curated Reactome pathways with known biological significance. if true, your query will consider Reactome pathways that have been expanded by including all available protein-protein interactors from the IntAct database.
- **page_size** (string) - Optional - page size
- **page** (string) - Optional - number of pages
- **species** (string) - Optional - list of species to filter the result (accepts taxonomy ids, species names and dbId)
- **sort_by** (string) - Optional - 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
- **order** (string) - Optional - order ASC or DESC
- **resource** (string) - Optional - the resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
- **p_value** (string) - Optional - defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
- **include_disease** (boolean) - Optional - set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
- **projection** (boolean) - Optional - if true, projects the identifiers to human and only shows the result in this species
- **max_entities** (None) - Optional - maximum number of contained entities per pathway (takes into account the resource)
- **min_entities** (None) - Optional - minimum number of contained entities per pathway (takes into account the resource)

### Returns
Json dictionary object
```

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

### mapping

Source: https://reactome.github.io/reactome2py/content.html

Map an identifier to pathways or reactions within a specified resource and species.

```APIDOC
## mapping

### Description
Map an identifier to pathways or reactions within a specified resource and species.

### Method
reactome2py.content.mapping(id='PTEN', resource='UniProt', species='9606', by='pathways')

### Parameters
#### Path Parameters
- **id** (string) - Optional - The identifier to be mapped
- **resource** (string) - Optional - The resource name for which the identifier is submitted
- **species** (string) - Optional - Species for which the result is filtered. Accepts taxonomy id, species name and dbId. Important Note - when identifier points to chemical, this becomes mandatory and if not provided, the default is ‘Homo sapiens’
- **by** (string) - Optional - 'pathways' or 'reactions'

### Returns
Json list object
```

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

### import_form

Source: https://reactome.github.io/reactome2py/genindex.html

Imports data from a form into the reactome2py.analysis module.

```APIDOC
## import_form()

### Description
Imports data from a form.

### Module
reactome2py.analysis
```

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

### Utils Service Functions

Source: https://reactome.github.io/reactome2py/genindex.html

Utility functions available in reactome2py.

```APIDOC
## unfound_entities()

### Description
Retrieves a list of unfound entities.

### Module
reactome2py.analysis
```

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

### query_ids

Source: https://reactome.github.io/reactome2py/genindex.html

Queries for multiple IDs from the reactome2py.content module.

```APIDOC
## query_ids()

### Description
Queries for multiple IDs.

### Module
reactome2py.content
```

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

### import_url

Source: https://reactome.github.io/reactome2py/genindex.html

Imports data from a URL into the reactome2py.analysis module.

```APIDOC
## import_url()

### Description
Imports data from a URL.

### Module
reactome2py.analysis
```

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

### interactors_psicquic_resources

Source: https://reactome.github.io/reactome2py/content.html

Retrieve a list of all active PSICQUIC registry services.

```APIDOC
## interactors_psicquic_resources

### Description
Retrieve a list of all active PSICQUIC registry services.

### Method
reactome2py.content.interactors_psicquic_resources()

### Returns
Json list object
```

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

### pathway_factor_graph

Source: https://reactome.github.io/reactome2py/utils.html

Fetch Pathway as a factor graph.

```APIDOC
## pathway_factor_graph

### Description
Fetch Pathway as a factor graph.

### Parameters
* **release** (string) - Optional - release year for Functional Interactions (FI) data. Defaults to '2019'.
* **stId** (string) - Optional - stable Identifier (stID) of a pathway. Defaults to 'R-HSA-177929'.
* **pattern** (string) - Optional - reactome's stable Identifier (stID) string tag for Human "R-HSA-". Defaults to 'R-HSA-'.
```

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

### search_facet

Source: https://reactome.github.io/reactome2py/content.html

Retrieves faceting information on the entire Reactome search data.

```APIDOC
## search_facet

### Description
This method retrieves faceting information on the whole Reactome search data.

### Returns
Json dictionary object of all facets corresponding to the whole Reactome search data
```

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

### species

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves species information from the reactome2py.content module.

```APIDOC
## species()

### Description
Retrieves species information.

### Module
reactome2py.content
```

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

### db_name

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves the database name from the reactome2py.analysis module.

```APIDOC
## db_name()

### Description
Retrieves the database name.

### Module
reactome2py.analysis
```

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

### pathways_low_entity

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves pathways with low-level entities from the reactome2py.content module.

```APIDOC
## pathways_low_entity()

### Description
Retrieves pathways with low-level entities.

### Module
reactome2py.content
```

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

### pathway_fi

Source: https://reactome.github.io/reactome2py/utils.html

Fetch Pathway's Functional Interactions (FI).

```APIDOC
## pathway_fi

### Description
Fetch Pathway's Functional Interactions (FI) https://www.ncbi.nlm.nih.gov/pubmed/20482850.

### Parameters
* **release** (string) - Optional - release year for Functional Interactions (FI) data. Defaults to '2019'.
* **stId** (string) - Optional - stable Identifier (stID) of a pathway. Defaults to 'R-HSA-177929'.
* **pattern** (string) - Optional - reactome's stable Identifier (stID) string tag for Human "R-HSA-". Defaults to 'R-HSA-'.
```

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

### interactors_psicquic_resources

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves available PSICQUIC resources for interactors from the reactome2py.content module.

```APIDOC
## interactors_psicquic_resources()

### Description
Retrieves available PSICQUIC resources for interactors.

### Module
reactome2py.content
```

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

### pathway_drug_target

Source: https://reactome.github.io/reactome2py/utils.html

Query drug-target interactions for a PhysicalEntity.

```APIDOC
## pathway_drug_target

### Description
Query drug-target interactions for a PhysicalEntity.

### Parameters
* **release** (string) - Optional - release year for Functional Interactions (FI) data. Defaults to '2019'.
* **source** (string) - Optional - drugcentral or targetome. Defaults to 'drugcentral'.
* **pdId** (string) - Optional - stable Identifier (stID) of a pathway. Defaults to '507988'.
* **pattern** (string) - Optional - reactome's stable Identifier (stID) string tag for Human "R-HSA-". Defaults to 'R-HSA-'.
```

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

### search_diagram_pathway_flag

Source: https://reactome.github.io/reactome2py/content.html

Traverses content to find flag targets by checking main identifiers and cross-references within a diagram.

```APIDOC
## search_diagram_pathway_flag

### Description
This method traverses the content and checks not only for the main identifier but also for all the cross-references to find the flag targets.

### Parameters
- **diagram** (string) - Required - diagram/pathway stable id
- **query** (string) - Required - query names by this string

### Returns
Json dictionary object of diagram entities plus pathways from the provided list containing the specified identifier
```

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

### search_diagram

Source: https://reactome.github.io/reactome2py/genindex.html

Searches for diagrams within the reactome2py.content module.

```APIDOC
## search_diagram()

### Description
Searches for diagrams.

### Module
reactome2py.content
```

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

### gene_mappings

Source: https://reactome.github.io/reactome2py/utils.html

Maps reactome pathway stId and name to its associated gene list (HGNC).

```APIDOC
## gene_mappings

### Description
Maps reactome pathway stId and name to its associated gene list (HGNC).

### Returns
dictionary of reactome pathways and HGNC gene mappings to the pathway.
```

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

### export_reaction

Source: https://reactome.github.io/reactome2py/genindex.html

Exports a reaction from the reactome2py.content module.

```APIDOC
## export_reaction()

### Description
Exports a reaction.

### Module
reactome2py.content
```

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

### species

Source: https://reactome.github.io/reactome2py/content.html

Queries species information from Reactome. Can return all species or be filtered by specific criteria.

```APIDOC
## species

### Description
Query species by:

### Parameters
- **by** (string) - Optional - 'all' returns list of all species in Reactome

### Returns
list of all species in Reactome
```

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

### entity_structures

Source: https://reactome.github.io/reactome2py/genindex.html

Retrieves entity structures from the reactome2py.content module.

```APIDOC
## entity_structures()

### Description
Retrieves entity structures.

### Module
reactome2py.content
```

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

### export_diagram

Source: https://reactome.github.io/reactome2py/content.html

Exports a diagram for a given event identifier with various customization options.

```APIDOC
## export_diagram

### Description
Exports a diagram for a given event identifier with various customization options.

### Parameters
* **id** (string) - Required - Identifier for the Event class instance.
* **ext** (string) - Optional - Extension for the exported diagram (e.g., 'png').
* **quality** (string) - Optional - Quality setting for the diagram.
* **flag_interactors** (boolean) - Optional - Flag to include interactors.
* **title** (boolean) - Optional - Whether to include a title.
* **margin** (string) - Optional - Margin around the diagram.
* **ehld** (boolean) - Optional - Flag for enhanced diagram features.
* **diagram_profile** (string) - Optional - Profile for the diagram rendering.
* **resource** (string) - Optional - Resource to use for the diagram.
* **analysis_profile** (string) - Optional - Profile for analysis rendering.
* **token** (any) - Optional - Token for authentication or specific operations.
* **flag** (any) - Optional - General flag parameter.
* **sel** (list) - Optional - Selection parameter, likely for highlighting elements.
* **exp_column** (any) - Optional - Column export parameter.
* **file** (string) - Optional - Base filename for the export.
* **path** (string) - Optional - Path for saving the exported file.
```

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

### interactors_psicquic_url

Source: https://reactome.github.io/reactome2py/content.html

Registry a custom PSICQUIC resource using its name and URL.

```APIDOC
## interactors_psicquic_url

### Description
Registry a custom PSICQUIC resource.

### Method
reactome2py.content.interactors_psicquic_url(name, psicquic_url)

### Parameters
#### Path Parameters
- **name** (string) - Required - Name which identifies the custom psicquic
- **psicquic_url** (string) - Required - A URL pointing to the Custom PSICQUIC Resource

### Returns
Registry custom PSICQUIC resource
```

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

### export_fireworks

Source: https://reactome.github.io/reactome2py/genindex.html

Exports fireworks visualization from the reactome2py.content module.

```APIDOC
## export_fireworks()

### Description
Exports fireworks visualization.

### Module
reactome2py.content
```

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

### interactors_upload_content

Source: https://reactome.github.io/reactome2py/genindex.html

Uploads content for interactor analysis from the reactome2py.content module.

```APIDOC
## interactors_upload_content()

### Description
Uploads content for interactor analysis.

### Module
reactome2py.content
```

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

### pathway2df

Source: https://reactome.github.io/reactome2py/genindex.html

Converts pathway data to a DataFrame from the reactome2py.analysis module.

```APIDOC
## pathway2df()

### Description
Converts pathway data to a DataFrame.

### Module
reactome2py.analysis
```

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

### reactome2py.analysis.token

Source: https://reactome.github.io/reactome2py/analysis.html

Retrieves analysis results associated with a token, with options for pagination, sorting, filtering by resource, and including/excluding disease pathways.

```APIDOC
## reactome2py.analysis.token

### Description
Returns the result associated with token. Use page and pageSize to reduce the amount of data retrieved. Use sortBy and order to sort the result by your preferred option. The resource field will filter the results to show only those corresponding to the preferred molecule type (TOTAL includes all the different molecules type).

### Parameters
- **token** (string) - Required - The token associated with the data result.
- **species** (string) - Optional - List of species to filter the result (accepts taxonomy ids, species names and reactome dbId) - default is 'Homo sapiens'.
- **page_size** (string) - Optional - Page size - default is '1'.
- **page** (string) - Optional - Page number - default is '1'.
- **sort_by** (string) - Optional - 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 - default is 'ENTITIES_FDR'.
- **order** (string) - Optional - Order ASC or DESC - default is 'ASC'.
- **resource** (string) - Optional - The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND.
- **p_value** (string) - Optional - Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned - default is '1'.
- **include_disease** (boolean) - Optional - Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics) - default is True.
- **min_entities** (any) - Optional - Minimum number of contained entities per pathway (takes into account the resource).
- **max_entities** (any) - Optional - Maximum number of contained entities per pathway (takes into account the resource).

### Returns
Json dictionary object.
```

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

### import_json

Source: https://reactome.github.io/reactome2py/genindex.html

Imports data from a JSON file into the reactome2py.analysis module.

```APIDOC
## import_json()

### Description
Imports data from a JSON file.

### Module
reactome2py.analysis
```

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

### token_unfound_identifiers

Source: https://reactome.github.io/reactome2py/analysis.html

Returns a list of identifiers that were not found for a given token.

```APIDOC
## token_unfound_identifiers

### Description
Returns a list of the identifiers not found for a given token.

### Parameters
* **token** (string) - Required - The token associated with the data result.
* **page_size** (string) - Optional - Page size, default is '1'.
* **page** (string) - Optional - Number of pages, default is '1'.

### Returns
list
```

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

### pathway_factor_graph

Source: https://reactome.github.io/reactome2py/genindex.html

Generates a factor graph for a pathway from the reactome2py.utils module.

```APIDOC
## pathway_factor_graph()

### Description
Generates a factor graph for a pathway.

### Module
reactome2py.utils
```