Samples
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Why is the ‘Finish’ or ‘Confirm’ button missing after manifest upload?
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This issue occurs because in the manifest uploaded, one or more of the
permit required fields or columns is set to Y. This means that permit
files are required for the sample(s) within the manifest.
Resolution: Upload the permit files using the 
button first then,
The Finish button will be displayed in the Upload Sample Spreadsheet dialogue (once there are no errors) if uploading the manifest for the first time.
Alternatively, if the manifest is being updated, the Confirm button will be displayed in the Upload Sample Spreadsheet dialogue (once there are no errors).
How do I update submitted samples?
Reupload the amended manifest.
Note
The manifest must be reuploaded in the same profile that the samples were submitted in.
If the manifest requires permits, the permits must also be reuploaded so that the samples’ updates can be processed.
The desired value(s) will be updated once the field value is not a compliance field [1]. See the Updating Samples: Important Notes section for information about which field values can be updated.
How can a sample submitter check the status of accepted or rejected samples?
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Option 1: The Status column in the samples data table will display different the status of the sample record on the Samples page.
Option 2: The Error column in the samples data table will display an error message if the sample record has been rejected or if there are any errors associated with the sample record.
Can submitted samples be deleted?
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No, samples cannot be deleted after the manifest have been submitted.
Can I retrieve submitted samples or manifests?
Is there a maximum number of samples allowed in a single manifest?
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Yes, there is a limit to the number of samples that can be included in a single manifest uploaded to COPO.
A threshold of 1,000 samples is recommended with larger sets split across multiple manifests under the same profile or different profiles. This is because the validation process can be lengthy and resource-intensive, requiring significant memory, which may cause the page to crash or lag if there are too many rows to process.
Why does the downloaded sample manifest have incorrect samples or metadata?
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When you click the 
button, the samples
downloaded are associated with a specific manifest ID, which can be found
in the Manifest Identifier column of the data table.
If multiple manifests are uploaded to the same profile, each will have a
different manifest ID, so ensure you click the
button for the record corresponding to
the manifest ID you need.
Guidance: Check the Manifest Identifier column to ensure the
manifest ID is the same for all the samples you wish to download. If you
identify records with different manifest IDs, click on each record with a
manifest ID and then click the button to
download the samples associated with that specific ID.
In summary, if there are records with varying manifest IDs, you will need
to click each record one by one then, click the
button for each to download the correct
manifest.
How can I view uploaded image?
How can I download uploaded permits?
Which formats can I use to download samples?
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The following are the formats that samples can be downloaded in:
-
Spreadsheet format (
.xlsx)See the Downloading manifest in spreadsheet format section for more information.
-
Comma-separated values (csv) format (
.csv)On the Samples page, click the
button to download a manifest in csv format.Refer to the relevant section below, depending on the type of profile that you are working on.
How do I submit virtual samples?
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Virtual samples are research objects that are submitted to COPO under a Biodata profile.
See the Submitting Virtual Samples section for more information.
Which types of genomic metadata submissions can be made?
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Note
Data files related to your desired genomic metadata submission type must be uploaded via the Files page before submission.
See the Uploading Data Files section for more information.
The following are types of genomic metadata submissions that can be made in COPO. Please click the desired link to view more information about each submission type.
Genomic metadata submissions can be made via the following methods:
Under a Biodata profile - this method is applicable if the genomic data to be submitted is not associated with any particular project brokered by COPO.
Under a Tree of Life (ToL) profile - this approach is applicable if the genomic data to be submitted is associated with a project brokered by COPO and there are existing or submitted sample metadata.
Why does the ‘PROXY_TISSUE_VOUCHER_ID_FOR_BIOBANKING’ error appear?
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If you encounter the error,
The ID should be in the format of institute
unique name:collection code:id or institute unique name:id and separated
by "|" and the ID should be registered already
when trying to upload or update the field, PROXY_TISSUE_VOUCHER_ID_FOR_BIOBANKING, in a manifest, please ensure that the format of the ID is
institution_unique_name:collection_code:voucher_idinstitution_unique_name:voucher_Id.
Are accessions assigned after sample manifests are uploaded?
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No, accessions are assigned after sample submissions have been accepted by a sample manager.
The acceptance makes the submissions public and available for viewing on repositories such as the European Nucleotide Archive (ENA) and National Centre for Biotechnology Information (NCBI).
See the Finding Data Submission IDs section for more information.
How do you submit sample metadata so that it appears in public repositories?
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Note
Click the button below to view its content.
Prerequisites
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Request to be added to a manifest group associated with your desired project by sending an email to the COPO team at
Hint
Visit the Supported Projects section to see a list of COPO-brokered projects.
-
Complete a manifest which is a spreadsheet containing metadata for the desired project.
If you do not have a blank manifest for the project, you can refer to the Data Templates and Instructions section for guidance on downloading one to record the metadata.
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Log into the COPO website then, you’ll be navigated to the Work profiles page
Refer to the Accessing COPO section for guidance.
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Create a profile.
For more information, check the Tree of Life Profile or profile-walkthrough-tol.
-
Click the
button in the Components column
to navigate to the Samples page.-
For additional information, please see the relevant section below, depending on the type of profile that you are working on.
-
-
Upload the completed manifest.
Visit the Submitting Samples section for guidance on submitting samples.
Note
Choose the desired type of submission listed in that section to be directed to the page for submitting the manifest of that type.
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COPO validates the uploaded manifest.
-
If there are errors and/or warnings during the validation process, our system will provide messages to help resolve them.
If you encounter errors that you are unable resolve, we are happy to assist. Contact the detailing the issue(s) encountered.
If you encounter warnings, they are just informational and will not prevent the upload process from proceeding, as long as there are no errors. Once there are no errors related to the field and you are satisfied with the value, the upload process will continue when you click the
button if it is the first time you are uploading the
manifest or the 
button if you are updating the
manifest.
-
-
If applicable, upload permits and/or images after uploading the sample manifest in the same attempt. Use the appropriate button in the Upload Sample Spreadsheet dialogue to complete this step.
Important
This process must be completed in one go; you cannot close the dialogue and return later to upload the permits and/or images. The permits and/or images rely on metadata from the sample manifest and as such they must be added in the same session.
Note
The Upload Sample Spreadsheet title of the dialogue will change depending on the type of submission that you are making e.g. Upload ERGA Sample Spreadsheet.
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Sample managers will be notified of the submission and will review it to accept or reject the samples.
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The metadata of accepted samples is deposited to ENA, where accession numbers are assigned and reflected in COPO. These samples can then be queried in public repositories like European Nucleotide Archive (ENA) and National Centre for Biotechnology Information (NCBI) using the assigned accession numbers.
The accession numbers are displayed in the columns – Biosample Accession, SRA Accession and Submission Accession – in the data table on the Samples page in COPO. While each accession uniquely identifies a sample record, the biosample accession is primarily used as the identifier.
Additionally, each cell/value in the aforementioned accession columns contains a hyperlink to the metadata on ENA, allowing you to directly access the data there.
For more details on retrieving accession numbers, please refer to the Retrieving Accessions section.
See also
Are accessions assigned in sample submissions after sample manifests are uploaded? FAQ
If you intend to submit other types of metadata in COPO such as assemblies, sequence annotations, barcoding manifests and reads submissions and would like to make the submitted metadata available in public repositories, please refer to the Releasing Profiles (Studies) section for more information.
How is genomic metadata linked to samples and shared publicly?
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Note
Click the button below to view its content.
Prerequisites
Please refer to the What are the steps for submitting sample metadata in COPO and ensure it appears in public repositories? FAQ for guidance on submitting sample metadata in COPO. The genomic metadata submission process depends on the sample metadata submission process.
In COPO, genomic metadata can be associated with submitted or existing sample metadata through the steps below:
-
Upload the data files associated with the type of genomic metadata to be submitted on the Files page.
See the Uploading Data Files section for guidance.
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Upload the genomic metadata to the same profile used for the sample manifest submission on the Work profiles page.
Each genomic metadata submission type requires wither a form or manifest (spreadsheet). Some fields may be linked to previously submitted sample metadata.
Navigate to the Components column of a profile then, click the appropriate option -
button, 
button, 
button
or 
to navigate to the relevant
page.
See also
Publishing Data Which types of genomic metadata submissions can be made? FAQ for guidance on the types of genomic metadata
Why am I seeing multiple errors after uploading a sample manifest?
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These Invalid column errors are likely due to the uploaded manifest not matching the desired sample type.
Samples uploaded to a Biodata profile - please ensure that the correct sample type is selected from the checklist dropdown menu on the Samples page before uploading a manifest.
-
Samples uploaded to a Tree of Life (ToL) profile - the sample type is determined by the type of ToL profile that you are uploading to.
Please make sure that the manifest you upload matches the sample type associated with that profile.
Refer to Profile Types Legend to identify the colour of the add manifest button (for example,
). The colour of
this button changes depending on the
profile type. For example, it may be 
for an
ASG
profile or 
for an ERGA profile.
Footnotes