Find Pathways By Xref — findPathwaysByXref • rWikiPathways
Description: Retrieve pathways containing the query Xref by identifier and system code.

# Find Pathways By Xref

Source: `R/findPathwaysByXref.R`
`findPathwaysByXref.Rd`

Retrieve pathways containing the query Xref by identifier and system code.

    findPathwaysByXref(identifier, systemCode)

## Arguments

identifier | (`character`) The official ID specified by a data source or system
systemCode | (`character`) The BridgeDb code associated with the data source or system, e.g., En (Ensembl), L (Entrez), Ch (HMDB), etc. See column two of https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.bio/src/main/resources/org/bridgedb/bio/datasources.tsv.

## Value

A `dataframe` of pathway attributes in addition to query result score

## Details

Note: there will be multiple listings of the same pathway if the Xref is present mutiple times.

The score is from a lucene index search engine, ranging from 0 to 1 with higher scores for better matches.

## Examples

    {
    findPathwaysByXref('ENSG00000232810','En')
    }
    #>         score     id                                                   url
    #>  1: 0.3951413 WP3893 https://www.wikipathways.org/index.php/Pathway:WP3893
    #>  2: 0.3951413 WP2882 https://www.wikipathways.org/index.php/Pathway:WP2882
    #>  3: 0.3951413 WP1584 https://www.wikipathways.org/index.php/Pathway:WP1584
    #>  4: 0.3951413 WP2431 https://www.wikipathways.org/index.php/Pathway:WP2431
    #>  5: 0.3951413 WP4673 https://www.wikipathways.org/index.php/Pathway:WP4673
    #>  6: 0.3951413 WP2059 https://www.wikipathways.org/index.php/Pathway:WP2059
    #>  7: 0.3951413 WP3599 https://www.wikipathways.org/index.php/Pathway:WP3599
    #>  8: 0.3951413 WP3863 https://www.wikipathways.org/index.php/Pathway:WP3863
    #>  9: 0.3951413 WP4008 https://www.wikipathways.org/index.php/Pathway:WP4008
    #> 10: 0.3951413 WP3865 https://www.wikipathways.org/index.php/Pathway:WP3865
    #> 11: 0.3951413 WP3624 https://www.wikipathways.org/index.php/Pathway:WP3624
    #> 12: 0.3951413 WP4341 https://www.wikipathways.org/index.php/Pathway:WP4341
    #> 13: 0.3951413 WP4298 https://www.wikipathways.org/index.php/Pathway:WP4298
    #> 14: 0.3951413 WP4666 https://www.wikipathways.org/index.php/Pathway:WP4666
    #> 15: 0.3951413 WP3941 https://www.wikipathways.org/index.php/Pathway:WP3941
    #> 16: 0.3951413 WP2813 https://www.wikipathways.org/index.php/Pathway:WP2813
    #> 17: 0.3951413  WP262  https://www.wikipathways.org/index.php/Pathway:WP262
    #> 18: 0.3951413 WP2873 https://www.wikipathways.org/index.php/Pathway:WP2873
    #> 19: 0.3951413 WP2571 https://www.wikipathways.org/index.php/Pathway:WP2571
    #> 20: 0.3951413 WP4329 https://www.wikipathways.org/index.php/Pathway:WP4329
    #> 21: 0.3951413 WP4136 https://www.wikipathways.org/index.php/Pathway:WP4136
    #> 22: 0.3951413 WP4864 https://www.wikipathways.org/index.php/Pathway:WP4864
    #> 23: 0.3951413 WP3287 https://www.wikipathways.org/index.php/Pathway:WP3287
    #> 24: 0.3951413 WP4066 https://www.wikipathways.org/index.php/Pathway:WP4066
    #> 25: 0.3951413 WP4063 https://www.wikipathways.org/index.php/Pathway:WP4063
    #> 26: 0.3951413 WP4969 https://www.wikipathways.org/index.php/Pathway:WP4969
    #> 27: 0.2794071 WP2795 https://www.wikipathways.org/index.php/Pathway:WP2795
    #> 28: 0.2794071 WP4847 https://www.wikipathways.org/index.php/Pathway:WP4847
    #> 29: 0.2794071  WP129  https://www.wikipathways.org/index.php/Pathway:WP129
    #> 30: 0.2794071  WP314  https://www.wikipathways.org/index.php/Pathway:WP314
    #> 31: 0.2794071 WP2513 https://www.wikipathways.org/index.php/Pathway:WP2513
    #> 32: 0.2794071 WP1449 https://www.wikipathways.org/index.php/Pathway:WP1449
    #> 33: 0.2794071 WP4481 https://www.wikipathways.org/index.php/Pathway:WP4481
    #> 34: 0.2794071 WP1544 https://www.wikipathways.org/index.php/Pathway:WP1544
    #> 35: 0.2794071 WP4482 https://www.wikipathways.org/index.php/Pathway:WP4482
    #> 36: 0.2794071 WP3297 https://www.wikipathways.org/index.php/Pathway:WP3297
    #> 37: 0.2794071  WP530  https://www.wikipathways.org/index.php/Pathway:WP530
    #> 38: 0.2794071 WP4891 https://www.wikipathways.org/index.php/Pathway:WP4891
    #> 39: 0.2794071  WP236  https://www.wikipathways.org/index.php/Pathway:WP236
    #> 40: 0.2794071 WP4747 https://www.wikipathways.org/index.php/Pathway:WP4747
    #> 41: 0.2794071  WP176  https://www.wikipathways.org/index.php/Pathway:WP176
    #> 42: 0.2794071  WP727  https://www.wikipathways.org/index.php/Pathway:WP727
    #> 43: 0.2794071 WP4496 https://www.wikipathways.org/index.php/Pathway:WP4496
    #> 44: 0.2794071  WP254  https://www.wikipathways.org/index.php/Pathway:WP254
    #> 45: 0.2794071 WP1533 https://www.wikipathways.org/index.php/Pathway:WP1533
    #> 46: 0.2794071   WP75   https://www.wikipathways.org/index.php/Pathway:WP75
    #> 47: 0.2794071 WP4478 https://www.wikipathways.org/index.php/Pathway:WP4478
    #> 48: 0.2794071 WP2328 https://www.wikipathways.org/index.php/Pathway:WP2328
    #> 49: 0.2794071 WP3851 https://www.wikipathways.org/index.php/Pathway:WP3851
    #> 50: 0.2794071  WP231  https://www.wikipathways.org/index.php/Pathway:WP231
    #> 51: 0.2794071 WP3617 https://www.wikipathways.org/index.php/Pathway:WP3617
    #> 52: 0.2794071 WP2036 https://www.wikipathways.org/index.php/Pathway:WP2036
    #> 53: 0.2794071 WP3611 https://www.wikipathways.org/index.php/Pathway:WP3611
    #> 54: 0.2794071  WP560  https://www.wikipathways.org/index.php/Pathway:WP560
    #> 55: 0.2794071 WP4816 https://www.wikipathways.org/index.php/Pathway:WP4816
    #> 56: 0.2794071 WP2864 https://www.wikipathways.org/index.php/Pathway:WP2864
    #> 57: 0.2794071 WP4304 https://www.wikipathways.org/index.php/Pathway:WP4304
    #> 58: 0.2794071 WP4857 https://www.wikipathways.org/index.php/Pathway:WP4857
    #> 59: 0.2794071   WP15   https://www.wikipathways.org/index.php/Pathway:WP15
    #> 60: 0.2794071 WP2586 https://www.wikipathways.org/index.php/Pathway:WP2586
    #> 61: 0.2794071 WP4493 https://www.wikipathways.org/index.php/Pathway:WP4493
    #> 62: 0.2794071 WP4396 https://www.wikipathways.org/index.php/Pathway:WP4396
    #> 63: 0.2794071 WP4480 https://www.wikipathways.org/index.php/Pathway:WP4480
    #> 64: 0.2794071  WP706  https://www.wikipathways.org/index.php/Pathway:WP706
    #> 65: 0.2794071 WP2447 https://www.wikipathways.org/index.php/Pathway:WP2447
    #> 66: 0.2794071  WP382  https://www.wikipathways.org/index.php/Pathway:WP382
    #> 67: 0.2794071 WP5044 https://www.wikipathways.org/index.php/Pathway:WP5044
    #> 68: 0.2794071 WP2751 https://www.wikipathways.org/index.php/Pathway:WP2751
    #> 69: 0.2794071 WP3380 https://www.wikipathways.org/index.php/Pathway:WP3380
    #> 70: 0.2794071 WP3398 https://www.wikipathways.org/index.php/Pathway:WP3398
    #> 71: 0.2794071 WP4066 https://www.wikipathways.org/index.php/Pathway:WP4066
    #> 72: 0.2794071 WP4063 https://www.wikipathways.org/index.php/Pathway:WP4063
    #> 73: 0.2794071 WP4754 https://www.wikipathways.org/index.php/Pathway:WP4754
    #> 74: 0.2794071 WP5039 https://www.wikipathways.org/index.php/Pathway:WP5039
    #>         score     id                                                   url
    #>                                                                                        name
    #>  1:                                         Development and heterogeneity of the ILC family
    #>  2:                                                          Nuclear Receptors Meta-Pathway
    #>  3:                                                               Type II diabetes mellitus
    #>  4:                                                                      Spinal Cord Injury
    #>  5:                                                      Genes involved in male infertility
    #>  6:                                                                      Alzheimers Disease
    #>  7:                                         Transcription factor regulation in adipogenesis
    #>  8:            T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection
    #>  9:                                                    NO/cGMP/PKG mediated Neuroprotection
    #> 10:                     Novel intracellular components of RIG-I-like receptor (RLR) pathway
    #> 11:                                                                           Lung fibrosis
    #> 12:                                         Non-genomic actions of 1,25 dihydroxyvitamin D3
    #> 13:                                                                 Viral Acute Myocarditis
    #> 14:                                                                   Hepatitis B infection
    #> 15:                                                                        Oxidative Damage
    #> 16:                Mammary gland development pathway - Embryonic development (Stage 1 of 4)
    #> 17:                                                                      EBV LMP1 signaling
    #> 18:                                                       Aryl Hydrocarbon Receptor Pathway
    #> 19:                                                       Polycystic Kidney Disease Pathway
    #> 20:                                     miRNAs involvement in the immune response in sepsis
    #> 21:                                          Fibrin Complement Receptor 3 Signaling Pathway
    #> 22:                           Host-pathogen interaction of human corona viruses - apoptosis
    #> 23:                                                        Overview of nanoparticle effects
    #> 24:                                              Interleukin-4 and Interleukin-13 signaling
    #> 25:                                                                Interleukin-10 signaling
    #> 26:                                                 RAS and Bradykinin pathways in COVID-19
    #> 27:                                                           Cardiac Hypertrophic Response
    #> 28:                                                                   AXL signaling pathway
    #> 29:                                                               Matrix Metalloproteinases
    #> 30:  Fas Ligand (FasL) pathway and Stress induction of Heat Shock Proteins (HSP) regulation
    #> 31:                                               Nanoparticle triggered regulated necrosis
    #> 32:                                      Regulation of toll-like receptor signaling pathway
    #> 33:                                                 Resistin as a regulator of inflammation
    #> 34:                                                  MicroRNAs in cardiomyocyte hypertrophy
    #> 35:                                                      Vitamin D in inflammatory diseases
    #> 36:                              EV release from cardiac cells and their functional effects
    #> 37:                                                     Cytokines and Inflammatory Response
    #> 38:                                                        COVID-19 Adverse Outcome Pathway
    #> 39:                                                                            Adipogenesis
    #> 40:                                                          Netrin-UNC5B signaling Pathway
    #> 41:                                                                       Folate Metabolism
    #> 42:                                                                     Monoamine Transport
    #> 43:                                                        Signal transduction through IL1R
    #> 44:                                                                               Apoptosis
    #> 45:                                                                  Vitamin B12 Metabolism
    #> 46:                                                    Toll-like Receptor Signaling Pathway
    #> 47:                                                      LTF danger signal response pathway
    #> 48:                                                                     Allograft Rejection
    #> 49:                                                            TLR4 Signaling and Tolerance
    #> 50:                                                             TNF alpha Signaling Pathway
    #> 51:                                   Photodynamic therapy-induced NF-kB survival signaling
    #> 52:                         TNF related weak inducer of apoptosis (TWEAK) Signaling Pathway
    #> 53:                                   Photodynamic therapy-induced AP-1 survival signaling.
    #> 54:                                                             TGF-beta Receptor Signaling
    #> 55:                                     TGF-beta Receptor Signalling in Skeletal Dysplasias
    #> 56:                       Apoptosis-related network due to altered Notch3 in ovarian cancer
    #> 57: Oligodendrocyte specification and differentiation, leading to Myelin Components for CNS
    #> 58:                                                                      Endothelin Pathway
    #> 59:                                                          Selenium Micronutrient Network
    #> 60:                                                       Aryl Hydrocarbon Receptor Netpath
    #> 61:                      Cells and Molecules involved in local acute inflammatory response
    #> 62:                                                        Nonalcoholic fatty liver disease
    #> 63:                        Role of Altered Glycolysation of MUC1 in Tumour Microenvironment
    #> 64:                             Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways
    #> 65:                                                     Amyotrophic lateral sclerosis (ALS)
    #> 66:                                                                  MAPK Signaling Pathway
    #> 67:                                     Kynurenine Pathway and links to Cellular Senescence
    #> 68:                           Transcriptional regulation of white adipocyte differentiation
    #> 69:                                                                           TNF signaling
    #> 70:                                                       TNFR2 non-canonical NF-kB pathway
    #> 71:                                              Interleukin-4 and Interleukin-13 signaling
    #> 72:                                                                Interleukin-10 signaling
    #> 73:                                                                 IL-18 signaling pathway
    #> 74:                    SARS-CoV-2 Innate Immunity Evasion and Cell-specific immune response
    #>                                                                                        name
    #>          species revision
    #>  1: Homo sapiens   106386
    #>  2: Homo sapiens   103038
    #>  3: Homo sapiens   111210
    #>  4: Homo sapiens   106712
    #>  5: Homo sapiens   106810
    #>  6: Homo sapiens   108233
    #>  7: Homo sapiens   105845
    #>  8: Homo sapiens   106753
    #>  9: Homo sapiens   110707
    #> 10: Homo sapiens   106524
    #> 11: Homo sapiens   110182
    #> 12: Homo sapiens   107169
    #> 13: Homo sapiens   110705
    #> 14: Homo sapiens   107486
    #> 15: Homo sapiens   106568
    #> 16: Homo sapiens   102405
    #> 17: Homo sapiens   106391
    #> 18: Homo sapiens   106304
    #> 19: Homo sapiens   108308
    #> 20: Homo sapiens   101725
    #> 21: Homo sapiens   106418
    #> 22: Homo sapiens   113801
    #> 23: Homo sapiens   113822
    #> 24: Homo sapiens   115055
    #> 25: Homo sapiens   115095
    #> 26: Homo sapiens   115143
    #> 27: Homo sapiens   106724
    #> 28: Homo sapiens   111812
    #> 29: Homo sapiens   106640
    #> 30: Homo sapiens   109375
    #> 31: Homo sapiens   110691
    #> 32: Homo sapiens   106494
    #> 33: Homo sapiens   102529
    #> 34: Homo sapiens   108800
    #> 35: Homo sapiens   112969
    #> 36: Homo sapiens   106734
    #> 37: Homo sapiens   111164
    #> 38: Homo sapiens   111616
    #> 39: Homo sapiens   105873
    #> 40: Homo sapiens   108877
    #> 41: Homo sapiens   107123
    #> 42: Homo sapiens   107191
    #> 43: Homo sapiens   102693
    #> 44: Homo sapiens   106302
    #> 45: Homo sapiens   107121
    #> 46: Homo sapiens   111250
    #> 47: Homo sapiens   103756
    #> 48: Homo sapiens   106557
    #> 49: Homo sapiens   105835
    #> 50: Homo sapiens   111053
    #> 51: Homo sapiens   106541
    #> 52: Homo sapiens   105837
    #> 53: Homo sapiens    90923
    #> 54: Homo sapiens   106477
    #> 55: Homo sapiens   111739
    #> 56: Homo sapiens   108133
    #> 57: Homo sapiens   112156
    #> 58: Homo sapiens   111629
    #> 59: Homo sapiens   107118
    #> 60: Homo sapiens   107439
    #> 61: Homo sapiens   102660
    #> 62: Homo sapiens    98945
    #> 63: Homo sapiens   107458
    #> 64: Homo sapiens   113813
    #> 65: Homo sapiens   113794
    #> 66: Homo sapiens   113991
    #> 67: Homo sapiens   114613
    #> 68: Homo sapiens   114880
    #> 69: Homo sapiens   114940
    #> 70: Homo sapiens   115048
    #> 71: Homo sapiens   115055
    #> 72: Homo sapiens   115095
    #> 73: Homo sapiens   115147
    #> 74: Homo sapiens   115153
    #>          species revision