The BioSample package set version 1.4.0 was released.

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 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