published_date |
date |
The date the object was published in Onyx. |
• Output format: iso-8601 |
site |
choice |
Laboratory, organisation or agency the sample has been submitted by. |
• Choices: APHA, CGPS, FSA, FSS, PHS, SSSCDRL, UKHSA |
climb_id |
text |
Unique identifier for a project record in Onyx. |
|
biosample_id |
text |
The sequencing providers identifier for a sample. |
|
biosample_source_id |
text |
Unique identifier for an individual to permit multiple samples from the same individual to be linked. |
|
run_id |
text |
The unique identifier assigned to the run by the sequencing instrument. |
|
platform |
choice |
The platform used to sequence the data. |
• Choices: illumina |
submitted_species |
choice |
The NCBI taxonomy id provided for the sample. |
• Choices: 1639, 28901, 562 |
sample_accession |
text |
Sample accession number if sequence is publically available in SRA. |
|
enterobase_barcode |
text |
Sample barcode if sequence is publically available in EnteroBase. |
|
collection_date |
date |
Date of sample collection. |
• Output format: YYYY-MM |
receipt_date |
date |
Date of receipt of the sample. |
• Output format: YYYY-MM |
month |
integer |
Month of sample collected if available or month of receipt otherwise. |
|
year |
integer |
Year of sample collected if available or year of sample receipt otherwise. |
|
sequence_org |
choice |
Laboratory, organisation or agency the sample has been sequenced by. |
• Choices: APHA, FSA, FSS, OTHER, PHS, PHW, SEPA, SSSCDRL, UKHSA |
sequence_org_other |
text |
Additional laboratory, organisation or agency the sample has been sequenced by. |
|
data_steward |
choice |
Laboratory, organisation or agency that hold the data for the sample. |
• Choices: APHA, FSA, FSS, OTHER, PHS, PHW, SEPA, SSSCDRL, UKHSA |
data_steward_other |
text |
Additional laboratory, organisation or agency that hold the data for the sample. |
|
source_type |
choice |
Source of the sample. |
• Choices: animal, animal_associated_environment, environment, food, food_associated_environment, human, human_associated_environment, missing, not_applicable, not_collected, not_provided, other, other_environment, restricted_access |
country |
choice |
The country that the sample was collected in, using ISO-3166-1 alpha-2 codes (https://en.wikipedia.org/wiki/List_of_ISO_3166_country_codes), unless within United Kingdom. If so, use ISO-3166-2:GB (https://en.wikipedia.org/wiki/ISO_3166-2:GB). |
• Choices: GB, GB-ENG, GB-NIR, GB-SCT, GB-WLS |
county |
choice |
County that the sample was collected in, using the second level subdivision codes of ISO-3166-2:GB (https://www.iso.org/obp/ui/#iso:code:3166:GB). |
• Choices: GB-ABC, GB-ABD, GB-ABE, GB-AGB, GB-AGY, GB-AND, GB-ANN, GB-ANS, GB-BAS, GB-BBD, GB-BCP, GB-BDF, GB-BDG, GB-BEN, GB-BEX, GB-BFS, GB-BGE, GB-BGW, GB-BIR, GB-BKM, ... |
sample_purpose |
choice |
The purpose of the sample collection. |
• Choices: active_surveillance, not_applicable, not_collected, not_provided, other, outbreak_initiated_surveillance, outbreak_investigation, population_based_surveillance, research, restricted_access, routine_diagnostics, routine_surveillance |
sample_purpose_other |
text |
Additional purpose of the sample collection. |
|
sequencing_kit |
text |
The sequencing kit used. |
|
library_kit |
text |
The library kit used to prep the sample. |
|
is_multiplexed |
bool |
Whether the sample was multiplexed. |
|
type_of_sample |
choice |
Type of sample used to produce the sequence. |
• Choices: genomic |
assembly |
text |
Assembly FASTA file. |
|
pathogenwatch_uuid |
text |
UUID from Pathogenwatch. |
|