Public
Edited
Apr 5, 2023
fetch_general
gene_of_interest = 'Rho'
// gene_of_interest = 'PARP14'
// gene_of_interest = 'Lgr4'
// gene_of_interest = 'Smo'
// gene_of_interest = 'Clasp1'
// gene_of_interest = 'tp53'
// gene_of_interest = 'egfr'
// gene_of_interest = 'dclk3'
// gene_of_interest = 'stk32A'
inst_organism = 'human'
inst_gene_name = JSON.parse(fetch_hzome.body).name
inst_gene_description = JSON.parse(fetch_hzome.body).description
fetch_hzome = {
let base_url = 'https://amp.pharm.mssm.edu/Harmonizome/api/1.0/gene/' ;
let full_url = base_url + gene_of_interest;
const response = await fetch(
full_url, {
method: 'GET'
}
);
return {
ok: response.ok,
body: await response.text()
};
}
real_protein = fetch_accession
.body
// has evidence at protein level
.filter(d => d.proteinExistence === 'Evidence at protein level')
// has a comments section
.filter(d => 'comments' in d)
// has a FUNCTION section in the comments
.filter(d => d.comments.map(c => c.type).includes('FUNCTION'))
// has gene
.filter(d => 'gene' in d)
// matches gene name in first entry (lowercase string)
.filter(d => d.gene[0].name.value.toLowerCase() === gene_of_interest.toLowerCase())
real_protein[0].gene[0].name.value.toLowerCase()
fetch_accession = {
let base_url = 'https://www.ebi.ac.uk/proteins/api/proteins?offset=0&size=' + num_matches + '&exact_gene=' + gene_of_interest + '&organism=' + inst_organism ;
let full_url = base_url // + gene_of_interest + '';
const response = await fetch(
full_url, {
method: 'GET',
headers: {
"Accept" : "application/json",
'Content-Type': 'application/json',
}
}
);
return {
ok: response.ok,
body: await response.json()
};
}
// inst_accession = 'P08100'
inst_accession = real_protein[0].accession
num_matches = 25
fetch_general = {
let base_url = 'https://rest.uniprot.org/uniprotkb/' + inst_accession + '.json' ;
let full_url = base_url ;
const response = await fetch(
full_url, {
method: 'GET',
headers: {
"Accept" : "application/json",
'Content-Type': 'application/json',
}
}
);
return {
ok: response.ok,
body: await response.json()
};
}
uniprot_full_name = fetch_general.body.proteinDescription.recommendedName.fullName.value
fetch_general.body
fetch_general.body.comments[0].texts[0].value
fetch_general.body.comments[0].texts[0].evidences[0]
// fetch_uniprot = {
// let base_url = 'https://rest.uniprot.org/uniprotkb/' + inst_accession + '.json' ;
// let full_url = base_url ;
// const response = await fetch(
// full_url, {
// method: 'GET',
// headers: {
// "Accept" : "application/json",
// 'Content-Type': 'application/json',
// }
// }
// );
// return {
// ok: response.ok,
// body: await response.json()
// };
// }
// // see https://www.biostars.org/p/5311/
// fetch_quickgo = {
// let base_url = 'https://www.ebi.ac.uk/QuickGO/services/annotation/search?geneProductId=' + inst_accession + '&aspect=None' ;
// let full_url = base_url ;
// const response = await fetch(
// full_url, {
// method: 'GET',
// headers: {
// "Accept" : "application/json",
// 'Content-Type': 'application/json',
// }
// }
// );
// return {
// ok: response.ok,
// body: await response.json()
// };
// }
library_name = 'GO_Biological_Process_2021'
// see https://www.biostars.org/p/5311/
fetch_gmt = {
let base_url = 'https://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=' + library_name ;
let full_url = base_url ;
const response = await fetch(
full_url, {
method: 'GET',
headers: {
"Accept" : "application/json",
'Content-Type': 'application/json',
}
}
);
var response_text = await response.text()
var gmt_dict = {}
response_text.split('\n').map(d => d.split('\t'))
.forEach(d => {
var term = d[0]
var gene_set = d.slice(2,)
gmt_dict[term] = gene_set
})
// return {
// ok: response.ok,
// body: response_text
// };
return gmt_dict
}
Object.keys(fetch_gmt)
{
var gmt_dict = {}
fetch_gmt.body.split('\n').map(d => d.split('\t'))
.forEach(d => {
var term = d[0]
var gene_set = d.slice(2,)
gmt_dict[term] = gene_set
// return {term: gene_set}
})
return gmt_dict
}
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