This document contains a list of all required fields in the HCA metadata schema. For a fulldescription of each schema, please refer to the relevant entity specification document.
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
file_name
The name of the file.
string
File name
R1.fastq.gz; codebook.json
format
The format of the file.
string
File format
fastq.gz; tif
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
protocol_id
A unique ID for the protocol.
string
Protocol ID
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
project_short_name
A short name for the project.
string
Project label
CoolOrganProject.
project_title
An official title for the project.
string
Project title
Study of single cells in the human body.
project_description
A longer description of the project which includes research goals and experimental approach.
string
Project description
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
biomaterial_id
A unique ID for the biomaterial.
string
Biomaterial ID
ncbi_taxon_id
A taxonomy ID (taxonID) from NCBI.
array
NCBI taxon ID
9606
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
process_id
A unique ID for the process.
string
Process ID
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
file
file_core
Core file-level information.
object
See core file_core File core
read_index
The sequencing read this file represents.
string
Read index
read1, read2, read3, read4, index1, index2, single-end, non-indexed
Should be one of: read1, read2, index1, index2
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
file
file_core
Core file-level information.
object
See core file_core File core
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
file
file_core
Core file-level information.
object
See core file_core File core
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
file
file_core
Core file-level information.
object
See core file_core File core
genome_assembly_version
Name of the genome assembly used to generate this file.
string
Genome version
GRCh38, GRCh37, GRCm39, GRCm38, GRCm37, Not Applicable
Should be one of: GRCh38, GRCh37, GRCm39, GRCm38, GRCm37, Not Applicable
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
file
file_core
Core file-level information.
object
See core file_core File core
ncbi_taxon_id
A taxonomy ID (taxonID) from NCBI.
integer
NCBI taxon ID
9606; 10090
genus_species
The scientific binomial name for the species of this reference.
object
See module species_ontology Genus species
reference_type
The type of the reference file.
string
Reference type
genome sequence, transcriptome sequence, annotation reference, transcriptome index, genome sequence index
Should be one of: genome sequence, transcriptome sequence, annotation reference, transcriptome index, or genome sequence index.
assembly_type
The assembly type of the genome reference file.
string
Genome assembly type
primary assembly, complete assembly, patch assembly
Should be one of: primary assembly, complete assembly, or patch assembly.
reference_version
The genome version of the reference file.
string
Reference version
GencodeV27; Ensembl 87
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
instrument_manufacturer_model
The manufacturer and model of the sequencer.
object
See module instrument_ontology Instrument manufacturer and model
paired_end
Whether the sequenced molecule was sequenced from both ends.
boolean
Paired end
Should be one of: yes, or no.
method
The general method for sequencing.
object
See module sequencing_ontology Sequencing method
Library preparation protocol
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
input_nucleic_acid_molecule
Starting nucleic acid molecule isolated for sequencing.
object
See module biological_macromolecule_ontology Input nucleic acid molecule
nucleic_acid_source
Source cells or organelles from which nucleic acid molecules were collected.
string
Nucleic acid source
bulk cell, single cell, single nucleus, bulk nuclei, mitochondria
Should be one of: single cell, bulk cell, single nucleus, bulk nuclei, or mitochondria.
library_construction_method
The general method for sequencing library construction.
object
See module library_construction_ontology Library construction method
end_bias
The type of tag or end bias the library has.
string
End bias
3 prime tag, 3 prime end bias, 5 prime tag, 5 prime end bias, full length
Should be one of: 3 prime tag, 3 prime end bias, 5 prime tag, 5 prime end bias, or full length.
strand
Library strandedness.
string
Strand
first, second, unstranded, not provided
Should be one of: first, second, unstranded, or not provided.
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
type
The type of protocol.
object
See module process_type_ontology Protocol type
Aggregate generation protocol
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
formation_method
Method used to form cell aggregates.
string
Aggregate formation method
rocking; suspension cultures; hanging drops; spinner flasks
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
method
The method by which enrichment was achieved.
object
See module process_type_ontology Enrichment method
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
method
How cells or organelles were dissociated.
object
See module process_type_ontology Dissociation method
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
method
Induction method applied to primary cell culture to induce pluripotent stem cell generation.
string
Induction method
lentivirus, sendai virus, Gun particle, piggyBac transposon, miRNA viral, adenovirus, cre-loxP, plasmid, retroviral
Should be one of: lentivirus, sendai virus, Gun particle, piggyBac transposon, miRNA viral, adenovirus, cre-loxP, plasmid, or retroviral.
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
method
Method used to collect the biomaterial.
object
See module process_type_ontology Collection method
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
method
Method applied to cell culture to induce a specific differentiation response.
string
Differentiation method
Embryoid Body; Monolayer; Inductive Co-Culture
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
method
Method applied to cell culture to induce a specific treatment response.
array
See module treatment_method_ontology Treatment method
Imaging preparation protocol
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
protocol
protocol_core
Core protocol-level information.
object
See core protocol_core Protocol core
microscopy_technique
The type of microscopy.
object
See module microscopy_ontology Microscopy technique
magnification
Magnification of the objective used for imaging.
string
Magnification
60x; 100x
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
project
project_core
Core project-level information.
object
See core project_core Project core
funders
Funding source(s) supporting the project.
array
See module funder Funding source(s)
data_use_restriction
Data use restrictions that apply to the project.
string
Data use restriction
NRES, GRU, GRU-NCU
GRU
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
biomaterial
biomaterial_core
Core biomaterial-level information.
object
See core biomaterial_core Biomaterial core
organ
The organ that the biomaterial came from.
object
See module organ_ontology Organ
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
biomaterial
biomaterial_core
Core biomaterial-level information.
object
See core biomaterial_core Biomaterial core
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
biomaterial
biomaterial_core
Core biomaterial-level information.
object
See core biomaterial_core Biomaterial core
type
The type of cell line.
string
Cell line type
primary, immortalized, stem cell, stem cell-derived, induced pluripotent, synthetic
Should be one of: primary, immortalized, stem cell, stem cell-derived, induced pluripotent, or synthetic.
model_organ
Organ for which this cell line is a model.
object
See module organ_ontology Organ model
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
biomaterial
biomaterial_core
Core biomaterial-level information.
object
See core biomaterial_core Biomaterial core
slice_thickness
Thickness of the imaged slice in micrometres.
number
Imaged slice thickness
14
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
biomaterial
biomaterial_core
Core biomaterial-level information.
object
See core biomaterial_core Biomaterial core
sex
The biological sex of the organism.
string
Biological sex
female, male, mixed, unknown
Should be one of: male, female, mixed, or unknown.
is_living
Whether organism was alive at time of biomaterial collection.
string
Alive at collection
yes, no, unknown, not applicable
Should be one of: yes, no, not applicable, or unknown.
development_stage
A classification of the developmental stage of the organism.
object
See module development_stage_ontology Development stage
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
biomaterial
biomaterial_core
Core biomaterial-level information.
object
See core biomaterial_core Biomaterial core
model_organ
Organ for which this organoid is a model system.
object
See module organ_ontology Organ model
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
process
process_core
Core process-level information.
object
See core process_core Process core
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
schema_type
The type of the metadata schema entity.
string
process
process_core
Core process-level information.
object
See core process_core Process core
type
The type of process.
object
See module process_type_ontology Process type
inputs
Input parameters used in the pipeline run.
array
Input parameters
tasks
Information about steps in the workflow.
array
Workflow tasks
timestamp_start_utc
Initial start time of the full pipeline in UTC.
string
Start timestamp (UTC)
2018-01-21T09:34:27Z
timestamp_stop_utc
Terminal stop time of the full pipeline in UTC.
string
Stop timestamp (UTC)
2018-01-21T11:35:01Z
analysis_run_type
Whether the analysis was run or was copied forward as an optimization.
string
Analysis run type
run, copy-forward
Should be one of: run, or copy-forward.
reference_files
UUID of the file entities that contain the reference genome used in running the pipeline.
array
Reference files
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
channel_id
User given ID. If there is an accompanying codebook, this name should correspond to the channel id used in the codebook.
string
Channel ID
1; A
excitation_wavelength
Excitation wavelength of the lightsource in nanometers.
number
Excitation wavelength
640
filter_range
Emission filter in nanometers.
string
Filter range
461/70
multiplexed
Whether multiple targets were detected simultaneously in this channel.
string
Multiplexed experiment
yes, no
Should be one of: yes, or no.
exposure_time
Acquisition time for a single image per channel, in milliseconds.
number
Exposure time
400
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
probe_label
The label of a probe used to detect target in this experiment.
string
Probe label
ACTA1; cFos
target_label
An identifier for the target molecule.
string
Target label
CHEBI:85345; ENSG00000170345
assay_type
Type of assay used to detect target.
object
See module process_type_ontology Assay type
MERFISH; in situ sequencing
There are no required properties in schema Matrix
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
General description of the contents of the file.
string
Content description
DNA sequence (raw); Sequence alignment
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a length unit being used.
string
Length unit
micrometer; meter
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a cell cycle of the cells in the specimen.
string
Cell cycle
meiotic cell cycle; mitotic G1 phase
Library amplification ontology
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a library amplification approach being used.
string
Library amplification
PCR; in vitro transcription
Contributor role ontology
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The primary role of the contributor in the project.
string
Contributor role
principal investigator; experimental scientist
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The ethnicity of the human donor.
string
Ethnicity
European; Hispanic or Latin American
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of the treatment target pathway.
string
Target pathway
positive regulation of memory T cell differentiation
Treatment method ontology
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a treatment method or approach being used.
string
Treatment method
T cell activation assay
Cellular component ontology
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a subcellular structure.
string
Subcellular structure
cytoplasm; nucleus
Library construction ontology
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a library construction approach being used.
string
Library construction
10X v2 sequencing; Smart-seq2
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a process type being used.
string
Process type
enzymatic dissociation; blood draw
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The gender identity of the human donor at the time of the experiment.
string
Gender identity
Female Gender; Agender; Non-Binary Gender
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a sequencing approach being used.
string
Sequencing approach
tag based single cell RNA sequencing; full length single cell RNA sequencing
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of the species to which the organism belongs.
string
Species
Homo sapiens; Mus musculus
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The text for the term as the user provides it.
string
Disease
type 2 diabetes mellitus; normal
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of the strain to which the organism belongs.
string
Strain
C57BL/6; BALB/c
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
Medication(s) the individual was taking at time of biomaterial collection.
string
Medication
Ibuprofen Lysine; Bisoprolol; Ambroxol Hydrochloride
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of the file format.
string
File format
FASTQ; JSON
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of an enrichment approach being used.
string
Enrichment
fluorescence-activated cell sorting; Ficoll-Hypaque method
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The text for the term as the user provides it.
string
Organ part
bone marrow; islet of Langerhans
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of the type of microscopy used in an imaging experiment.
string
Microscopy
confocal microscopy; fluorescence microscopy
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a time unit being used.
string
Time unit
second; week
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a protocol type used.
string
Protocol type
dissociation protocol; enrichment protocol
Development stage ontology
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of the development stage of the organism.
string
Development stage
human adult stage; Theiler stage 28
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The full name of the instrument used.
string
Instrument
Illumina HiSeq 2500; ONT MinION
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a mass unit being used.
string
Mass unit
kilogram; microgram
Biological macromolecule ontology
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of the biological macromolecule being used.
string
Biological macromolecule
polyA RNA; mRNA
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The name of a cell type supplied by a user.
string
Cell type
bone marrow hematopoietic cell; cardiac muscle cell
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
text
The text for the term as the user provides it.
string
Organ
heart; immune system
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
grant_id
The unique grant identifier or reference.
string
Grant ID
BB/P0000001/1
organization
The name of the funding organization.
string
Funding organization
Biotechnology and Biological Sciences Research Council (BBSRC); California Institute of Regenerative Medicine (CIRM)
There are no required properties in schema HCA Bionetwork
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
name
Name of individual who has contributed to the project.
string
Contact name
John,D,Doe; Jane,,Smith
institution
Name of primary institute where the individual works.
string
Institute
EMBL-EBI; University of Washington
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
authors
A list of authors associated with the publication.
array
Authors
Doe JD
title
The title of the publication.
string
Publication title
Study of single cells in the human body.
official_hca_publication
Has the publication been accepted as an official HCA publication, according to the process described in https://www.humancellatlas.org/publications/ ?
boolean
Official HCA Publication
yes; no
There are no required properties in schema Human-specific
There are no required properties in schema Growth conditions
There are no required properties in schema Medical tests
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
name
Name of the institute where the biomaterial was collected on.
string
Collection institute name
institute_1; Addenbrooke's Hospital; University of California, San Francisco
There are no required properties in schema Disease profile
There are no required properties in schema Reproductive history
There are no required properties in schema Preservation and storage
There are no required properties in schema Lifestyle
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
cause_of_death
Conditions resulting in death.
string
Cause of death
Hypoxic brain damage; Sudden cardiac arrest
There are no required properties in schema Familial relationship
There are no required properties in schema Medical history
There are no required properties in schema Blood test
There are no required properties in schema Residence
There are no required properties in schema Cell morphology
There are no required properties in schema State of specimen
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
value
The numerical value in Timecourse unit associated with a time interval used in the experiment.
string
Timecourse value
2; 5.5-10.5
unit
The unit in which the Timecourse value is expressed.
object
See module time_unit_ontology Timecourse unit
There are no required properties in schema Mouse-specific
There are no required properties in schema Purchased reagents
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
insdc_experiment_accession
An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession.
string
INSDC experiment accession
SRX0000000
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
barcode_read
The read in which the barcode is found.
string
Barcode-containing read
Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index
Should be one of: Read 1, Read 2, i7 Index, or i5 Index.
barcode_offset
The 0-based offset of start of barcode in read.
integer
Barcode offset
0
barcode_length
Length of barcode in nucleotides.
integer
Barcode length
28
There are no required properties in schema 10x-specific
Property name
Description
Type
Object reference?
User friendly name
Allowed values
Example
plate_label
A label or name for the plate on which the well is located.
string
Plate label
2217