search

alabarga / biohackathon-jp-2023

biohackathon-jp-2023
GNU General Public License v3.0
0 stars 0 forks source link

Create knowledge graph for multiomics #1

Open alabarga opened 1 year ago

alabarga commented 1 year ago
alabarga commented 1 year ago 
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX vg: <http://biohackathon.org/resource/vg#>
PREFIX uniprotkb: <http://purl.uniprot.org/uniprot/>
PREFIX uberon: <http://purl.obolibrary.org/obo/uo#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX sp: <http://spinrdf.org/sp#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX sh: <http://www.w3.org/ns/shacl#>
PREFIX schema: <http://schema.org/>
PREFIX sachem: <http://bioinfo.uochb.cas.cz/rdf/v1.0/sachem#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
PREFIX patent: <http://data.epo.org/linked-data/def/patent/>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX orthodbGroup: <http://purl.orthodb.org/odbgroup/>
PREFIX orthodb: <http://purl.orthodb.org/>
PREFIX orth: <http://purl.org/net/orth#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX np: <http://nextprot.org/rdf#>
PREFIX nextprot: <http://nextprot.org/rdf/entry/>
PREFIX mnx: <https://rdf.metanetx.org/schema/>
PREFIX mnet: <https://rdf.metanetx.org/mnet/>
PREFIX mesh: <http://id.nlm.nih.gov/mesh/>
PREFIX lscr: <http://purl.org/lscr#>
PREFIX lipidmaps: <https://www.lipidmaps.org/rdf/>
PREFIX keywords: <http://purl.uniprot.org/keywords/>
PREFIX insdcschema: <http://ddbj.nig.ac.jp/ontologies/nucleotide/>
PREFIX insdc: <http://identifiers.org/insdc/>
PREFIX identifiers: <http://identifiers.org/>
PREFIX glyconnect: <https://purl.org/glyconnect/>
PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
PREFIX genex: <http://purl.org/genex#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX eunisSpecies: <http://eunis.eea.europa.eu/rdf/species-schema.rdf#>
PREFIX ensembltranscript: <http://rdf.ebi.ac.uk/resource/ensembl.transcript/>
PREFIX ensemblterms: <http://rdf.ebi.ac.uk/terms/ensembl/>
PREFIX ensemblprotein: <http://rdf.ebi.ac.uk/resource/ensembl.protein/>
PREFIX ensemblexon: <http://rdf.ebi.ac.uk/resource/ensembl.exon/>
PREFIX ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/>
PREFIX ec: <http://purl.uniprot.org/enzyme/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dc: <http://purl.org/dc/terms/>
PREFIX chebislash: <http://purl.obolibrary.org/obo/chebi/>
PREFIX chebihash: <http://purl.obolibrary.org/obo/chebi#>
PREFIX cco: <http://rdf.ebi.ac.uk/terms/chembl#>
PREFIX busco: <http://busco.ezlab.org/schema#>
PREFIX bibo: <http://purl.org/ontology/bibo/>
PREFIX allie: <http://allie.dbcls.jp/>
PREFIX SWISSLIPID: <https://swisslipids.org/rdf/SLM_>
PREFIX GO: <http://purl.obolibrary.org/obo/GO_>
PREFIX ECO: <http://purl.obolibrary.org/obo/ECO_>
PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>

SELECT ?protein ?transcript ?ensprotein ?gene ?rhea ?equation ?chebi
WHERE 
{
  ?protein rdfs:seeAlso ?transcript .
  ?protein a up:Protein .
  ?protein up:reviewed true .
  ?protein up:organism taxon:9606 .
  ?transcript a up:Transcript_Resource .
  ?transcript up:translatedTo ?ensprotein .
  ?transcript up:transcribedFrom ?gene .

}
alabarga commented 1 year ago

image

alabarga commented 1 year ago

Map miRNA - target data

alabarga commented 1 year ago

Querying Ensembl

mysql://ensembldb.ensembl.org

image

SELECT transcript.stable_id transcript_id, xref.display_label refseq_id
FROM transcript, object_xref, xref,external_db
WHERE transcript.transcript_id = object_xref.ensembl_id
  AND object_xref.ensembl_object_type = 'Transcript'
  AND object_xref.xref_id = xref.xref_id
  AND xref.external_db_id = external_db.external_db_id
  AND external_db.db_name = 'RefSeq_mRNA';
alabarga commented 1 year ago

Map proteomics data

alabarga commented 1 year ago

Mirbase RDF

mariacastillo982 commented 1 year ago

library(affy) library(oligo) library(Biobase) library("GEOquery") library(openxlsx) library("dplyr") library("readxl")

File path

setwd('/Users/mariacastillo/Desktop/MULTIOMICS/Hackaton') MTI <- read_excel("hsa_MTI.xlsx") gene_ENS <- AnnotationDbi::select(org.Hs.eg.db, keys = as.character(MTI$'Target Gene (Entrez ID)'), columns = "ENSEMBL", keytype = "ENTREZID") newname<-list("Target Gene (Entrez ID)",'ENSEMBL') names(gene_ENS)<-newname gene_list <- merge(MTI, gene_ENS, by = "Target Gene (Entrez ID)", all = TRUE)

Save variables

write.xlsx(gene_list, "hsa_MTI_ENSEMBL.xlsx")

alabarga commented 1 year ago

Map transcriptomic data

Agilent 028004 SurePrint G3 Human GE 8x60K Microarray

https://www.ebi.ac.uk/biostudies/arrayexpress/arrays/A-MEXP-2104

has Ensembl Transcript Id