{
"opencollection": "1.0.0",
"info": {
"name": "Pathway Analysis Service database search API",
"version": "2.0"
},
"items": [
{
"info": {
"name": "search",
"type": "folder"
},
"items": [
{
"info": {
"name": "Performs a Solr query (diagram widget scoped) for a given QueryObject",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/diagram/:diagram",
"params": [
{
"name": "diagram",
"value": "R-HSA-8848021",
"type": "path"
},
{
"name": "query",
"value": "MAD",
"type": "query"
},
{
"name": "types",
"value": "",
"type": "query",
"description": "Types to filter"
},
{
"name": "start",
"value": "",
"type": "query",
"description": "Start row"
},
{
"name": "rows",
"value": "",
"type": "query",
"description": "Number of rows to include"
},
{
"name": "scope",
"value": "",
"type": "query",
"description": "Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types"
},
{
"name": "includeInteractors",
"value": "",
"type": "query",
"description": "Whether the result should consider interactors as part of a diagram"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "Performs a Solr query (diagram widget scoped) for a given QueryObject"
},
{
"info": {
"name": "Performs a Solr query (diagram widget scoped) for a given QueryObject",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/diagram/:diagram/occurrences/:instance",
"params": [
{
"name": "diagram",
"value": "R-HSA-68886",
"type": "path"
},
{
"name": "instance",
"value": "R-HSA-141433",
"type": "path"
},
{
"name": "types",
"value": "",
"type": "query",
"description": "Types to filter"
},
{
"name": "includeInteractors",
"value": "",
"type": "query",
"description": "Whether the result should consider interactors as part of a diagram"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "Performs a Solr query (diagram widget scoped) for a given QueryObject"
},
{
"info": {
"name": "A list of diagram entities plus pathways from the provided list containing the specified identifier",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/diagram/:pathwayId/flag",
"params": [
{
"name": "pathwayId",
"value": "R-HSA-446203",
"type": "path",
"description": "The pathway to find items to flag"
},
{
"name": "query",
"value": "CTSA",
"type": "query",
"description": "The identifier for the elements to be flagged"
},
{
"name": "includeInteractors",
"value": "",
"type": "query",
"description": "Whether the result should consider interactors as part of a diagram"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "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"
},
{
"info": {
"name": "A list of facets corresponding to the whole Reactome search data",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/facet",
"params": [
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "This method retrieves faceting information on the whole Reactome search data."
},
{
"info": {
"name": "A list of facets corresponding to a specific query",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/facet_query",
"params": [
{
"name": "query",
"value": "TP53",
"type": "query",
"description": "Search term"
},
{
"name": "species",
"value": "",
"type": "query",
"description": "Species name"
},
{
"name": "types",
"value": "",
"type": "query",
"description": "Types to filter"
},
{
"name": "compartments",
"value": "",
"type": "query",
"description": "Compartments to filter"
},
{
"name": "keywords",
"value": "",
"type": "query",
"description": "Keywords"
},
{
"name": "scope",
"value": "",
"type": "query",
"description": "Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types"
},
{
"name": "Force filters",
"value": "",
"type": "query",
"description": "Force filters
In case where applied filters yield to no results, filters are removed by default to grant results as much as possible. Set Force filters to true to avoid this behaviour"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "This method retrieves faceting information on a specific query"
},
{
"info": {
"name": "Performs a Solr query (fireworks widget scoped) for a given QueryObject",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/fireworks",
"params": [
{
"name": "query",
"value": "BRAF",
"type": "query"
},
{
"name": "species",
"value": "Homo sapiens",
"type": "query",
"description": "Species name"
},
{
"name": "types",
"value": "",
"type": "query",
"description": "Types to filter"
},
{
"name": "start",
"value": "",
"type": "query",
"description": "Start row"
},
{
"name": "scope",
"value": "",
"type": "query",
"description": "Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types"
},
{
"name": "includeInteractors",
"value": "",
"type": "query",
"description": "Whether the result should consider interactors as part of a diagram"
},
{
"name": "rows",
"value": "",
"type": "query",
"description": "Number of rows to include"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "Performs a Solr query (fireworks widget scoped) for a given QueryObject"
},
{
"info": {
"name": "Performs a Solr query (fireworks widget scoped) for a given QueryObject",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/fireworks/flag",
"params": [
{
"name": "query",
"value": "KNTC1",
"type": "query"
},
{
"name": "species",
"value": "",
"type": "query"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "Performs a Solr query (fireworks widget scoped) for a given QueryObject"
},
{
"info": {
"name": "Find the different pathways containing a specific entity determined by its dbId. Can customise the output using fields",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/pathways/of/:dbId",
"params": [
{
"name": "dbId",
"value": "227785",
"type": "path"
},
{
"name": "includeInteractors",
"value": "",
"type": "query",
"description": "Whether the result should consider interactors as part of a diagram"
},
{
"name": "directlyInDiagram",
"value": "",
"type": "query",
"description": "Whether the result should exclude higher level diagrams containing pathways, themselves containing the targeted entity"
},
{
"name": "species",
"value": "Homo sapiens",
"type": "query",
"description": "Species name to filter results for"
},
{
"name": "fields",
"value": "",
"type": "query",
"description": "Fields to include in the response. If empty, retrieves all field available (not recommended)"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "Find the different pathways containing a specific entity determined by its dbId. Can customise the output using fields"
},
{
"info": {
"name": "Queries Solr against the Reactome knowledgebase",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/query",
"params": [
{
"name": "query",
"value": "Biological oxidations",
"type": "query",
"description": "Search term"
},
{
"name": "species",
"value": "",
"type": "query",
"description": "Species name"
},
{
"name": "types",
"value": "",
"type": "query",
"description": "Types to filter"
},
{
"name": "compartments",
"value": "",
"type": "query",
"description": "Compartments to filter"
},
{
"name": "keywords",
"value": "",
"type": "query",
"description": "Keywords"
},
{
"name": "cluster",
"value": "true",
"type": "query",
"description": "Cluster results"
},
{
"name": "parserType",
"value": "STD",
"type": "query",
"description": "Query parser to use"
},
{
"name": "Start row",
"value": "0",
"type": "query",
"description": "Start row"
},
{
"name": "rows",
"value": "10",
"type": "query",
"description": "Number of rows to include"
},
{
"name": "scope",
"value": "",
"type": "query",
"description": "Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types"
},
{
"name": "Force filters",
"value": "",
"type": "query",
"description": "Force filters
In case where applied filters yield to no results, filters are removed by default to grant results as much as possible. Set Force filters to true to avoid this behaviour"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "This method performs a Solr query on the Reactome knowledgebase. Results can be provided in a paginated format."
},
{
"info": {
"name": "Queries Solr against the Reactome knowledgebase",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/query/paginated",
"params": [
{
"name": "query",
"value": "Biological oxidations",
"type": "query",
"description": "Search term"
},
{
"name": "page",
"value": "1",
"type": "query",
"description": "Page, should be strictly positive"
},
{
"name": "rowCount",
"value": "10",
"type": "query",
"description": "Rows per page"
},
{
"name": "species",
"value": "",
"type": "query",
"description": "Species name"
},
{
"name": "types",
"value": "",
"type": "query",
"description": "Types to filter"
},
{
"name": "compartments",
"value": "",
"type": "query",
"description": "Compartments to filter"
},
{
"name": "keywords",
"value": "",
"type": "query",
"description": "Keywords"
},
{
"name": "cluster",
"value": "true",
"type": "query",
"description": "Cluster results"
},
{
"name": "scope",
"value": "",
"type": "query",
"description": "Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types"
},
{
"name": "parserType",
"value": "STD",
"type": "query",
"description": "Query parser to use"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "This method performs a Solr query on the Reactome knowledgebase. Results are in a paginated format, pages count starting from 1."
},
{
"info": {
"name": "Spell-check suggestions for a given query",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/spellcheck",
"params": [
{
"name": "query",
"value": "repoduction",
"type": "query",
"description": "Search term"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "This method retrieves a list of spell-check suggestions for a given search term."
},
{
"info": {
"name": "Auto-suggestions for a given query",
"type": "http"
},
"http": {
"method": "GET",
"url": "/AnalysisService/search/suggest",
"params": [
{
"name": "query",
"value": "platele",
"type": "query",
"description": "Search term"
},
{
"name": "view",
"value": "",
"type": "query",
"description": "Global parameter - Customise the view to be more concise and/or aggregate relationships"
},
{
"name": "includeRef",
"value": "",
"type": "query",
"description": "Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}"
}
]
},
"docs": "This method retrieves a list of suggestions for a given search term."
}
]
}
],
"bundled": true
}