AHWikipathwaysDbs 0.99.4
AnnotationHubThe AHWikipathwaysDbs package provides the metadata for all Wikipathways
tibble databases in AnnotationHub. First we load/update the
AnnotationHub resource.
library(AnnotationHub)
ah <- AnnotationHub()Next we list all Wikipathways entries from AnnotationHub.
query(ah, "wikipathways")## AnnotationHub with 25 records
## # snapshotDate(): 2021-05-06
## # $dataprovider: WikiPathways
## # $species: Zea mays, Sus scrofa, Solanum lycopersicum, Saccharomyces cerevi...
## # $rdataclass: Tibble
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
## # rdatapath, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["AH91793"]]'
##
## title
## AH91793 | wikipathways_Anopheles_gambiae_metabolites.rda
## AH91794 | wikipathways_Arabidopsis_thaliana_metabolites.rda
## AH91795 | wikipathways_Bacillus_subtilis_metabolites.rda
## AH91796 | wikipathways_Bos_taurus_metabolites.rda
## AH91797 | wikipathways_Caenorhabditis_elegans_metabolites.rda
## ... ...
## AH91813 | wikipathways_Rattus_norvegicus_metabolites.rda
## AH91814 | wikipathways_Saccharomyces_cerevisiae_metabolites.rda
## AH91815 | wikipathways_Solanum_lycopersicum_metabolites.rda
## AH91816 | wikipathways_Sus_scrofa_metabolites.rda
## AH91817 | wikipathways_Zea_mays_metabolites.rdaWe can confirm the metadata in AnnotationHub in Bioconductor S3 bucket
with mcols().
mcols(query(ah, "wikipathways"))## DataFrame with 25 rows and 15 columns
## title dataprovider species taxonomyid
## <character> <character> <character> <integer>
## AH91793 wikipathways_Anophel.. WikiPathways Anopheles gambiae 7165
## AH91794 wikipathways_Arabido.. WikiPathways Arabidopsis thaliana 3702
## AH91795 wikipathways_Bacillu.. WikiPathways Bacillus subtilis 1423
## AH91796 wikipathways_Bos_tau.. WikiPathways Bos taurus 9913
## AH91797 wikipathways_Caenorh.. WikiPathways Caenorhabditis elegans 6239
## ... ... ... ... ...
## AH91813 wikipathways_Rattus_.. WikiPathways Rattus norvegicus 10116
## AH91814 wikipathways_Sacchar.. WikiPathways Saccharomyces cerevi.. 4932
## AH91815 wikipathways_Solanum.. WikiPathways Solanum lycopersicum 4081
## AH91816 wikipathways_Sus_scr.. WikiPathways Sus scrofa 9823
## AH91817 wikipathways_Zea_may.. WikiPathways Zea mays 4577
## genome description coordinate_1_based
## <character> <character> <integer>
## AH91793 NA Metabolite names lin.. 1
## AH91794 NA Metabolite names lin.. 1
## AH91795 NA Metabolite names lin.. 1
## AH91796 NA Metabolite names lin.. 1
## AH91797 NA Metabolite names lin.. 1
## ... ... ... ...
## AH91813 NA Metabolite names lin.. 1
## AH91814 NA Metabolite names lin.. 1
## AH91815 NA Metabolite names lin.. 1
## AH91816 NA Metabolite names lin.. 1
## AH91817 NA Metabolite names lin.. 1
## maintainer rdatadateadded preparerclass
## <character> <character> <character>
## AH91793 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91794 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91795 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91796 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91797 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## ... ... ... ...
## AH91813 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91814 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91815 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91816 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## AH91817 Kozo Nishida <kozo.n.. 2021-05-04 AHWikipathwaysDbs
## tags rdataclass rdatapath
## <list> <character> <character>
## AH91793 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91794 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91795 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91796 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91797 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## ... ... ... ...
## AH91813 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91814 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91815 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91816 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## AH91817 CAS,ChEBI,ChemSpider,... Tibble AHWikipathwaysDbs/wi..
## sourceurl sourcetype
## <character> <character>
## AH91793 https://www.wikipath.. XML
## AH91794 https://www.wikipath.. XML
## AH91795 https://www.wikipath.. XML
## AH91796 https://www.wikipath.. XML
## AH91797 https://www.wikipath.. XML
## ... ... ...
## AH91813 https://www.wikipath.. XML
## AH91814 https://www.wikipath.. XML
## AH91815 https://www.wikipath.. XML
## AH91816 https://www.wikipath.. XML
## AH91817 https://www.wikipath.. XMLWe query only the Wikipathways tibble for species Homo sapiens.
qr <- query(ah, c("wikipathways", "Homo sapiens"))
qr## AnnotationHub with 1 record
## # snapshotDate(): 2021-05-06
## # names(): AH91805
## # $dataprovider: WikiPathways
## # $species: Homo sapiens
## # $rdataclass: Tibble
## # $rdatadateadded: 2021-05-04
## # $title: wikipathways_Homo_sapiens_metabolites.rda
## # $description: Metabolite names linked to Wikipathways Homo sapiens pathway...
## # $taxonomyid: 9606
## # $genome: NA
## # $sourcetype: XML
## # $sourceurl: https://www.wikipathways.org/index.php/Download_Pathways
## # $sourcesize: NA
## # $tags: c("CAS", "ChEBI", "ChemSpider", "CustomDBSchema", "Drugbank",
## # "FunctionalAnnotation", "HMDB", "KEGG", "metabolites", "Pathways")
## # retrieve record with 'object[["AH91805"]]'There are a tibble in the result. Let’s get a tibble of it here.
hsatbl <- qr[[1]]## loading from cachehsatbl## # A tibble: 5,085 x 14
## wpid wpid_version pathway_name metabolite_name HMDB_ID KEGG_ID ChEBI_ID
## <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 WP100 107114 Glutathione m… g-L-Glutamyl-L-c… "HMDB00… C00669 17515
## 2 WP100 107114 Glutathione m… L-Cysteine "HMDB00… C00097 CHEBI:3…
## 3 WP100 107114 Glutathione m… Cysteinyl-glycine "HMDB00… C01419 4047
## 4 WP100 107114 Glutathione m… Glycine "HMDB00… C00037 CHEBI:1…
## 5 WP100 107114 Glutathione m… 5-Oxoproline "HMDB00… C01879 CHEBI:1…
## 6 WP100 107114 Glutathione m… L-Glutamate "HMDB00… C00025 CHEBI:1…
## 7 WP100 107114 Glutathione m… NADPH "HMDB00… C00005 CHEBI:1…
## 8 WP100 107114 Glutathione m… (5-L-Glutamyl)-L… "HMDB06… C03740 50619
## 9 WP100 107114 Glutathione m… R-S-Mercapturona… "" C05727 CHEBI:4…
## 10 WP100 107114 Glutathione m… L-Amino acid "" C00151 CHEBI:1…
## # … with 5,075 more rows, and 7 more variables: DrugBank_ID <chr>,
## # PubChem_CID <chr>, ChemSpider_ID <chr>, KNApSAcK_ID <chr>,
## # Wikidata_ID <chr>, CAS <chr>, InChI_Key <chr>Each row shows information for one metabolite. This tibble indicates which pathway of Wikipathways has those metabolites. Each metabolite has a the name, HMDB_ID, KEGG_ID, ChEBI_ID, DrugBank_ID, PubChem_CID, ChemSpider_ID, KNApSAcK_ID, Wikidata_ID, CAS and InChI Key as well as the pathway information to which it belongs.
To get the metabolites defined for Amino Acid metabolism we can call.
hsatbl[hsatbl$`pathway_name`=="Amino Acid metabolism", ]## # A tibble: 108 x 14
## wpid wpid_version pathway_name metabolite_name HMDB_ID KEGG_ID ChEBI_ID
## <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 WP3925 115752 Amino Acid met… Ethanol HMDB000… C00469 16236
## 2 WP3925 115752 Amino Acid met… Methionine HMDB000… C00073 16643
## 3 WP3925 115752 Amino Acid met… Indoleacetate HMDB000… C00954 16411
## 4 WP3925 115752 Amino Acid met… Aconitate HMDB000… C00417 32805
## 5 WP3925 115752 Amino Acid met… Oxaloacetate HMDB000… C00036 30744
## 6 WP3925 115752 Amino Acid met… Aspartate HMDB000… C00049 CHEBI:1…
## 7 WP3925 115752 Amino Acid met… Leucine HMDB000… C00123 CHEBI:1…
## 8 WP3925 115752 Amino Acid met… Urea HMDB000… C00086 CHEBI:1…
## 9 WP3925 115752 Amino Acid met… Fumarate HMDB000… C00122 CHEBI:1…
## 10 WP3925 115752 Amino Acid met… isocitrate HMDB000… C00311 30887
## # … with 98 more rows, and 7 more variables: DrugBank_ID <chr>,
## # PubChem_CID <chr>, ChemSpider_ID <chr>, KNApSAcK_ID <chr>,
## # Wikidata_ID <chr>, CAS <chr>, InChI_Key <chr>This section describes the automated way to create Wikipathways tibble databases using GPML XML files.
To create the databases we use the createWikipathwaysMetabolitesDb function.
This function downloads the zip archive of “Wikipathways GPML” XML files.
Then, those XMLs are integrated into a table for each species and tibbleed.
The function has no parameters. In other words, it does not have the function of making tibble only for a specific species, but makes tibble for all species in Wikipathways.
library(AHWikipathwaysDbs)
scr <- system.file("scripts/make-data.R", package = "AHWikipathwaysDbs")
source(scr)
createWikipathwaysMetabolitesDb()The tibble is stored in the rda file and saved in the current working directory.