searchPc: Search Pathway Commons

Description

This command provides a text search using the Lucene query syntax.

Usage

searchPc(q, page = 0, datasource = NULL, organism = NULL, type = NULL,
  verbose = FALSE)

Arguments

a keyword, name, external identifier, or a Lucene query string.

page

an integer giving the search result page number (N>=0, default: 0)

datasource

a vector that is a filter by data source (use names or URIs of pathway data sources or of any existing Provenance object). If multiple data source values are specified, a union of hits from specified sources is returned. For example, datasource as c("reactome", "pid") returns hits associated with Reactome or PID.

organism

a vector that is an organism filter. The organism can be specified either by official name, e.g. "homo sapiens" or by NCBI taxonomy id, e.g. "9606". Similar to data sources, if multiple organisms are declared a union of all hits from specified organisms is returned. For example organism as c("9606", "10016") returns results for both human and mice. Only humans, "9606" is officially supported.

type

BioPAX class filter. See Details.

verbose

a boolean, display the command used to query Pathway Commons

Value

an XMLInternalDocument with results

concept

paxtoolsr

Details

Indexed fields were selected based on most common searches. Some of these fields are direct BioPAX properties, others are composite relationships. All index fields are (case-sensitive):comment, ecnumber, keyword, name, pathway, term, xrefdb, xrefid, dataSource, and organism. The pathway field maps to all participants of pathways that contain the keyword(s) in any of its text fields. This field is transitive in the sense that participants of all sub-pathways are also returned. Finally, keyword is a transitive aggregate field that includes all searchable keywords of that element and its child elements - e.g. a complex would be returned by a keyword search if one of its members has a match. Keyword is the default field type. All searches can also be filtered by data source and organism. It is also possible to restrict the domain class using the 'type' parameter. This query can be used standalone or to retrieve starting points for graph searches. Search strings are case insensitive unless put inside quotes.

BioPAX classes can be found at http://www.pathwaycommons.org/pc2/#biopax_types

Examples

Run this code

query <- "Q06609"
#results <- searchPc(query)

query <- "glycolysis"
#results <- searchPc(query, type="Pathway")

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