Species Namespace

This namespace contains endpoints to get data about all species on the database and also about a specific species.

Get the list of species

To get the list of species available in Chewie-NS you need to use the /species/list endpoint.

Click on the Try it out on the top-right corner of the endpoint and afterwards the Execute button.

An example of a possible response from Chewie-NS is the following

  [
{
  "species": {
    "type": "uri",
    "value": "https://127.0.0.1/NS/api/species/1"
  },
  "name": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "Yersinia pestis"
  }
},
{
  "species": {
    "type": "uri",
    "value": "https://127.0.0.1/NS/api/species/2"
  },
  "name": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "Streptococcus agalactiae"
  }
}
  ]

In the response we obtain the internal ID of the species, which is important if we want to Download a schema from Chewie-NS <https://chewbbaca.readthedocs.io/en/latest/user/modules/DownloadSchema.html>_ or Upload a schema to Chewie-NS <https://chewbbaca.readthedocs.io/en/latest/user/modules/LoadSchema.html>_. We also obtain the name of the species associated with each ID.

Alternatively, we can check if a species is already on Chewie-NS by filling the species_name field. If the species exists, the response will contain the associated ID.

For example if we search for Yersinia pestis and it already exists the response will be the following:

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

If it does not exist, the response will be the following:

{
    "NOT FOUND": "Species does not exists in the NS."
}

Getting all the loci for a species

To get all the loci of a species, we need to access the /species/{species_id}/loci and provide the ID of the species obtained in endpoint described above.

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"
    }
  }
]

Getting schemas information

The /species/{species_id}/schemas endpoint allows users to get all the schemas associated with a species. The response will contain:

The schema ID.
The schema name.

Example:

[
    {
        "schemas": {
            "type": "uri",
            "value": "https://127.0.0.1/NS/api/species/1/schemas/1"
        },
        "name": {
            "type": "typed-literal",
            "datatype": "http://www.w3.org/2001/XMLSchema#string",
            "value": "test_schema"
        }
    }
]

Getting chewBBACA parameters of a schema

The /species/{species_id}/schemas/{schema_id} will return the chewBBACA parameters used to create a schema.

Example:

  [
{
  "name": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "test_schema"
  },
  "bsr": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "0.6"
  },
  "chewBBACA_version": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "2.1.0"
  },
  "prodigal_training_file": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "<hash>"
  },
  "translation_table": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "11"
  },
  "minimum_locus_length": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "201"
  },
  "size_threshold": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "None"
  },
  "word_size": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "None"
  },
  "cluster_sim": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "None"
  },
  "representative_filter": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "None"
  },
  "intraCluster_filter": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "None"
  },
  "dateEntered": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "2020-04-09T19:35:38.287942"
  },
  "last_modified": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "2020-04-09T19:35:38.287942"
  },
  "Schema_lock": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "Unlocked"
  },
  "SchemaDescription": {
    "type": "typed-literal",
    "datatype": "http://www.w3.org/2001/XMLSchema#string",
    "value": "Schema description."
  }
}
  ]

Getting the loci of a schema

The /species/{species_id}/schemas/{schema_id}/loci will return the loci corresponding to a schema, instead of the loci of the species.

The response has the same format as described in Getting all the loci for a species.