The BioSample package set version 1.4.0 was released.
- Release note Github
- Package and attribute definition table ddbj_biosample_definition_table.xlsx
Packages addition
Standard packages used when it is not appropriate to use MIxS packages, and pathogen packages used for pathogen relevant to public health were added.
Other package is not available.
Standard packages
- SARS-CoV-2: clinical or host-associated
- SARS-CoV-2: wastewater surveillance
- Microbe
- Model organism or animal
- Metagenome or environmental
- Invertebrate
- Human
- Plant
- Virus
- Beta-lactamase
- Omics
Pathogen packages
- Pathogen: clinical or host-associated
- Pathogen: environmental/food/other
New MIxS packages were added.
- MIMAG: metagenome-assembled genome
- MISAG: single amplified genome
- MIUVIG: uncultivated virus genome
New MIxS environment package was added.
- built
The functional genomics package was renamed to Omics package becase it is used for MetaboBank metabolomics data in addition to GEA functional genomics data.
- Functional genomics → Omics package
At least one of attributes is mandatory
Either one mandatory -at least one of attributes is mandatory- check was added.
In the following packages, at least one of these attributes is necessary. For example, strain or isolate is necessary in the Microbe package.
In the BioSample submission tsv, mandatory attributes are marked with “*”, however, either-one-mandatory attributes are not marked. In the D-way submission system, validation will fail when a tsv with empty either-one-mandatory attributes is uploaded.
| Package | ‘either-one-mandatory’ attributes | ‘either-one-mandatory’ attributes |
|---|---|---|
| Microbe | strain, isolate | isolation_source, host |
| Model.organism.animal | strain, isolate, breed, cultivar, ecotype | age, dev_stage |
| Metagenome.environmental | isolation_source, host | |
| Invertebrate | isolate, breed | isolation_source, host |
| Plant | isolate, cultivar, ecotype | age, dev_stage |
| Virus | host, lab_host | |
| Beta-lactamase | strain, isolate | |
| Pathogen.cl | strain, isolate | |
| Pathogen.env | strain, isolate |
Attribute name change
In the MIxS package, following attribute names are changed.
- env_biome → env_broad_scale
- env_feature → env_local_scale
- env_material → env_medium