Standards - GSA - CNCB-NGDC

1. Metadata

1.1 BioProject

BioProject is a searchable collection of complete and incomplete (in-progress) large-scale molecular projects including genome sequencing and assembly, transcriptome, metagenomic, annotation, expression and mapping projects.

1.1.1 ID System

BioProject accession No. is prefixed with 'PRJC' and followed by 1 Capital letters and 6 digits. For example, PRJCA000001.

1.1.2 Attributes

See the Standard of BioProject metadata for detailed information.

1.2 BioSample

BioSample contains descriptions of biological source materials used in studies that have data in other National Genomics Data Center databases such as Genome Sequence Archive, Genome Warehouse, Gene Expression Nebulas, Genome Variation Map, Methylation Bank, etc. The National Genomics Data Center, working collaboratively with multiple partner institutions/laboratories, develops a family of standards for big omics data representation, analysis, search and exchange.

1.2.1 ID System

BioSample accession No. is prefixed with 'SAMC', and followed by6 digits. For example, SAMC000001.

1.2.2 Sample Types

Pathogen

Used for pathogen samples that are relevant to public health. Required attributes include those considered useful for the rapid analysis and trace back of pathogens.

Clinical or host-associated

Environmental, food or other

Microbe

Used for bacteria or other microbes when it is not appropriate or advantageous to use for Pathogen or Virus packages.

Animal

Used for multicellular samples or cell lines derived from common laboratory model organisms, e.g., mouse, rat, Drosophila, worm, fish, frog, or large mammals including zoo and farm animals.

Human

Human genetic related raw sequence reads should be submitted to the GSA for Human database.

Plant

Used for any plant sample or cell line.

Virus

Used for all virus samples not directly associated with disease. Viral pathogens should be submitted using the Pathogen: Clinical or host-associated pathogen package.

Metagenome/Environmental Sample (GSC MIMS unsupported)

Use for metagenome/environmental samples when it is not appropriate or advantageous to use the GSC (Genome Standards Consortium) MIMS (Minimum Information about a MetaGenome Sequence) standards.

Metagenome/Environmental Sample (GSC MIMS compliant)

Describe and standardize sample metadata, defined by the GSC (Genome Standards Consortium) MIMS (Minimum Information about a MetaGenome Sequence) standards for metagenome/environmental samples.

human-gut

soil

water

1.2.3 Attributes

See the Standard of BioSample metadata for detailed information.