2.1. BioProject & BioSample submission

Introduction

Registering project and biological samples at the K-BDS BioProject and the BioSample databases is a prerequisite for any public KVar submission. The BioProject and BioSample databases store data that relate to organizational and biological aspects of sequencing experiments.

BioProject submission describes the goal of the sequencing study, whereas BioSample submission records the attributes of the biological material that had been sequenced

However, for human-derived material data (KHBDB), do not create BioProject or BioSample; instead, follow the KHBDB's guidelines.

BioProject Submission Quick guide

BioProject describes the goal of your research effort. Each study is limited to a single database submission in K-BDS, aligning with the policy that only one data type can be registered per project. you may accumulate data that are suitable for submission in multiple K-BDS databases. To be eligible for KVar submission the project (1) must exist; (2) should not be an umbrella project

1. Log in first to register the BioProject.

2. Click on the Submit menu of BioProject or KVar main page

3. Enter entire section of the BioProject divided into 4 steps. Be sure to fill in fields marked with an asterisk(*)

   1. Submitter (Submitter & Group information)

   2. Project type (Project type & Release date)

   3. Project information (General & Grant & Publication and patent information)

   4. Review & Submit

   👉 All fields must be entered in English and numbers, and required fields must be filled out.

4. Click on the Continue at the bottom of each step after completing the writing

   1. Each step will automatically undergo validation — if any errors are detected, the corresponding fields will be highlighted in red, and you will not be able to proceed to the next step until all issues are resolved.

   2. Once validation is successfully completed, you can move to the next step.

5. After completing all steps, review your information on the final “Review & Submit” step, then click Save at the bottom of the screen to finalize and submit your BioProject.

6. When the BioProject is submitted, you can check the submitted content in Manage data of My data of My page

   👉 For general BioProjects, once validation is successfully completed and submission is finalized, the BioProject is approved and accession number (KAP#) is immediately assigned.

Please refer to BioProject Documentation for details

BioSample Submission Quick guide

BioSample is a record of biological isolate with unique physical properties. Biological and technical replicates (in most cases) should not be considered unique BioSamples.

Examples:

• 23,000 unique 16S amplicons from a single seawater collection point – 1 BioSample (1 sample was collected and then analyzed to deduce 16S diversity)

• 3 "identical" transgenic mice treated with the same drug as part of an experiment – 1 BioSample

• CHO cells infected with a virus and sampled at 0, 2, 4, and 8 hours post infection – 4 BioSamples (4 time points)

• RNA-Seq data from a single male anteater taken from the brain, heart, lungs, testes, and liver – 5 BioSamples (5 different tissues isolated)

Majority of KVar submissions require more than one sample. Make sure that organism/metagenome, tissue type, time point, etc., have their own sample. Select most appropriate taxonomy for organism/metagenome in the NCBI Taxonomy browser. Providing the exact and most specific name for the organism/metagenome will simplify your BioSample submission. For metagenome or environmental samples look up appropriate taxonomy in the NCBI Taxonomy browser Unspecified sequences taxonomy.

1. Log in first to register the BioSample.

2. Click on the Submit menu of BioSample or KVar main page

3. Enter entire section of the BioSample divided into 4 steps. Be sure to fill in fields marked with an asterisk(*)

   1. BioProject (BioProject accession number & Release date)

   2. Sample packages

   3. Attributes

   4. Review & Submit

   👉 All fields must be entered in English and numbers, and required fields must be filled out. However, if an appropriate English term does not exist (e.g., cultivar), Korean may be used instead

Prerequisites of sample packages & attributes

• The sample package consists of a total of 10 types (Human, organism or animal, Invertebrate, Plant, Microbe, Virus, Clinical or host-associated pathogen, Environmental food or other pathogen, Metagenome or environmental, MIMS Metagenome/Environmental)

• The MIMS Metagenome/Environmental package is further divided into 23 sub-categories depending on the specific environment from which the sample was collected.

• Excel template is different for each sample package, so care must be taken when writing metadata

• Each sample name must be meaningful and unique within linked BioProject. Please do not name sample by your sequence data filename

1. Click on the Continue at the bottom of each step after completing the writing

   1. Each step will automatically undergo validation — if any errors are detected, the corresponding fields will be highlighted in red, and an error report detailing the cause of the failure will be displayed in the Attribute step.

   2. You will not be able to proceed to the next step until all issues are resolved.

   3. Once validation is successfully completed, you can move to the next step.

2. After completing all steps, review your information on the final “Review & Submit” step, then click Save at the bottom of the screen to finalize and submit your BioSample.

3. When the BioSample is submitted, you can check the submitted content in Manage data of My data of My page

   👉 Once validation is successfully completed and submission is finalized, the BioSample is approved and accession number (KAS#) is immediately assigned.

⚠️ Note: Even after the BioSample registration is completed, the corresponding BioData will remain hidden until it is reviewed and approved by the administrator. Please note that, upon the administrator’s request, certain details may need to be supplemented or revised after registration.

Please refer to BioSample Documetation for details

Contact K-BDS staff

If you need assistance or updates regarding BioProject and BioSample submission, please send an email to [e-mail]