Samples Metadata Only
This page describes how to upload a spreadsheet containing sample information to the COG-UK storage

1. To bulk upload multiple samples, download the template and fill in the fields.

There are several alternative templates
  1. 1.
    A simple template with column headings only. Download directly from the website or from here (N.B You must be logged in first) This file is in CSV format. Please ensure that when editing in Excel you set all fields to be 'text format' not the default 'General format'. In particular pay attention to date fields that they remain as YYYY-MM-DD.
  2. 2.
    The Excel template with explanatory text that the Wellcome Sanger Institute is sending to collecting centres
  3. 3.
    This simple Excel sheet created by Tanya Golubchik (University of Oxford) that has some validation and tooltips to guide data entry
An explanation for the fields can be found in the table below
Column heading
Required
Description
central_sample_id
yes
The centrally shared ID that you will use to refer to this sample inside the consortium.
adm1
yes
The administrative region. One of: UK-ENG,UK-SCT,UK-WLS,UK-NIR
collection_date
no
The date the sample was collected. YYYY-MM-DD format only.
received_date
no
The date the sample was received. YYYY-MM-DD only.
ONE of collection_date, received_date
Date sample was first received by any lab. This date should be as close to possible to collection_date. This date must be provided if collection_date is missing.
source_age
no
Age of the patient in years
source_sex
no
Sex of the patient. One of: F,M,Other
is_surveillance
yes
Is this sample one chosen according to the surveillance sampling strategy. ONE of Y or N Y = sample is a random surveillance sample and not part of a targeted cluster
one of a targeted cluster can be Y
N = sample is part of a targeted cluster
collection_pillar
no
The pillar under which this sample was collected (e.g. 1, 2). This is likely 1, but leave blank if unsure.
is_hcw
no
Is the sample from a healthcare worker?
ONE of Y or N
employing_hospital_name
no
If a HCW, the name of the hospital
employing_hospital_trust_or_board
no
If a HCW, the name of hospital trust (in England) or hospital organisation
is_hospital_patient
no
Is the sample from a patient in hospital?
ONE of Y or N or blank
is_icu_patient
no
Is the sample from a patient that was or is in a ICU due to COVID_19 irrespective of when the sample was taken?
ONE of Y or N or blank
admitted_with_covid_diagnosis
no
Was the patient in admitted to hospital with a positive diagnosis for covid?
ONE of Y or N or blank
admitted_hospital_name
no
If a hospital patient, the name of the hospital
admitted_hospital_trust_or_board
no
If a hospital patient, the name of hospital trust (in England) or hospital organisation
is_care_home_worker
no
Is the sample from a care home worker?
ONE of Y or N or blank
is_care_home_resident
no
Is the sample from a care home resident?
ONE of Y or N or blank
anonymised_care_home_code
no
A code identifying the care home but which does not contain any identifying information about the care home, e.g. 'A'
adm2
no
The county that the patient lives in (no abbreviations or short hand)
adm2_private
no
The outer postcode for the patient’s home address (first half of the postcode only)
biosample_source_id
no
Unique identifier of patient or environmental sample. Do not use an NHS number here. This field will be backfilled later by PHx and HDR-UK.
collecting_org
no
The site (eg. hospital or surgery) that this sample was originally collected by. Use the first line of the ‘sender’ from the E28 form.
root_sample_id
no
Identifier assigned to this sample from one of the health agencies (eg. PHE samples will be prefixed with H20). This is necessary for linking samples to private patient metadata later.
sample_type_collected
no
Sample type. One of: dry swab, swab, sputum, BAL, aspirate
sample_type_received
no
Sample type. One of primary, extract, lysate, culture
sender_sample_id
no
If this sample was renamed by a local organisation (eg. hospital virology lab, sequencing lab), provide this identifier here. Otherwise leave blank.
swab_site
no
Swab site. One of: nose, throat, nose-throat, endotracheal, rectal
epi_cluster
no
Identifier for an epidemiological cluster
investigation_cluster
no
An optional identifier for a cluster within an investigation
ct_1_ct_value
no
Ct value for samples (test 1)
ct_1_test_target
no
The target for the qPCR test (test 1) (see here for valid values)
"E", "N", "ORF1AB", "ORF8", "RDRP", "RDRP+N", "S", null
ct_1_test_platform
no
The platform used for the qPCR test (test 1) (see here for valid values)
"ABBOTT_M2000", "ALTONA", "ALTOSTAR_AM16", "APPLIED_BIO_7500", "AUSDIAGNOSTICS", "BD_MAX", "CEPHEID_XPERT", "ELITE_INGENIUS", "INHOUSE", "PANTHER", "QIAGEN_ROTORGENE", "QIASTAT_DX", "ROCHE_COBAS", "ROCHE_FLOW", "ROCHE_LIGHTCYCLER", "SEEGENE_NIMBUS", null
ct_1_test_kit
no
The kit used for the qPCR test (test 1) (see here for valid values)
"ALTONA", "ABBOTT", "AUSDIAGNOSTICS", "BOSPHORE", "ROCHE", "INHOUSE", "SEEGENE", "VIASURE", "BD" , "XPERT", null
ct_2_ct_value
no
Ct value for samples (test 2)
ct_2_test_target
no
The target for the qPCR test (test 2) (see above for valid values)
ct_2_test_platform
no
The platform used for the qPCR test (test 2) (see above for valid values)
ct_2_test_kit
no
The kit used for the qPCR test (test 2) (see above for valid values)

2. Upload the completed spreadsheet to the website by dragging file onto dotted box or clicking 'Select files to upload.

3. The spreadsheet will be rendered in the web page with a pending status. Click the 'Start Upload' button.

4. If successful a sample will display a tick next to it

5. If there are errors, there will be a circular exclamation mark symbol displayed

6. Clicking on a row with an error will reveal a more detailed reason for the error

7. Correct these errors and re-upload the spreadsheet using the 'Upload another file' button

Last modified 1yr ago
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