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
}
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
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All information contributed to the SeqCode Registry is released under
the terms of the
Creative Commons Attribution (CC BY) 4.0
license