Validation and Conversion
The FAANG validation tool will validate required assay specific tabs for any of the assay types contained within the FAANG experiment metadata rules. You can upload your completed Experiment template, as was possible for your sample metadata template. This will alert you to any errors that need resolving before submission. Please contact FAANG DCC for guidance if required.
To start validation please follow these steps:
- Click on 'Choose file'' button to choose filled out template file
- Click on 'Upload a File' button to upload template to validation service
- Check 'Status' badge for updates. It might have three different values:
- If status has 'Success' value you can start validation. For this click on 'Start validation' button
- Check 'Status' badge in '3. Validation results:' section for updates.
It might have three different values:
- Review all 'Errors' and 'Warnings'. For this click on the cell that contains any issues, pop-up window will have detailed information about 'Errors' and 'Warnings'
'Errors' are problems that have to be dealt with. You will not be able to convert the FAANG experiments spreadsheet to the ENA XML format if the spreadsheet contains errors. 'Warnings' are items for you to review. They might be fine, but you need to decide. Any warnings left in a submission are likely to be reviewed by the FAANG DCC. You may be asked to update the experiment record later if the metadata group agrees a certain value should be improved.
For descriptions and explanations of the different error messages that the validation tool can provide please see FAANG validation error message explanations.
Metadata fields are organized into biologically-meaningful type schemas, for example a 'ATAC-seq' or 'DNase-seq'. Each type schema inherits a core schema, containing the minimal fields necessary for that type (standard rule group in experiments ruleset). Also template could have custom fields (defined by user) and module fields (ChIP-seq DNA-binding proteins and ChIP-seq input DNA).
For each of these types of schemas 'Errors' and 'Warnings' information will be provided in '3. Validation results' section, for example 'Core errors' or 'Type warnings'.
Having run the validation tool on your spreadsheet, you will need to update it to deal with the errors shown. Review the warnings and consider making changes to deal with these. Re-validate your spreadsheet, and repeat the process until there are no errors left and you are comfortable with everything that has triggered a warning. If there are some things that you cannot resolve, contact FAANG DCC for help. Eventually, you will have a set of metadata that passes the validation checks and is ready for conversion.
To start conversion you need to fix all 'Errors' in template. When data is ready follow these steps to get converted data in JSON format:
- Click on 'Get submission data' button (it will start conversion process)
- Check 'Status' badge in '4. Get data for submission:' section for updates.
- Click on 'Dowload data' button to get JSON file that is suitable for BioSamples submission.
The FAANG conversion tool converts your experiment template into the required XML documents that will be given to you as a zipped download. The conversion tool runs a number of additional checks to the validation tool that are specific for submission to the ENA, so you may need to resolve a number of other errors before the files are converted.
The FAANG conversion tool has been developed to support FAANG users submitting to the European Nucleotide Archive, as due to the requirements of FAANG you must submit using XML documents, you should also refer to the documentation from ENA and SRA to ensure you meet their requirements. To submit to ENA you require a number of XML documents. XML is a structured document language that will be used to describe your array data, these will be created for you by the FAANG validation tool. This validation tool is new, and may not currently support all requirements, please contact FAANG DCC if you have any issues in creating your XML files.
Before you start you MUST have submitted all of your sample data to BioSamples, please refer to the instructions to achieve this.
You may wish to refer to the ENA schema for additional information on certain data formats and attributes. If there are any fields that you require and are missing from the excel template, please contact FAANG DCC to see if we can add it.
Please contact FAANG DCC if you have any issues in creating your XML files.