Find Pathways By Literature — findPathwaysByLiterature • rWikiPathways
Description: Retrieve a list of pathways containing the query citation.

# Find Pathways By Literature

Source: `R/findPathwaysByLiterature.R`
`findPathwaysByLiterature.Rd`

Retrieve a list of pathways containing the query citation.

    findPathwaysByLiterature(query)

## Arguments

query | The `character` string to search for, e.g., a PMID, title keyword or author name.

## Value

A `list` of lists

## Examples

    {
    findPathwaysByLiterature('19649250')
    findPathwaysByLiterature('smith')
    findPathwaysByLiterature('cancer')
    }#> $`https://www.wikipathways.org/index.php/Pathway:WP4055`
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$score
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$score$`0`
    #> [1] "0.87241286"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$graphId
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$graphId$name
    #> [1] "graphId"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$graphId$values
    #> [1] "b1394"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$literature.pubmed
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$literature.pubmed$name
    #> [1] "literature.pubmed"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$literature.pubmed$values
    #> [1] "27798111"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$literature.title
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$literature.title$name
    #> [1] "literature.title"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$fields$literature.title$values
    #> [1] "The RING finger domain E3 ubiquitin ligases BRCA1 and the RNF20/RNF40 complex in global loss of the chromatin mark histone H2B monoubiquitination (H2Bub1) in cell line models and primary high-grade serous ovarian cancer."
    #>
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$id
    #> [1] "WP4055"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$url
    #> [1] "https://www.wikipathways.org/index.php/Pathway:WP4055"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$name
    #> [1] "E3 ubiquitin ligases ubiquitinate target proteins"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$species
    #> [1] "Homo sapiens"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP4055`$revision
    #> [1] "101599"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$score
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$score$`0`
    #> [1] "0.84895813"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$name
    #> [1] "graphId"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`0`
    #> [1] "fff85"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`1`
    #> [1] "f7745"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`2`
    #> [1] "f519f"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`3`
    #> [1] "e09f5"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`4`
    #> [1] "cf0c6"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`5`
    #> [1] "ab5ff"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`6`
    #> [1] "a40f0"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`7`
    #> [1] "d44c2"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`8`
    #> [1] "ca530"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`9`
    #> [1] "bdd39"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`10`
    #> [1] "a8cd5"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`12`
    #> [1] "ce11a"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`13`
    #> [1] "fba10"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`14`
    #> [1] "fab99"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`15`
    #> [1] "f929e"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`16`
    #> [1] "d5687"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`17`
    #> [1] "d4406"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`18`
    #> [1] "c9d1d"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`19`
    #> [1] "a2421"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`20`
    #> [1] "be903"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`21`
    #> [1] "f1834"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`22`
    #> [1] "dc24f"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`23`
    #> [1] "af130"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`24`
    #> [1] "df835"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$graphId$values$`25`
    #> [1] "bc131"
    #>
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$name
    #> [1] "literature.pubmed"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`0`
    #> [1] "21160078"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`2`
    #> [1] "15116089"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`3`
    #> [1] "24850843"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`4`
    #> [1] "17496923"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`5`
    #> [1] "11389083"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`6`
    #> [1] "17699850"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`7`
    #> [1] "20179196"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`8`
    #> [1] "21666749"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`9`
    #> [1] "16140923"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`10`
    #> [1] "18056464"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`11`
    #> [1] "20094046"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`12`
    #> [1] "19874848"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`13`
    #> [1] "21367659"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`14`
    #> [1] "21711248"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`15`
    #> [1] "12068308"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`16`
    #> [1] "17227708"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.pubmed$values$`17`
    #> [1] "18772890"
    #>
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$name
    #> [1] "literature.title"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`0`
    #> [1] "Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`2`
    #> [1] "Blocking of FGFR signaling inhibits breast cancer cell proliferation through downregulation of D-type cyclins."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`3`
    #> [1] "FGFR1/3 tyrosine kinase fusions define a unique molecular subtype of non-small cell lung cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`4`
    #> [1] "Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`5`
    #> [1] "High-throughput tissue microarray analysis of 3p25 (RAF1) and 8p12 (FGFR1) copy number alterations in urinary bladder cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`6`
    #> [1] "High-resolution single nucleotide polymorphism array analysis of epithelial ovarian cancer reveals numerous microdeletions and amplifications."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`7`
    #> [1] "FGFR1 amplification drives endocrine therapy resistance and is a therapeutic target in breast cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`8`
    #> [1] "Inhibitor-sensitive FGFR1 amplification in human non-small cell lung cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`9`
    #> [1] "Somatic mutations of the protein kinase gene family in human lung cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`10`
    #> [1] "Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`11`
    #> [1] "Fibroblast growth factor signalling: from development to cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`12`
    #> [1] "De-regulated FGF receptors as therapeutic targets in cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`13`
    #> [1] "Targeting mutant fibroblast growth factor receptors in cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`14`
    #> [1] "Fibroblast growth factors and their receptors in cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`15`
    #> [1] "Mutations of the BRAF gene in human cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`16`
    #> [1] "The role of Shp2 (PTPN11) in cancer."
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$fields$literature.title$values$`17`
    #> [1] "Comprehensive genomic characterization defines human glioblastoma genes and core pathways."
    #>
    #>
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$id
    #> [1] "WP3335"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$url
    #> [1] "https://www.wikipathways.org/index.php/Pathway:WP3335"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$name
    #> [1] "Signaling by FGFR1"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$species
    #> [1] "Homo sapiens"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP3335`$revision
    #> [1] "101309"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$score
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$score$`0`
    #> [1] "0.3762009"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$fields
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$fields$literature.pubmed
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$fields$literature.pubmed$name
    #> [1] "literature.pubmed"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$fields$literature.pubmed$values
    #> [1] "12893990"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$fields$literature.title
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$fields$literature.title$name
    #> [1] "literature.title"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$fields$literature.title$values
    #> [1] "UGT pharmacogenomics: implications for cancer risk and cancer therapeutics."
    #>
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$id
    #> [1] "WP961"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$url
    #> [1] "https://www.wikipathways.org/index.php/Pathway:WP961"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$name
    #> [1] "Irinotecan Pathway"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$species
    #> [1] "Pan troglodytes"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP961`$revision
    #> [1] "93193"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$score
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$score$`0`
    #> [1] "0.3762009"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$graphId
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$graphId$name
    #> [1] "graphId"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$graphId$values
    #> [1] "d6a1f" "a4c48" "b2ae0"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$literature.pubmed
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$literature.pubmed$name
    #> [1] "literature.pubmed"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$literature.pubmed$values
    #> [1] "12810652" "12730278" "12893990"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$literature.title
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$literature.title$name
    #> [1] "literature.title"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$fields$literature.title$values
    #> [1] "Differential effects of the breast cancer resistance protein on the cellular accumulation and cytotoxicity of 9-aminocamptothecin and 9-nitrocamptothecin."
    #> [2] "Functional characterization of human UDP-glucuronosyltransferase 1A9 variant, D256N, found in Japanese cancer patients."
    #> [3] "UGT pharmacogenomics: implications for cancer risk and cancer therapeutics."
    #>
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$id
    #> [1] "WP1080"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$url
    #> [1] "https://www.wikipathways.org/index.php/Pathway:WP1080"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$name
    #> [1] "Irinotecan Pathway"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$species
    #> [1] "Bos taurus"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP1080`$revision
    #> [1] "101977"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$score
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$score$`0`
    #> [1] "0.3762009"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$fields
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$fields$literature.pubmed
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$fields$literature.pubmed$name
    #> [1] "literature.pubmed"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$fields$literature.pubmed$values
    #> [1] "12893990"
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$fields$literature.title
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$fields$literature.title$name
    #> [1] "literature.title"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$fields$literature.title$values
    #> [1] "UGT pharmacogenomics: implications for cancer risk and cancer therapeutics."
    #>
    #>
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$id
    #> [1] "WP124"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$url
    #> [1] "https://www.wikipathways.org/index.php/Pathway:WP124"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$name
    #> [1] "Irinotecan Pathway"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$species
    #> [1] "Rattus norvegicus"
    #>
    #> $`https://www.wikipathways.org/index.php/Pathway:WP124`$revision
    #> [1] "93209"
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