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. 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. The Excel template with explanatory text that the Wellcome Sanger Institute is sending to collecting centres

  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