Loci Namespace

This namespace contains endpoints to get data about the loci of the database, such as its alleles, the FASTA sequence and the Uniprot annotation.

Get the list of all loci from Chewie-NS

The /loci/list endpoint will return all loci form Chewie-NS.

The obtained response contains:

• The name of the locus.

• The locus ID, which can be used to obtain more information in the Loci Namespace.

• The name of the file it was contained.

Example:

"Loci": [
  {
    "name": {
      "type": "literal",
      "value": "test_schema-000006"
    },
    "locus": {
      "type": "uri",
      "value": "https://127.0.0.1/NS/api/loci/6"
    },
    "original_name": {
      "type": "literal",
      "value": "original_file.fasta"
    }
  }
]

Warning

Using this endpoint with large databases will cause a considerable slow response from the server. Please don’t abuse it.

Get details about a loci

The /loci/{loci_id} will return detailed information about the locus, such as:

• The locus name.

• The name of the it was contained in.

• The Uniprot annotation.

• The Uniprot URI.

Example:

[
  {
    "name": {
      "type": "literal",
      "value": "test_schema-000001"
    },
    "original_name": {
      "type": "literal",
      "value": "protein1.fasta"
    },
    "UniprotName": {
      "type": "typed-literal",
      "datatype": "http://www.w3.org/2001/XMLSchema#string",
      "value": "chromosomal replication initiator protein DnaA"
    },
    "UniprotLabel": {
      "type": "typed-literal",
      "datatype": "http://www.w3.org/2001/XMLSchema#string",
      "value": "chromosomal replication initiator protein DnaA"
    },
    "UniprotURI": {
      "type": "typed-literal",
      "datatype": "http://www.w3.org/2001/XMLSchema#string",
      "value": "http://purl.uniprot.org/uniparc/UPI001012CEFD"
    }
  }
]

Get the allele IDs of a locus

The /loci/{loci_id}/alleles endpoint returns the alleles IDs associated with a locus.

Example:

{
    "alleles": {
    "type": "uri",
    "value": "https://127.0.0.1/NS/api/loci/1/alleles/1"
    }
}

Get details about an allele associated with a locus

The /loci/{loci_id}/alleles/{allele_id} returns detailed information about an allele.

The response contains:

• The sequence hash, which can be used in the Sequences Namespace.

• The source organism.

• The insertion date.

• The allele ID.

• The isolate count.

Example:

[
    {
        "sequence": {
        "type": "uri",
        "value": "https://127.0.0.1/NS/api/sequences/<hash>"
        },
        "source": {
        "type": "literal",
        "value": "Yersinia pestis"
        },
        "date": {
        "type": "typed-literal",
        "datatype": "http://www.w3.org/2001/XMLSchema#dateTime",
        "value": "2020-04-09T14:59:05.434355"
        },
        "id": {
        "type": "typed-literal",
        "datatype": "http://www.w3.org/2001/XMLSchema#integer",
        "value": "1"
        },
        "isolate_count": {
        "type": "typed-literal",
        "datatype": "http://www.w3.org/2001/XMLSchema#integer",
        "value": "0"
        }
    }
]

Getting the DNA sequence of all alleles associated with a locus

The /loci/{loci_id}/fasta endpoint returns the DNA sequence of all alleles belonging to a locus.

The response contains:

• The locus name.

• The allele ID.

• The nucleotide sequence.

• The length of the nucleotide sequence.

Example:

"Fasta": [
  {
    "name": {
      "type": "typed-literal",
      "datatype": "http://www.w3.org/2001/XMLSchema#string",
      "value": "test_schema-000001"
    },
    "allele_id": {
      "type": "typed-literal",
      "datatype": "http://www.w3.org/2001/XMLSchema#integer",
      "value": "1"
    },
    "nucSeq": {
      "type": "literal",
      "value": "ATGACTGAAAATGAACAAATTTTTTGGAACAGGGTCTTGGAATTAGCTCAGAGTCAAT
                TAAAACAGGCAACTTATGAATTTTTTGTTCATGATGCCCGTCTATTAAAGGTCGATAA
                GCATATTGCAACTATTTACTTAGATCAAATGAAAGAACTCTTTTGGGAAAAAAATCTT
                AAAGATGTTATTCTTACTGCTGGTTTTGAAGTTTATAACGCTCAAATTTCTGTTGACT
                ATGTTTTCGAAGAAGACCTAATGATTGAGCAAAATCAGACCAAAATCAATCAAAAACC
                TAAGCAGCAAGCCTTAAATTCTTTGCCTACTGTTACTTCAGATTTAAACTCGAAATAT
                AGTTTTGAAAACTTTATTCAAGGAGATGAAAATCGTTGGGCTGTTGCTGCTTCAATAG
                CAGTAGCTAATACTCCTGGAACTACCTATAATCCTTTGTTTATTTGGGGTGGCCCTGG
                GCTTGGGAAAACCCATTTATTAAATGCTATTGGTAATTCTGTACTATTAGAAAATCCA
                AATGCTCGAATTAAATATATCACAGCTGAAAACTTTATTAATGAGTTTGTTATCCATA
                TTCGCCTTGATACCATGGATGAATTGAAAGAAAAATTTCGTAATTTAGATTTACTCCT
                TATTGATGATATCCAATCTTTAGCTAAAAAAACGCTCTCTGGAACACAAGAAGAGTTC
                TTTAATACTTTTAATGCACTTCATAATAATAACAAACAAATTGTCCTAACAAGCGACC
                GTACACCAGATCATCTCAATGATTTAGAAGATCGATTAGTTACTCGTTTTAAATGGGG
                ATTAACAGTCAATATCACACCTCCTGATTTTGAAACACGAGTGGCTATTTTGACAAAT
                AAAATTCAAGAATATAACTTTATTTTTCCTCAAGATACCATTGAGTATTTGGCTGGTC
                AATTTGATTCTAATGTCAGAGATTTAGAAGGTGCCTTAAAAGATATTAGTCTGGTTGC
                TAATTTCAAACAAATTGACACGATTACTGTTGACATTGCTGCCGAAGCTATTCGCGCC
                AGAAAGCAAGATGGACCTAAAATGACAGTTATTCCCATCGAAGAAATTCAAGCGCAAG
                TTGGAAAATTTTACGGTGTTACCGTCAAAGAAATTAAAGCTACTAAACGAACACAAAA
                TATTGTTTTAGCAAGACAAGTAGCTATGTTTTTAGCACGTGAAATGACAGATAACAGT
                CTTCCTAAAATTGGAAAAGAATTTGGTGGCAGAGACCATTCAACAGTACTCCATGCCT
                ATAATAAAATCAAAAACATGATCAGCCAGGACGAAAGCCTTAGGATCGAAATTGAAAC
                CATAAAAAACAAAATTAAATAA"
    },
    "nucSeqLen": {
      "type": "typed-literal",
      "datatype": "http://www.w3.org/2001/XMLSchema#integer",
      "value": "1356"
    }
  }
]