Content Service¶

Content Service for Reactome knowledgebase. API calls are avaialble @ https://reactome.org/ContentService/#/

Data model key classes for id query are available @ https://reactome.org/documentation/data-model

reactome2py.content.discover(id='R-HSA-446203')¶

For each event (reaction or pathway) this method generates a json representing the dataset object as defined by schema.org (http). This is mainly used by search engines in order to index the data

Parameters: id -- An event identifier ex. pathway stable identifier (stId) of pathway
Returns: Json dictionary object of The schema.org for an Event in Reactome knowledgebase

reactome2py.content.disease(doid=False)¶

Query list of diseases

if doid is set to False
- it retrieves the list of diseases annotated in Reactome
if doid is set to True
- it retrieves the list of disease DOIDs annotated in Reactome

Parameters: doid -- Boolean param, if set to true - function returns a list of disease DOID
Returns: Json list object of diseases or disease DOID(s)

reactome2py.content.entities_complex(id='R-HSA-5674003', exclude_structures=False)¶

Retrieves the list of subunits that constitute any given complex. In case the complex comprises other complexes, this method recursively traverses the content returning each contained PhysicalEntity. Contained complexes and entity sets can be excluded setting the ‘exclude_structures’ optional parameter to ‘true’

Parameters

id -- The complex for which subunits are requested
exclude_structures -- Specifies whether contained complexes and entity sets are excluded in the response

Returns

Json list object with the entities contained in a given complex

reactome2py.content.entities_complexes(id='P00533', resource='UniProt')¶

Retrieves the list of complexes that contain a given (identifier, resource). The method deconstructs the complexes into all its participants to do so.

Parameters

id -- The resource's identifier for which complexes are requested
resource -- The resource of the identifier for complexes are requested

Returns

Json list object of complexes containing the pair (identifier, resource)

reactome2py.content.entity_other_form(id='R-HSA-199420')¶

Retrieves a list containing all other forms of the given PhysicalEntity. These other forms are PhysicalEntities that share the same ReferenceEntity identifier, ex. PTEN H93R[R-HSA-2318524] and PTEN C124R[R-HSA-2317439] are two forms of PTEN.

Parameters: id -- dbId or stId of a PhysicalEntity
Returns: Json list object

reactome2py.content.entity_structures(id='R-HSA-199420')¶

Retrieves the list of structures (Complexes and Sets) that include the given entity as their component. It should be mentioned that the list includes only simplified entries (type, names, ids) and not full information about each item.

Parameters: id -- stable Identifier (stID) of a PhysicalEntity ex. PTEN [cytosol] R-HSA-199420'
Returns: Json list object of larger structures containing the entity

reactome2py.content.event_ancestors(id='R-HSA-5673001')¶

The Reactome definition of events includes pathways and reactions. Although events are organised in a hierarchical structure, a single event can be in more than one location, i.e. a reaction can take part in different pathways while, in the same way, a sub-pathway can take part in many pathways. Therefore, this method retrieves a list of all possible paths from the requested event to the top level pathway(s).

Parameters: id -- The event for which the ancestors are requested
Returns: Json list object of the ancestors of a given event

reactome2py.content.event_species(species='9606')¶

Events (pathways and reactions) in Reactome are organised in a hierarchical structure for every species. By following all ‘hasEvent’ relationships, this method retrieves the full event hierarchy for any given species. The result is a list of tree structures, one for each TopLevelPathway. Every event in these trees is represented by a PathwayBrowserNode. The latter contains the stable identifier, the name, the species, the url, the type, and the diagram of the particular event.

Parameters: species -- Species name (ex: Homo sapiens) or species taxId (ex: 9606)
Returns: Json list object of the full event hierarchy for a given species

reactome2py.content.export_diagram(id='R-HSA-177929', ext='png', quality='5', flag_interactors=False, title=True, margin='15', ehld=True, diagram_profile='Modern', resource='Total', analysis_profile='Standard', token=None, flag=None, sel=[], exp_column=None, file='report', path='')¶

This method accepts identifiers for Event class instances.

When a diagrammed pathway is provided, the diagram is exported to the specified format.
When a subpathway is provided, the diagram for the parent is exported and the events that are part of the subpathways are selected.
When a reaction is provided, the diagram containing the reaction is exported and the reaction is selected.

Parameters

id -- Event identifier (it can be a pathway with diagram, a subpathway or a reaction)
ext -- File extension (defines the image format) available extensions: png, jpg, jpeg, svg, gif
quality -- Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)
flag -- Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
flag_interactors -- Defines whether to take into account interactors for the flagging default set to False
sel -- Highlight element(s) selection in the diagram. CSV line. comma seperate python list ex ['X', 'Y', 'Z']
token -- The analysis token with the results to be overlaid on top of the given diagram
title -- Sets whether the name of the pathway is shown as title
margin -- Defines the image margin between [0 - 20] (Default 15)
ehld -- Defines whether textbook-like illustration are taken into account
diagram_profile -- Diagram Color Profile: Modern or Standard
resource -- The analysis resource for which the results will be overlaid on top of the given pathways overview
exp_column -- Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay
analysis_profile -- Analysis Color Profile: Standard, Strosobar, Copper Plus
file -- Name of file default is 'report'
path -- Absolute path to save the file to

Returns

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

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='')¶

This method accepts identifiers for Event class instances. The generated document contains the details for the given event and, optionally, its children (see level parameter).

These details include:

A diagram image
Summation
Literature references
Edit history
Other details: type, location, compartments, diseases

Documents can also be overlaid with pathway analysis results (given a token)

Parameters

id -- Event identifier (it can be a pathway with diagram, a subpathway or a reaction)
level -- Number of levels to explore down in the pathways hierarchy [0 - 1]
diagram_profile -- Diagram Color Profile Modern or Standard
resource -- The analysis resource for which the results will be overlaid on top of the given pathways overview
analysis_profile -- Analysis Color Profile: Standard, Strosobar, Copper Plus
token -- The analysis token with the results to be overlaid on top of the given diagram
exp_column -- Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay
file -- Name of file default is 'report'
path -- Absolute path to save the file to

Returns

Exports the content of a given event (pathway or reaction) to a PDF document

reactome2py.content.export_event(id='R-HSA-177929', format='sbgn', file='report', path='')¶

Exports a given pathway or reaction to the format requested:

Systems Biology Graphical Notation (SBGN)
Systems Biology Markup Language (SBML)

Parameters

id -- DbId or StId of the requested pathway or reaction
format -- sbgn or sbml
file -- Name of file default is set to report
path -- Absolute path to save the file

Returns

Exports a given pathway or reaction to SBGN

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)¶

Exports a given pathway overview to the specified image format (png, jpg, jpeg, svg, gif) https://reactome.org/dev/pathways-overview/js

Parameters

species -- Species identifier (it can be the taxonomy id, species name or dbId)
ext -- File extension (defines the image format) available extensions: png, jpg, jpeg, svg, gif
file -- Name of file default is set to report
path -- Absolute path to save the file
quality -- Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)
flag -- Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
flag_interactors -- Defines whether to take into account interactors for the flagging
sel -- Highlight element(s) selection in the diagram. CSV line. comma seperate python list ex ['X', 'Y', 'Z']
title -- Sets whether the name of the pathway is shown below
margin -- Defines the image margin between [0 - 20] (Default 15)
resource -- The analysis resource for which the results will be overlaid on top of the given pathways overview
diagram_profile -- Diagram Color Profile available in: Copper, Copper plus, Barium lithium, Calcium salts
coverage -- Set to ‘true’ to overlay analysis coverage values default is set to false
token -- The analysis token with the results to be overlaid on top of the given pathways overview
exp_column -- 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)

reactome2py.content.export_reaction(id='R-HSA-6787403', 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)¶

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

Parameters

id -- Reaction identifier
ext -- File extension (defines the image format) available extensions: png, jpg, jpeg, svg, gif
file -- Name of file default is set to report
path -- Absolute path to save the file
quality -- Result image quality between [1 - 10]. It defines the quality of the final image (Default 5)
flag -- Gene name, protein or chemical identifier or Reactome identifier used to flag elements in the diagram
flag_interactors -- Defines whether to take into account interactors for the flagging
sel -- Highlight element(s) selection in the diagram. CSV line. comma seperate python list ex ['X', 'Y', 'Z']
title -- Sets whether the name of the pathway is shown below
margin -- Defines the image margin between [0 - 20] (Default 15)
resource -- The analysis resource for which the results will be overlaid on top of the given pathways overview
diagram_profile -- Diagram Color Profile available in: Copper, Copper plus, Barium lithium, Calcium salts
coverage -- Set to ‘true’ to overlay analysis coverage values default is set to false
token -- The analysis token with the results to be overlaid on top of the given pathways overview
exp_column -- Expression column. When the token is associated to an expression analysis, this parameter allows specifying the expression column for the overlay

Returns

reactome2py.content.interactors_acc_pathways(acc='Q9BXM7-1', species='Homo sapiens', only_diagrammed=False)¶

Retrieve a list of lower level pathways where the interacting molecules can be found

Parameters

acc -- Accession
species -- The species name for which the pathways are requested (e.g. ‘Homo sapiens’)
only_diagrammed -- Specifies whether the pathways has to have an associated diagram or not

Returns

Json list object

reactome2py.content.interactors_form(path, name)¶

Parse file and retrieve a summary associated with a token

Parameters

path -- Absolute path to file to be read with custom interactor
name -- Name which identifies the sample

Returns

reactome2py.content.interactors_psicquic_acc(resource='MINT', acc='Q13501', by='details')¶

if by details
- Retrieve clustered interaction, sorted by score, of a given accession by resource
if by summary
- Retrieve a summary of a given accession by resource

Parameters

resource -- Proteomics standards initiative common query interface (PSICQUIC) Resource use interactors_psicquic_resources to retrive all active resources
acc -- Single Accession
by -- details or summary (returns counts of details available)

Returns

Json dictionary object

reactome2py.content.interactors_psicquic_accs(proteins='EGFR', resource='MINT', by='details')¶

if by details
- Retrieve clustered interaction, sorted by score, of a given accession(s) by resource.
if by summary
- Retrieve a summary of a given accession list by resource.

Parameters

proteins -- Comma seperate list of Accessions in string format 'a1,a2,a3'
resource -- Proteomics standards initiative common query interface (PSICQUIC) Resource use interactors_psicquic_resources to retrive all active resources

Returns

Json dictionary object

reactome2py.content.interactors_psicquic_resources()¶

Retrieve a list of all Psicquic Registries services

Returns: Json list object

reactome2py.content.interactors_psicquic_url(name, psicquic_url)¶

Registry custom PSICQUIC resource

Parameters

name -- Name which identifies the custom psicquic
psicquic_url -- A URL pointing to the Custom PSICQUIC Resource

Returns

Registry custom PSICQUIC resource

reactome2py.content.interactors_static_acc(acc='Q13501', page='-1', page_size='-1', by='details')¶

if by details:
- retrieve a detailed interaction information of a given accession
if by summary:
- retrieve a summary of a given accession

Parameters

acc -- Interactor accession (or identifier)
page -- For paginating the results
page_size -- Number of results to be retrieved
by -- details or summary (returns counts of details available)

Returns

Json dictionary object

reactome2py.content.interactors_static_accs(accs='Q9BXM7-1', by='details', page='-1', page_size='-1')¶

if by details:
- Retrieve clustered interaction, sorted by score, of a given accession(s) by resource.
if by summary:
- Retrieve a summary of a given accession list by resource.

Parameters

accs -- Comma seperate list of Accessions in string format 'a1,a2,a3'
by -- details or summary (returns counts of details available)
page -- For paginating the results
page_size -- Number of results to be retrieved

Returns

Json dictionary object

reactome2py.content.interactors_upload_content(name, content)¶

Paste file content and get a summary associated with a token

Parameters

name -- Name which identifies the sample
content -- Paste custom interactors file content

Returns

Paste file content and get a summary associated with a token

reactome2py.content.interactors_url(name, interactors_url)¶

Send file via URL and get a summary associated with a token

Parameters

name -- Name which identifies the sample
interactors_url -- A URL pointing to the Interactors file

Returns

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

by pathways:
Entities play different roles in reactions, and reactions are events that conform a pathway. This method retrieves the pathways for which an identifier plays a role within one or more of their events. return: The lower level pathways where an identifier can be mapped to
by reactions:
Entities play different roles in reactions. This method retrieves the reactions for which an identifier plays a role . return: The reactions where an identifier can be mapped to

Parameters

id -- The identifier to be mapped
resource -- The resource name for which the identifier is submitted
species -- 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 -- pathways or reactions

Returns

Json list object

reactome2py.content.orthology(id='R-HSA-6799198', species='49633')¶

Reactome uses the set of manually curated human reactions to computationally infer reactions in twenty evolutionarily divergent eukaryotic species for which high-quality whole-genome sequence data are available, and hence a comprehensive and high-quality set of protein predictions exists. Thus, this method retrieves the orthology for any given event or entity in the specified species.

Parameters

id -- The event for which the orthology is requested
species -- The species id for which the orthology is requested

Returns

Json dictionary object of the orthology for a given event or entity

reactome2py.content.orthology_events(ids='R-HSA-6799198,R-HSA-168256,R-HSA-168249', species='49633')¶

Reactome uses the set of manually curated human reactions to computationally infer reactions in twenty evolutionarily divergent eukaryotic species for which high-quality whole-genome sequence data are available, and hence a comprehensive and high-quality set of protein predictions exists. Thus, this method retrieves the orthologies for any given set of events or entities in the specified species.

Parameters

ids -- The events identifiers for which the orthology is requested
species -- The species id for which the orthology is requested

Returns

Json dictionary object of the orthologies of a given set of events or entities

reactome2py.content.participants(id='5205685')¶

Participants contains a PhysicalEntity (dbId, displayName) and a collection of ReferenceEntities (dbId, name, identifier, url)

Parameters: id -- dbId or stId of a PhysicalEntity
Returns: Json list obj of participants for a given event

reactome2py.content.participants_physical_entities(id='R-HSA-5205685')¶

This method retrieves all the PhysicalEntities that take part in a given event. It is worth mentioning that because a pathway can contain smaller pathways (subpathways), the method also recursively retrieves the PhysicalEntities from every constituent

Parameters: id -- The event for which the participating PhysicalEntities are requested
Returns: Json list object of participating PhysicalEntities for a given event

reactome2py.content.participants_reference_entities(id='5205685')¶

PhysicalEntity instances that represent, e.g., the same chemical in different compartments, or different post-translationally modified forms of a single protein, share numerous invariant features such as names, molecular structure and links to external databases like UniProt or ChEBI. To enable storage of this shared information in a single place, and to create an explicit link among all the variant forms of what can also be seen as a single chemical entity, Reactome creates instances of the separate ReferenceEntity class. A ReferenceEntity instance captures the invariant features of a molecule. This method retrieves the ReferenceEntities of all PhysicalEntities that take part in a given event. It is worth mentioning that because a pathway can contain smaller pathways (subpathways), this method also recursively retrieves the ReferenceEntities for all PhysicalEntities in every constituent pathway.

Parameters: id -- The event for which the participating ReferenceEntities are requested
Returns: Json list object of participating ReferenceEntities for a given event

reactome2py.content.pathway_contained_event(id='R-HSA-5673001')¶

Events are the building blocks used in Reactome to represent all biological processes, and they include pathways and reactions. Typically, an event can contain other events. For example, a pathway can contain smaller pathways and reactions. This method recursively retrieves all the events contained in any given event.

Parameters: id -- The event for which the contained events are requested
Returns: Json list object of all the events contained in the given event

reactome2py.content.pathway_contained_event_atttibute(id='R-HSA-5673001', attribute='stId')¶

Events are the building blocks used in Reactome to represent all biological processes, and they include pathways and reactions. Typically, an event can contain other events. For example, a pathway can contain smaller pathways (subpathways) and reactions. This method recursively retrieves a single attribute for each of the events contained in the given event.

Parameters

id -- The event for which the contained events are requested
attribute -- Attribute to be filtered

Returns

List object of a single property for each event contained in the given event

reactome2py.content.pathways_low_diagram(id='R-HSA-199420', species=None, all_forms=False)¶

This method traverses the event hierarchy and retrieves the list of all lower level pathways that have a diagram and contain the given PhysicalEntity or Event.

if all_forms is set to true: it retrieves the given PhysicalEntity in any of its variant forms. These variant forms include for example different post-translationally modified versions of a single protein, or the same chemical in different compartments.

Parameters

id -- The entity that has to be present in the pathways
species -- The species for which the pathways are requested. Taxonomy identifier (eg: 9606) or species name (eg: ‘Homo sapiens’)
all_forms -- If true, it retrieves the given PhysicalEntity in any of its variant forms.

Returns

Json list object of lower level pathways with diagram containing a given entity or event

reactome2py.content.pathways_low_entity(id='R-HSA-199420', species=None, all_forms=False)¶

This method traverses the event hierarchy and retrieves the list of all lower level pathways that contain the given PhysicalEntity or Event.

if all_forms is set to true, it retrieves the list of all lower level pathways that contain the given PhysicalEntity in any of its variant forms. These variant forms include for example different post-translationally modified versions of a single protein, or the same chemical in different compartments.

Parameters

id -- The entity that has to be present in the pathways
species -- The species for which the pathways are requested. Taxonomy identifier (eg: 9606) or species name (eg: ‘Homo sapiens’)
all_forms -- If set to true, it retrieves the list of all lower level pathways that contain the given PhysicalEntity in any of its variant forms.

Returns

Json list object of lower level pathways containing a given entity or event

reactome2py.content.pathways_top_level(species='9606')¶

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

Parameters: species -- 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

reactome2py.content.person_id(id='0000-0001-5807-0069', by=None, attribute=None)¶

With only id parameter declared,
- Retrieves a person in Reactome by his/her OrcidId or DbId.
With id and query by declared with pathway or publication
- Retrieves a list of pathways authored by a given person. OrcidId, DbId or Email can be used to specify the person.
- Retrieves a list of publications authored by a given person. OrcidId, DbId or Email can be used to specify the person.
With id and attribute declared
- Retrieves a specific person’s property by his/her OrcidId or DbId.

Parameters

id -- Person identifier - Can be OrcidId or DbId
by -- if not None, query by authored: pathways or publications
attribute -- Attribute to be filtered ex. displayName

Returns

Json dictionary object

reactome2py.content.person_name(name='Steve Jupe', exact=False)¶

Retrieves a list of people in Reactome with either their first or last name partly matching the given name (string).

If exact is set to true, retrieves a list of people in Reactome with either their first or last name matching exactly the given name (string).

Parameters

name -- Person’s first or last name
exact --

Returns

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

reactome2py.content.query_id(id='R-HSA-60140', enhanced=False, attribute=None)¶

This method queries for an entry in Reactome knowledgebase based on the given identifier, i.e. stable id or database id. It is worth mentioning that the retrieved database object has all its properties and direct relationships (relationships of depth 1) filled.

if enhanced is set to true it also includes any second level relationships regarding regulations and catalysts.
if attribute name is present it queries the property of the attribute requested

Parameters

id -- DbId or StId of the requested database object
enhanced -- boolean value to make an enhanced query on id
attribute -- Attribute to be queried

Returns

Json dictionary object

reactome2py.content.query_ids(ids='R-HSA-60140', mapping=False)¶

This method queries for a set of entries in Reactome knowledgebase based on the given list of identifiers. The provided list of identifiers can include stable ids, database ids or a mixture of both. It should be underlined that any duplicated ids are eliminated while only requests containing up to 20 ids are processed.

if mapping is set, to true previous version of stable identifiers can be queried.

Parameters

ids -- A comma separated list of identifiers
mapping -- If set to true, retrieves a list of entries with their mapping to the provided identifiers

Returns

Json list object

reactome2py.content.references(id='15377')¶

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

Parameters: id -- Identifier for a given entity
Returns: Json list obkect of all ReferenceEntities for a given identifier

reactome2py.content.schema(name='Pathway', by='count', species='9606', page='-1', offset='20000')¶

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:
- counts the total number of entries in Reactome that belong to the specified schema class.
if by is min:
- the list of simplified entries in Reactome that belong to the specified schema class. A simplified entry may be considered as a minimised version of the full database object that includes its database id, stable id, displayName and type.
if by is reference:
- the list of simplified reference objects that belong to the specified schema class. A reference object includes its database id, external identifier, and external database name. ex. name='ReferenceMolecule'

Parameters

name -- Schema class name.
by -- if not None, by count, min, or reference (name needs to an instance of ReferenceEntity or ExternalOntology)
species -- Allowed species filter: SpeciesName (eg: Homo sapiens) SpeciesTaxId (eg: 9606)
offset -- Number of rows returned. Maximum = 25
page -- Page to be returned

Returns

int if by = count, json list if by = min or reference

reactome2py.content.search_diagram(diagram='R-HSA-8848021', query='MAD', types=[], start=None, rows=None)¶

Performs a Apache Solr query (diagram widget scoped) for a given QueryObject

Parameters

diagram -- diagram/pathway stable id
query -- query names by this string
types -- types to filter
start -- start row
rows -- number of rows to include

Returns

Json dictionary object

reactome2py.content.search_diagram_instance(diagram='R-HSA-68886', instance='R-HSA-141433', types=[])¶

Performs a Apache Solr query (diagram widget scoped) for a given QueryObject

Parameters

diagram -- diagram/pathway stable id
instance -- instance stable id
types -- types to filter

Returns

Json dictionary object

reactome2py.content.search_diagram_pathway_flag(diagram='R-HSA-446203', query='CTSA')¶

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 -- diagram/pathway stable id
query -- query names by this string

Returns

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

reactome2py.content.search_facet()¶

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

reactome2py.content.search_facet_query(query='TP53', species=[], types=[], compartments=[], keywords=[])¶

This method retrieves faceting information on a specific query

Parameters

query -- search term
species -- Species identifier (it can be the taxonomy id, species name or dbId) - python list of strings
types -- types to filter by - python list of strings
compartments -- compartments - python list of strings
keywords -- keywords - python list of strings

Returns

Json dictionary object

reactome2py.content.search_fireworks(query='BRAF', species='Homo sapiens', types=[], start=None, rows=None)¶

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

Parameters

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

Returns

Json dictionary object

reactome2py.content.search_fireworks_flag(query='KNTC1', species='Homo sapiens')¶

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

Parameters

query -- Search term
species -- Species identifier (it can be the taxonomy id, species name or dbId)

Returns

Json dictionary object

reactome2py.content.search_query(query='Biological oxidations', species=[], types=[], compartments=[], keywords=[], cluster=True, start=None, rows=None)¶

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

Parameters

query -- term to search
species -- list of species - python list of strings
types -- Types to filter by - python list of strings
compartments -- Compartments - python list of strings
keywords -- Keywords - python list of strings
cluster -- Cluster results
start -- Start row
rows -- number of rows to include

Returns

Json dictionary object

reactome2py.content.search_spellcheck(query='repoduction')¶

This method retrieves a list of spell-check suggestions for a given search term.

Parameters: query -- term to search
Returns: list of matched elements

reactome2py.content.search_suggest(query='platele')¶

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

Parameters: query -- term to search
Returns: list of matched elements

reactome2py.content.species(by='all')¶

Query species by:

all, returns list of all species in Reactome
main, return list of main species in Reactome

Parameters: by -- all or main
Returns: Json list object

reactome2py.content.token_interactors(token, proteins)¶

Retrieve custom interactions associated with a token

Parameters

token -- A token associated with a data submission
proteins -- Interactors accessions

Returns

Retrieve custom interactions associated with a token

Content Service¶

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