# Endpoint: https://rdfportal.org/sib/sparql
# Description: protein name, mnemonic and gene name of human
# Parameter: taxonomy: (example: taxonomy:9606)

PREFIX core: <http://purl.uniprot.org/core/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX taxonomy: <http://purl.uniprot.org/taxonomy/>

SELECT DISTINCT ?UniProt ?recommended_name ?submited_name ?mnemonic ?gene_name ?taxonomy
FROM <http://sparql.uniprot.org/uniprot>
FROM <http://sparql.uniprot.org/obsolete>
FROM <http://sparql.uniprot.org/citationmapping>
FROM <http://sparql.uniprot.org/taxonomy>
FROM <http://sparql.uniprot.org/citations>
FROM <http://sparql.uniprot.org/proteomes>
FROM <http://sparql.uniprot.org/go>
FROM <http://sparql.uniprot.org/enzyme>
FROM <http://sparql.uniprot.org/diseases>
FROM <http://sparql.uniprot.org/journal>
FROM <http://sparql.uniprot.org/pathways>
FROM <http://sparql.uniprot.org/keywords>
FROM <http://sparql.uniprot.org/locations>
FROM <http://sparql.uniprot.org/tissues>
FROM <http://sparql.uniprot.org/core>
FROM <http://sparql.uniprot.org/databases>
WHERE {
    VALUES ?taxonomy { taxonomy:9606 }
    ?UniProt a core:Protein ;
        core:mnemonic ?mnemonic ;
        core:organism ?taxonomy .
    OPTIONAL {
        ?UniProt core:recommendedName / core:fullName ?recommended_name .
    }
    OPTIONAL {
        ?UniProt core:submittedName / core:fullName ?submited_name .
    }
    OPTIONAL {
        ?UniProt core:encodedBy / skos:prefLabel ?gene_name .
    }
}
LIMIT 100

# Endpoint: https://rdfportal.org/sib/sparql
# Description: PTM sites and descriptions of an UniProt
# Parameter: UniProt: (example: up:Q9BYF8)

PREFIX core: <http://purl.uniprot.org/core/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX faldo: <http://biohackathon.org/resource/faldo#>
PREFIX up: <http://purl.uniprot.org/uniprot/>

SELECT ?UniProt ?mod_desc ?mod_begin ?mod_end
FROM <http://sparql.uniprot.org/uniprot>
FROM <http://sparql.uniprot.org/obsolete>
FROM <http://sparql.uniprot.org/citationmapping>
FROM <http://sparql.uniprot.org/taxonomy>
FROM <http://sparql.uniprot.org/citations>
FROM <http://sparql.uniprot.org/proteomes>
FROM <http://sparql.uniprot.org/go>
FROM <http://sparql.uniprot.org/enzyme>
FROM <http://sparql.uniprot.org/diseases>
FROM <http://sparql.uniprot.org/journal>
FROM <http://sparql.uniprot.org/pathways>
FROM <http://sparql.uniprot.org/keywords>
FROM <http://sparql.uniprot.org/locations>
FROM <http://sparql.uniprot.org/tissues>
FROM <http://sparql.uniprot.org/core>
FROM <http://sparql.uniprot.org/databases>
WHERE {
    VALUES ?UniProt { up:Q9BYF8 }
    ?UniProt a core:Protein ;
        core:annotation ?ModifiedResidueAnnotation .
    ?ModifiedResidueAnnotation a core:Modified_Residue_Annotation .
    OPTIONAL {
        ?ModifiedResidueAnnotation rdfs:comment ?mod_desc ;
            core:range [
                a faldo:Region ;
                faldo:begin [
                    a faldo:Position ;
                    faldo:position ?mod_begin ;
                ] ;
                faldo:end [
                    a faldo:Position ;
                    faldo:position ?mod_end ;
                ] ;
            ] .
    }
}
LIMIT 100

# Endpoint: https://rdfportal.org/sib/sparql
# Description: corresponding HGNC ID of human
# Parameter: database: (example: database:HGNC)
#            taxonomy: (example: taxonomy:9606)

PREFIX core: <http://purl.uniprot.org/core/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX database: <http://purl.uniprot.org/database/>
PREFIX taxonomy: <http://purl.uniprot.org/taxonomy/>

SELECT ?UniProt ?db_resource ?database ?taxonomy
FROM <http://sparql.uniprot.org/uniprot>
FROM <http://sparql.uniprot.org/obsolete>
FROM <http://sparql.uniprot.org/citationmapping>
FROM <http://sparql.uniprot.org/taxonomy>
FROM <http://sparql.uniprot.org/citations>
FROM <http://sparql.uniprot.org/proteomes>
FROM <http://sparql.uniprot.org/go>
FROM <http://sparql.uniprot.org/enzyme>
FROM <http://sparql.uniprot.org/diseases>
FROM <http://sparql.uniprot.org/journal>
FROM <http://sparql.uniprot.org/pathways>
FROM <http://sparql.uniprot.org/keywords>
FROM <http://sparql.uniprot.org/locations>
FROM <http://sparql.uniprot.org/tissues>
FROM <http://sparql.uniprot.org/core>
FROM <http://sparql.uniprot.org/databases>
WHERE {
    VALUES ?database { database:HGNC }
    VALUES ?taxonomy { taxonomy:9606 }
    VALUES ?db_resource__class { core:Resource core:Nucleotide_Resource core:Transcript_Resource core:Structure_Resource }
    ?db_resource a ?db_resource__class ;
        core:database ?database .
    ?UniProt a core:Protein ;
        core:organism ?taxonomy .
    OPTIONAL {
        ?UniProt rdfs:seeAlso ?db_resource .
    }
}
LIMIT 100