Overview

This page will guide you through the process of submitting your samples to BioSamples in order to receive your sample accession IDs. We have provided templates and tools to help validate your samples metadata. If you have any questions about this process please contact FAANG Data Coordination Centre for help.

Prerequisites

Please familiarise yourself with the latest sample ruleset specification and the FAANG data sharing principles.

IMPORTANT: The data validation service is not compatible with templates prepared using Libre Office Calc, please use Microsoft Excel saving as xslx or Google sheets exporting as xslx.

In order to submit samples to BioSamples first you need to complete Excel template with information about your sample following these two steps:

  1. Download the Excel template
  2. Complete the template

1. Download the Excel template

2. Complete the template

Complete the template following the instructions below on this page and referring to the latest sample ruleset specification. The rules for each attribute define if it is mandatory or optional, what sort of data is expected (numeric, date, text, etc.), what units are permitted, and whether or not an ontology term is required.

The Excel template contains a series of separate worksheet tabs to capture information about the organisms, specimens and cells. Do not alter or delete any of the existing column headings or tabs from the file.
However it is fine to add or duplicate column headings for the purpose of capturing customized extra information and providing multiple values for one field respectively (where it's allowed, see ruleset specification "Allow multiple?" field).

Submission tab

Provide a submission title and submission description. * Submission Title. The suggested title format is "EBI-FAANG-HARRISON-Sheep-160414". This is constructed from your organisation/group abbreviation, the "FAANG" project (to help identify your samples), submitters surname, common species name and date of submission. * Note please check the organisation/group abbreviation page to find or add your organisation/group abbreviation for consistency across institutes. * Submission Description. Briefly describe the samples and study.
This description will be displayed on BioSamples to describe all of the samples in your BioSamples group so it is important that it is informative and accurately describes the samples in the study. Please ensure that the common species name is included in this description.

Person tab

Add the full details and email address of the people responsible for producing the data. At least one person must be listed. For each person a role should be provided from the list of possible organization roles.

A person can have more than one role by listing them twice in full, see the example of John Smith below. At least one person should be listed as the submitter (this is you!).

Person Last Name Person Initials Person First Name Person Email Person role
Smith J John john@someplace.ac.uk submitter
Smith J John john@someplace.ac.uk experiment performer
Bloggs LE Laura laura@someplace.ac.uk data analyst
Organization tab

Add the full details of the organisations and funding bodies responsible for producing the data. At least one organisation must be listed.

For each organisation a role should be provided from the same list as the person tab above.

Multiple organizations can be recorded here as appropriate, one per line.
If an organization has more than one role, then it should be listed in full on multiple lines, see example for Roslin Institute below.

Organization Name Organization Address Organization URI Organization Role
EMBL-EBI Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom http://www.ebi.ac.uk/ curator
The Roslin Institute and Royal Dick School of Veterinary Studies Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, United Kingdom http://www.roslin.ed.ac.uk/ institution
The Roslin Institute and Royal Dick School of Veterinary Studies Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, United Kingdom http://www.roslin.ed.ac.uk/ biomaterial provider
BBSRC Polaris House, North Star Avenue, Swindon, Wiltshire, SN2 1UH, United Kingdom http://www.bbsrc.ac.uk/ funder
Sample Name

Sample Name should contain a short species code, an abbreviated name for the institute/lab, and a unique ID for each sample, e.g. 'ECA_ROSLIN_H1'

Accepted short species codes (please contact FAANG DCC if you are submitting a species not listed there)

Please check the organisation/group abbreviation page to find or add your organisation/group abbreviation for consistency across institutes.

Sample Description

Briefly describe the sample.

Material and Term Source ID

For recording specimen material and term source ID please use this table

Project

Always use "FAANG" as the project so that your samples are in the correct group in BioSamples. The project tag is important, as the data coordination centre (DCC) will use it to find your records.

Availability

This is optional for all sample types. Use this to inform people how they can get access to the sample. This can either be as a URL, or an e-mail address to contact for further information. This information will persist in the archives, so please choose e-mail addresses or web sites that will be available for a long time. These are example values for the availability attribute (non-FAANG):

  • https://cells.ebisc.org/EDi001-A/
  • mailto:samplesgroup@example.ac.uk
Same as

BioSample ID for an equivalent sample record, created before the FAANG metadata specification was available. This is optional and not intended for general use, please contact the data coordination centre before using it.

Material specific fields

For information about material specific fields please follow ruleset specification:

Multiple values

Some metadata attributes permit multiple values. For example, you may wish to describe several health status traits for an animal. In this case, insert extra columns for the attribute into the template. Take care to copy all related columns. e.g. for an animal with foot and mouth disease and endocarditis, you would use four columns:

Health Status Term Source ID Health Status Term Source ID
endocarditis EFO_0000465 foot and mouth disease EFO_0007277

Where there isn’t a term that is precisely right, consider using the ID for a term that is close enough, combined with text to say exactly what you mean. This will be marked with a warning at validation, but you can choose to ignore this. You can also request a new term from the ontology. Guidance on this is available on the FAANG wiki. Contact FAANG DCC if assistance is needed. As requesting a new term can sometimes take a while to resolve, you can use the best approximation first, and update with the more accurate term at a later date. You don’t have to just wait for the new term to be assigned.

Guidelines on describing crossbred animals.

There are additional instructions for describing crossbred animals

Derived From / Child of

Used to describe familial relationships between samples or what samples were derived from. For example, a tissue specimen is derived from an animal.

These must either:

  • Refer exactly to the 'Sample Name' of an appropriate sample within the same excel spreadsheet
  • Refer to an appropriate sample that already exists in the BioSamples database using its BioSample ID, e.g. 'SAMEA4447799'.
Specimen Collection Protocol / Purification Protocol / Cell Culture Protocol / Culture Protocol

The FAANG sample and experiment metadata specification requires your protocols to be publicly available.

It is best these are hosted in a location which will be available in the long term so locations such as lab pages are inadvisable as web addresses change and hosting goes away.

FAANG is happy to host protocols in the data portal

If you wish FAANG to host your protocols, please send PDF copies of your protocols to FAANG DCC. Please consult the FAANG metadata validation privacy notice for the processing of your personal information in relation to protocol submission https://www.ebi.ac.uk/data-protection/privacy-notice/faang-metadata-validation

Please name your files using this convention INSTITUTE_SOP_PROTOCOLNAME_YYYYMMDD.pdf e.g INRA_SOP_sorting_swine_CD_cells_20160504.pdf. This is a protocol for Sorting Swine CD cells, the protocol comes from the French National Institute for Agricultural Research and the protocol was written on the 4th May 2016.

Please check the organisation/group abbreviation page to find or add your organisation/group abbreviation for consistency across institutes.

If you have any questions about protocols and the form they should take, please email the FAANG Animal, Samples and Assays group

3. Specific metadata instructions for tracking embryos and pregnancy

For samples taken from pregnant animals:

  • Include that the animal was 'pregnant' in the Sample Description.
  • The 'Animal Age At Collection' is the age of the mother
  • The gestational age and unit should also be supplied. (TODO: check this)

For embryo samples, on the specimen from organism sheet 'Organism Part' should be listed as "embryo", the 'Term Source ID' as "UBERON_0000922". The 'Animal Age At Collection' should list the embryos age in days since conception.

4. Adding custom columns to your spreadsheet

It is possible to add additional custom fields to your BioSamples records, simply add the columns to the end of the appropriate tab.

Please contact FAANG DCC with your requirements as it may be something we wish to support by default in future.

If it is possible to attach an ontology term to control the nomenclature of these custom fields then 'Term Source Ref' and 'Term Source ID' columns should also be added. If you are using an ontology not listed by default under the term source tab then it needs to be added to the term source tab and you also need to contact FAANG DCC to let us know which ontology you have additionally used.

5. Missing values

Where data cannot be included in a submission, submit one of these text values instead:

  • not applicable
  • not collected (i.e. will always be missing)
  • not provided (i.e. may be added later)
  • restricted access (i.e. it isn't missing, we just can't include it in a public document)

The use of these values will interact with the metadata validation system as follows:

  • if an attribute is required:
    • not applicable, not collected, not provided - validation will regard these as an error
    • restricted access - validation will generate a warning
  • if an attribute is recommended:
    • not collected, not provided - validation will generate a warning
    • restricted access, not applicable - pass
  • if an attribute is optional:
    • validation will fail with any of missing values terms. As this is an optional field it should be left blank if no real data is being provided.

If an attribute is optional and you can’t supply it, you should just leave the column blank.

Assume that the DCC will ask about anything that seems implausible. e.g. 'restricted access' for species would be queried.

6. Pools of specimens

Each specimen within the pool should have its own specimen record. For each specimen in the pool add its 'Sample Name' (if detailed in the same file), or BioSample ID if it already exists in the BioSamples database, to the 'Derived From' field. Add as many 'Derived From' fields as are required to record all of the specimens that are part of the pool.