Complex substance of biological origin

derived_from

Description: The biological substance the complex substance is derived from
Required: yes
Type: enumerator (string)
Options: ('Body fluid', 'Cell fraction', 'Virion')

source_organism

Description: Identification of the organism to the lowest taxonomic rank possible e.g. strain. Note that this is based on the NCBI taxonomy
Required: yes
Type: object (vocabulary)
Contains see Organism

preparation_protocol

Description: List of the steps performed during the preparation of the complex substance
Required: yes
Type: array of object (Step)
Contains see Step

storage

Description: Information about how the complex substance was stored between being acquired and measured, including temperature and duration
Required: no
Type: object (Storage)
Contains see Storage

additional_specifications

Description: Additional information about the complex substance can be specified here
Required: no
Type: array of string (fulltext)

The fields from one of the following objects

Body fluid:

fluid

Description: The body fluid the complex substance is derived from
Required: yes
Type: enumerator (string)
Options: ('Blood', 'Fecal matter', 'Milk', 'Plasma', 'Saliva', 'Serum', 'Urine', 'Plant extract')

health_status

Description: Health status of the donor organism where the body fluid was derived (e.g. healthy, sick, patient with Diabetes type 2)
Required: yes
Type: string (keyword)

Cell fraction

fraction

Description: The subcelluar component e.g. (Ribosome)
Required: yes
Type: enumerator (string)
Options: ('Ribosome', 'Cell wall', 'Vesicle' ' Cell lysate/Cytoplasm', 'Cell Membrane', 'Extracellular matrix', 'Lysosome', 'Golgi Apparatus', 'Mitochondrion', 'Nucleus', 'Rough Endoplasmic Reticulum', 'Smooth Endoplasmic Reticulum', 'Vacuole','Chloroplast')

organ

Description: The organ the cell fraction was derived from (e.g. heart)
Required: no
Type: string (keyword)

tissue

Description: The tissue type the cell fraction was derived from
Required: no
Type: string (keyword)

cell_type

Description: The cell type the cell fraction was derived from
Required: no
Type: string (keyword)

health_status

Description: Health status of the donor organism where the body fluid was derived (e.g. healthy, sick, patient with Diabetes type 2)
Required: yes
Type: string (keyword)

Virion

genetic_material

Description: The genetic material carried by the virions (None, virus genome, synthetic)
Required: yes
Type: enumerator (string)
Options: ('No genetic material', 'Virus genome', 'Synthetic')

capsid_type

Description: The type of virion capsid
Required: yes
Type: enumerator (string)
Options: ('None', 'Native', 'Genetically Engineered', 'Synthetic')

envelope_type

Description: The type of virion envelope
Required: yes
Type: enumerator (string)
Options: ('None', 'Native', 'Genetically Engineered', 'Synthetic')

host_organism

Description: The host organism the virion was produced in. Note that information is based on the NCBI taxonomy
Required: no
Type: object (vocabulary)
Contains see Organism

host_cell_type

Description: The host organism the virion was produced in. Note that information is based on the NCBI taxonomy
Required: no
Type: string (fulltext)