REST API Documentation

Public endpoint

The public endpoint is located at https://api.seqco.de/v1/.

Global Models

All the following models can also take the value of null:

bool: Boolean, one of true or false
int: Integer. Example: 3
float: Double (floating point number). Example: 3.14
str: String. Example: "e.g."
date: Date and time, in format ISO 8601 (without time). Example: "2019-04-15"
date_time: Date and time, in format ISO 8601 (including seconds). Example: "2019-04-15T18:47:15.734Z"

Generic

Model: `text_with_format`

{
  "raw": str,
  "html": str
}

Model: `response`

{
  "status": "ok",
  "message_type": str
}

Model: `response_paginated`

{
  "status": "ok",
  "message_type": str,
  "count": int,
  "current_page": int,
  "total_pages": int,
  "next": str
}

`GET /seqcode/page/status.json`

Description

Checks that the API is accessible

Parameters

None

Response

{ "status": "ok" }

Example

https://api.seqco.de/v1/page/status.json

Names

Model: `name_item`

{
  "id": int,
  "name": str,
  "url": str,
  "uri": str
}

Model: `classification`

[
  {
    "id": int,
    "name": str,
    "rank": str,
    "status_name": str,
    "priority_date": date_time,
    "type_material": type_material,
    "created_at": date_time,
    "updated_at": date_time,
    "url": str,
    "uri": str
  },
  ...
]

The classification model is an array ordered from highest to lowest taxonomic rank, where the first value typically corresponds to a name with the rank of "domain"

Model: `type_material`

{
  "class": str,
  "id": int,
  "url": str,
  "uri": str,
  "display": str
}

class can take any value from "unknown", "Name", or "Genome"

Model: `qc_warning`

{
  "message": str,
  "rules": [
    str,
    ...
  ],
  "recommendations": [
    str,
    ...
  ],
  "rule_notes": [
    str,
    ...
  ],
  "can_endorse": bool,
  "checklist": str
}

message is the only mandatory field in this model
rules, recommendations, and rule_notes are (optional) arrays indicating which rules, recommendations, or rule notes (respectively) from the SeqCode are being contravened by the name in its current status
can_endorse indicates if the name can be endorsed despite the warning. If missing, warnings citing rules don't allow endorsement, and all other warnings do
checklist indicates (if present) that the warning was registered by manual curation of this type, one of "nomenclature" or "genomics"

`GET /seqcode/names.json`

Description

Retrieve a list of names

Parameters

page [int, opt]: Page of the list of names
status [str, opt]: Filter names by status, one of public, automated, SeqCode, ICNP, ICN, or valid

Response

{
  "response": response_paginated,
  "values": [
    name_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/names.json?status=SeqCode

`GET /seqcode/names/(id).json`

Description

Retrieve data about the name (id) [int]

Parameters

None

Response

{
  "response": response,
  name_item,
  "rank": str,
  "status_name": str,
  "syllabication": str,
  "priority_date": date_time,
  "description": text_with_format,
  "formal_styling": text_with_format,
  "etymology": str,
  "type_material": type_material,
  "notes": text_with_format,
  "proposed_in": publication_item,
  "not_validly_proposed_in": [
    publication_item,
    ...
  ],
  "corrigendum_in": publication_item,
  "corrigendum_from": str,
  "emended_in": [
    publication_item,
    ...
  ],
  "classification": classification,
  "children": [
    name_item,
    ...
  ],
  "register": register_item,
  "qc_warnings": [
    qc_warning,
    ...
  ],
  "register": register_item,
  "created_at": date_time,
  "updated_at": date_time
}

The following fields are optional: description, notes, proposed_in, not_validly_proposed_in, corrigendum_in, corrigendum_from, emended_in, register, and qc_warnings

Example

https://api.seqco.de/v1/names/1.json

Genomes

Model: `genome_item`

{
  "id": int,
  "database": str,
  "accession": str,
  "kind": str,
  "url": str,
  "uri": str
}

database can take any of the values: "assembly" or "nuccore"
kind can take any of the values: "isolate", "enrichment", "mag", "sag", or null

`GET /seqcode/genomes.json`

Description

Retrieve a list of genomes

Parameters

page [int, opt]: Page of the list of genomes

Response

{
  "response": response_paginated,
  "values": [
    genome_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/genomes.json

`GET /seqcode/genomes/(id).json`

Description

Retrieve data about genome (id) [int]

Parameters

None

Response

{
  "response": response,
  genome_item,
  "sample": {
    "source_database": str,
    "source_accessions": [
      str,
      ...
    ]
  },
  "genomic_features": {
    "auto_check": bool,
    "seq_depth": int,
    "gc_content": float,
    "most_complete_16s": float,
    "number_of_16s": int,
    "most_complete_23s": float,
    "number_of_23s": int,
    "number_of_trnas": int,
    "coding_density": float,
    "codon_table": int,
    "n50": float,
    "contigs": int,
    "largest_contig": int,
    "assembly_length": int,
    "ambiguous_fraction": float
  },
  "names": [
    name_item,
    ...
  ],
  "created_at": date_time,
  "updated_at": date_time
}

sample.source_database can take any of the values: "biosample", "sra", "", or null (the last two should be interpreted as equivalent)
genomic_features.codon_table follows the NCBI codon table numbering, and typically would take a value of 11, 4, or null

Example

https://api.seqco.de/v1/genomes/1.json

`GET /seqcode/type-genomes.json`

Description

Retrieve a list of type genomes from validly published names and their corresponding names

Parameters

page [int, opt]: Page of the list genomes and corresponding validly published names

Response

{
  "response": response_paginated,
  "values": [
    {
      "id": int,
      "name": str,
      "rank": str,
      "status_name": str,
      "priority_date": date_time,
      "type_material": {
        str: str,
        type_material
      },
      "classification": classification,
      "created_at": date_time,
      "updated_at": date_time,
      "url": str
    },
    ...
  ]
}

The first key-value pair in values[*].type_material corresponds to database and accession, where the database (key) is "nuccore" or "assembly"
values[*].id and all other direct children of values[*] correspond to features of the name, not features of the type genome

Example

https://api.seqco.de/v1/type-genomes.json

Registers

Model: `register_item`

{
  "acc_url": str,
  "title": str,
  "priority_date": date_time,
  "url": str,
  "uri": str
}

`GET /seqcode/registers.json`

Description

Retrieve a list of (validated) register lists

Parameters

page [int, opt]: Page of the list

Response

{
  "response": response_paginated,
  "values": [
    register_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/registers.json

`GET /seqcode/registers/(acc).json`

Description

Retrieve a data from register list (acc) [str]

Parameters

page [int, opt]: Page of the list of names in the register list

Response

{
  "response": response_paginated,
  register_item,
  "submitted": bool,
  "validated": bool,
  "validated_by": str,
  "submitter": str,
  "effective_publication": publication_item,
  "doi": str,
  "created_at": date_time,
  "updated_at": date_time,
  "names": [
    name_item,
    ...
  ]
}

doi is only present for validated register lists

Example

https://api.seqco.de/v1/registers/r:sy5jeiw2.json

Publications

Model: `author_item`

{
  "id": int,
  "given": str,
  "family": str,
  "created_at": date_time,
  "updated_at": date_time,
  "url": str
}

Model: `publication_item`

{
  "id": int,
  "citation": str,
  "doi": str,
  "url": str
}

Model: `subject_item`

{
  "id": int,
  "name": str,
  "url": str
}

`GET /seqcode/authors.json`

Description

Retrieve a list of publication authors

Parameters

page [int, opt]: Page of the list of authors

Response

{
  "response": response_paginated,
  "values": [
    author_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/authors.json

`GET /seqcode/authors/(id).json`

Description

Retrieve data about the author (id) [int]

Parameters

page [int, opt]: Page of the list of publications from the author

Response

{
  "response": response_paginated,
  author_item,
  "publications": [
    publication_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/authors/1.json

`GET /seqcode/journals.json`

Description

Retrieve a list of publication journals

Parameters

page [int, opt]: Page of the list of journals

Response

{
  "response": response_paginated,
  "values": [
    {
      "name": str,
      "url": str
    },
    ...
  ]
}

Example

https://api.seqco.de/v1/journals.json

`GET /seqcode/journals/(name).json`

Description

Retrieve data about the journal (name) [str]

Parameters

page [int, opt]: Page of the list of publications from the journal

Response

{
  "response": response_paginated,
  "name": str,
  "url": str,
  "publications": [
    publication_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/journals/Acta Horticulturae.json

`GET /seqcode/publications.json`

Description

Retrieve a list of publications

Parameters

page [int, opt]: Page of the list of publications

Response

{
  "response": response_paginated,
  "values": [
    publication_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/publications.json

`GET /seqcode/publications/(id).json`

Description

Retrieve data about publication (id) [int]

Parameters

None

Response

{
  "response": response,
  publication_item,
  "link_ext": str,
  "title": str,
  "journal": str,
  "journal_loc": str,
  "journal_date": date,
  "pub_type": str,
  "abstract": str,
  "long_citation_html": str,
  "created_at": date_time,
  "updated_at": date_time,
  "authors": [
    author_item,
    ...
  ],
  "names": [
    name_item,
    ...
  ],
  "subjects": [
    subject_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/publications/1.json

`GET /seqcode/subjects.json`

Description

Retrieve a list of publication subjects

Parameters

page [int, opt]: Page of the list

Response

{
  "response": response_paginated,
  "values": [
    subject_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/subjects.json

`GET /seqcode/subjects/(id).json`

Description

Retrieve data from publication subject (id) [int]

Parameters

page [int, opt]: Page of the list of publications with the subject

Response

{
  "response": response_paginated,
  subject_item,
  "created_at": date_time,
  "updated_at": date_time,
  "publications": [
    publication_item,
    ...
  ]
}

Example

https://api.seqco.de/v1/subjects/1.json

© 2022-2024 The SeqCode Initiative
All information contributed to the SeqCode Registry is released under the terms of the Creative Commons Attribution (CC BY) 4.0 license

REST API Documentation

Public endpoint

Global Models

Generic

Model: text_with_format

Model: response

Model: response_paginated

GET /seqcode/page/status.json

Names

Model: name_item

Model: classification

Model: type_material

Model: qc_warning

GET /seqcode/names.json

GET /seqcode/names/(id).json

Genomes

Model: genome_item

GET /seqcode/genomes.json

GET /seqcode/genomes/(id).json

GET /seqcode/type-genomes.json

Registers

Model: register_item

GET /seqcode/registers.json

GET /seqcode/registers/(acc).json

Publications

Model: author_item

Model: publication_item

Model: subject_item

GET /seqcode/authors.json

GET /seqcode/authors/(id).json

GET /seqcode/journals.json

GET /seqcode/journals/(name).json

GET /seqcode/publications.json

GET /seqcode/publications/(id).json

GET /seqcode/subjects.json

GET /seqcode/subjects/(id).json

Model: `text_with_format`

Model: `response`

Model: `response_paginated`

`GET /seqcode/page/status.json`

Model: `name_item`

Model: `classification`

Model: `type_material`

Model: `qc_warning`

`GET /seqcode/names.json`

`GET /seqcode/names/(id).json`

Model: `genome_item`

`GET /seqcode/genomes.json`

`GET /seqcode/genomes/(id).json`

`GET /seqcode/type-genomes.json`

Model: `register_item`

`GET /seqcode/registers.json`

`GET /seqcode/registers/(acc).json`

Model: `author_item`

Model: `publication_item`

Model: `subject_item`

`GET /seqcode/authors.json`

`GET /seqcode/authors/(id).json`

`GET /seqcode/journals.json`

`GET /seqcode/journals/(name).json`

`GET /seqcode/publications.json`

`GET /seqcode/publications/(id).json`

`GET /seqcode/subjects.json`

`GET /seqcode/subjects/(id).json`