Last updated: 2020-04-20
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In this section we will introduce you the SPARQL endpoint from Bgee. You are able to use the sparql endpoint from Bgee in R to retrieve all information from the database.
library(SPARQL)
library(stringr)
library(data.table)The Bgee SPARQL endpoint is accessible in a stable manner through the stable URL address.
sparqlEndPoint <- "https://bgee.org/sparql14_1"Using the sparql endpoint from Bgee you are able to retrieve information about each species by specifying the respective uniprot taxon.
species_taxon <- "PREFIX up: <http://purl.uniprot.org/core/>
SELECT * {
?species a up:Taxon .
?species up:scientificName ?name .
?species up:rank up:Species .
}"
species_taxonTable <- unique(SPARQL(url=sparqlEndPoint, species_taxon)$results)
paste0("Number of the species present in Bgee database: ", nrow(species_taxonTable))[1] "Number of the species present in Bgee database: 29"As a recommendation and for forward analysis you maybe should clean the first row of the table.
species_taxonTable$species <- sub('<http://purl.uniprot.org/taxonomy/(\\d+).*', '\\1', species_taxonTable$species)
head(species_taxonTable) species name
1 10090 Mus musculus
9 10116 Rattus norvegicus
17 10141 Cavia porcellus
25 13616 Monodelphis domestica
33 28377 Anolis carolinensis
41 6239 Caenorhabditis elegansTo show you how to query particular data from species, genes or anatomical entitites, in this section we will use information collected from the TopAnat analysis, so this means we will use Bus taurus as a specie target.
You can retrieve data by specifying your target species and the target developmental stage by retrieving all anatomic entities. Here we will use as example the Bus taurus (cattle) and as developmental stage the ‘prime adult stage’.
anatEnt_devStage <- "PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT DISTINCT ?anatName FROM <https://bgee.org/rdf_v14_1> {
?cond genex:hasAnatomicalEntity ?anatEntity .
?anatEntity rdfs:label ?anatName .
?cond genex:hasDevelopmentalStage ?stage .
?stage rdfs:label ?stageName .
?cond obo:RO_0002162 ?taxon .
?taxon up:commonName ?commonName .
FILTER ( LCASE(?commonName) = LCASE('cattle')).
FILTER ( CONTAINS(?stageName, 'prime adult stage'))
}"
anatEnt_devStageTable <- SPARQL(url=sparqlEndPoint, anatEnt_devStage)
print(paste0("Number of anatomical entities found: ", length(anatEnt_devStageTable$results)))[1] "Number of anatomical entities found: 319"Now using one of the statistical significant genes from TopAnat you should be able to retrieve all anatomical entites in Bgee. For that you should specify in your query the target species and the target gene.
anatEnt_gene_species <- "PREFIX orth: <http://purl.org/net/orth#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX genex: <http://purl.org/genex#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX lscr: <http://purl.org/lscr#>
PREFIX dct: <http://purl.org/dc/terms/>
SELECT DISTINCT ?anatEntity ?anatName FROM <https://bgee.org/rdf_v14_1> {
values ?ensembl_gene { <http://rdf.ebi.ac.uk/resource/ensembl/ENSBTAG00000005333> }
?seq a orth:Gene .
?seq lscr:xrefEnsemblGene ?ensembl_gene.
?seq rdfs:label ?geneName .
?seq genex:isExpressedIn ?cond .
?cond genex:hasAnatomicalEntity ?anatEntity .
?anatEntity rdfs:label ?anatName .
?cond obo:RO_0002162 <http://purl.uniprot.org/taxonomy/9913> .
}"
anatEnt_gene_speciesTable <- SPARQL(url=sparqlEndPoint, anatEnt_gene_species)
print(paste0("Number of anatomical entities: ", length(anatEnt_gene_speciesTable$results$anatEntity)))[1] "Number of anatomical entities: 13"print(unique(anatEnt_gene_speciesTable$results$anatEntity)) [1] "<http://purl.obolibrary.org/obo/UBERON_0000082>"
[2] "<http://purl.obolibrary.org/obo/UBERON_0000451>"
[3] "<http://purl.obolibrary.org/obo/UBERON_0000948>"
[4] "<http://purl.obolibrary.org/obo/UBERON_0000955>"
[5] "<http://purl.obolibrary.org/obo/UBERON_0001111>"
[6] "<http://purl.obolibrary.org/obo/UBERON_0001134>"
[7] "<http://purl.obolibrary.org/obo/UBERON_0001155>"
[8] "<http://purl.obolibrary.org/obo/UBERON_0002048>"
[9] "<http://purl.obolibrary.org/obo/UBERON_0002106>"
[10] "<http://purl.obolibrary.org/obo/UBERON_0001295>"
[11] "<http://purl.obolibrary.org/obo/UBERON_0001401>"
[12] "<http://purl.obolibrary.org/obo/UBERON_0002000>"
[13] "<http://purl.obolibrary.org/obo/UBERON_0034908>"Use the genes to target description and species.
Target the genes that have muscle as a term condiction, from this verify if the gene “ENSBTAG00000014614” was detected. Note that this genes was statistically significant in the TopAnat analysis.
genes_muscles <- "PREFIX up: <http://purl.uniprot.org/core/>
PREFIX orth: <http://purl.org/net/orth#>
PREFIX dcterms: <http://purl.org/dc/terms/>
SELECT ?geneName ?geneId FROM <https://bgee.org/rdf_v14_1> {
?gene a orth:Gene .
?gene rdfs:label ?geneName .
?gene dcterms:identifier ?geneId .
?gene dcterms:description ?desc .
FILTER CONTAINS ( ?desc, 'muscle' )
}"
genes_musclesTable <- SPARQL(url=sparqlEndPoint, genes_muscles)
## gene just in Bus taurus
genes_musclesTable$results[genes_musclesTable$results$geneId %like% "ENSBTAG", ] geneName geneId
28 PYGM ENSBTAG00000001032
29 MUSK ENSBTAG00000002744
30 MYH7B ENSBTAG00000003512
31 ACTC1 ENSBTAG00000005714
32 MYH2 ENSBTAG00000007090
33 MYH8 ENSBTAG00000009702
34 MYH7 ENSBTAG00000009703
35 ANKRD1 ENSBTAG00000011734
36 CAPZA3 ENSBTAG00000013207
37 CKM ENSBTAG00000013921
38 MBNL3 ENSBTAG00000014088
39 PERM1 ENSBTAG00000014540
40 SMPX ENSBTAG00000015204
41 MYLPF ENSBTAG00000021218
42 MURC ENSBTAG00000021992
43 ENSBTAG00000030186
44 MYH4 ENSBTAG00000037794
45 ACTA1 ENSBTAG00000046332
453 PFKM ENSBTAG00000000286
454 ATP2A2 ENSBTAG00000001398
455 MRAS ENSBTAG00000001497
456 PKM ENSBTAG00000001601
457 ATP5A1 ENSBTAG00000002507
458 MYH14 ENSBTAG00000002580
459 CAPZA2 ENSBTAG00000004072
460 CAPZB ENSBTAG00000004554
461 MBNL1 ENSBTAG00000004564
462 ENO3 ENSBTAG00000005534
463 ACYP2 ENSBTAG00000006852
464 GEM ENSBTAG00000007596
465 PHKG1 ENSBTAG00000008195
466 ENSBTAG00000009713
467 CNN1 ENSBTAG00000011207
468 PAMR1 ENSBTAG00000012630
469 ANKRD2 ENSBTAG00000012720
470 CAPZA1 ENSBTAG00000014295
471 MYLK ENSBTAG00000014567
472 ACTA2 ENSBTAG00000014614
473 COX7A1 ENSBTAG00000014878
474 CFL2 ENSBTAG00000015053
475 ACTG2 ENSBTAG00000015441
476 PHKA1 ENSBTAG00000015848
477 FABP3 ENSBTAG00000016819
478 MBNL2 ENSBTAG00000018313
479 MYH10 ENSBTAG00000021151
480 LMOD1 ENSBTAG00000021576Verify if the geneId “ENSBTAG00000014614” with gene name ACTA2 is also present in others species.
gene_present_species <- "PREFIX up: <http://purl.uniprot.org/core/>
PREFIX orth: <http://purl.org/net/orth#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT ?name FROM <https://bgee.org/rdf_v14_1> {
?gene a orth:Gene .
?gene rdfs:label ?geneName .
?gene orth:organism ?organism . #orth v2
?organism obo:RO_0002162 ?taxon . #label: in taxon .
?taxon up:scientificName ?name .
FILTER ( UCASE(?geneName) = UCASE('ACTA2') )
}"
gene_present_speciesTable <- SPARQL(url=sparqlEndPoint, gene_present_species)
print(paste0("Number of species detected: ",length(gene_present_speciesTable$results)))[1] "Number of species detected: 18"t(gene_present_speciesTable$results) [,1]
name "Danio rerio"
name.1 "Homo sapiens"
name.2 "Mus musculus"
name.3 "Rattus norvegicus"
name.4 "Sus scrofa"
name.5 "Xenopus tropicalis"
name.6 "Anolis carolinensis"
name.7 "Bos taurus"
name.8 "Canis lupus familiaris"
name.9 "Cavia porcellus"
name.10 "Equus caballus"
name.11 "Erinaceus europaeus"
name.12 "Felis catus"
name.13 "Ornithorhynchus anatinus"
name.14 "Oryctolagus cuniculus"
name.15 "Gorilla gorilla"
name.16 "Macaca mulatta"
name.17 "Monodelphis domestica"
sessionInfo()R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.12.8 stringr_1.4.0 SPARQL_1.16 RCurl_1.98-1.1
[5] XML_3.99-0.3 workflowr_1.6.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4.6 knitr_1.28 whisker_0.4 magrittr_1.5
[5] R6_2.4.1 rlang_0.4.5 tools_3.6.0 xfun_0.13
[9] git2r_0.26.1 htmltools_0.4.0 yaml_2.2.1 digest_0.6.25
[13] rprojroot_1.3-2 later_1.0.0 promises_1.1.0 fs_1.4.1
[17] bitops_1.0-6 glue_1.4.0 evaluate_0.14 rmarkdown_2.1
[21] stringi_1.4.6 compiler_3.6.0 backports_1.1.6 httpuv_1.5.2