Fields common to all schemas in this document
| Property name | Description | Type | Required? | Example |
|---|---|---|---|---|
| describedBy | The URL reference to the schema. | string | no | |
| schema_version | The version number of the schema in major.minor.patch format. | string | no | 4.6.1 |
A file of read sequences generated by a sequencing experiment.
Location: type/file/sequence_file.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | file | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| file_core | Core file-level information. | object | yes | See core file_core | File core | ||
| read_index | The sequencing read this file represents. | string | yes | Read index | read1, read2, read3, read4, index1, index2, single-end, non-indexed | Should be one of: read1, read2, index1, index2 | |
| lane_index | The lane that this file was sequenced from. | integer | no | Lane index | 1 | ||
| read_length | The length of a sequenced read in this file, in nucleotides. | integer | no | Read length | 51 | ||
| insdc_run_accessions | An International Nucleotide Sequence Database Collaboration (INSDC) run accession. | array | no | INSDC run accession | SRR0000000 | ||
| library_prep_id | A unique ID for the library preparation. | string | no | Library preparation ID | tech_rep_group_001 |
Information about an image file generated by an imaging experiment.
Location: type/file/image_file.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | file | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| file_core | Core file-level information. | object | yes | See core file_core | File core |
Supplementary files belonging to a project.
Location: type/file/supplementary_file.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | file | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| file_core | Core file-level information. | object | yes | See core file_core | File core | ||
| file_description | A short description of the file contents. | string | no | File description | Protocol for FACS enrichment; Image of spleen sample collection location |
A file analysis results produced by a secondary analysis pipeline.
Location: type/file/analysis_file.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | file | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| file_core | Core file-level information. | object | yes | See core file_core | File core | ||
| matrix_cell_count | Number of cells analyzed in a matrix file. | integer | no | Matrix cell count | 1; 2100 | ||
| genome_assembly_version | Name of the genome assembly used to generate this file. | string | yes | Genome version | GRCh38, GRCh37, GRCm39, GRCm38, GRCm37, Not Applicable | Should be one of: GRCh38, GRCh37, GRCm39, GRCm38, GRCm37, Not Applicable | |
| genome_patch_version | Patch version of the genome assembly used to generate this file. | string | no | Patch version | p11; p14 |
A reference file used by a secondary reference pipeline.
Location: type/file/reference_file.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | file | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| file_core | Core file-level information. | object | yes | See core file_core | File core | ||
| ncbi_taxon_id | A taxonomy ID (taxonID) from NCBI. | integer | yes | NCBI taxon ID | 9606; 10090 | ||
| genus_species | The scientific binomial name for the species of this reference. | object | yes | See module species_ontology | Genus species | ||
| reference_type | The type of the reference file. | string | yes | 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 | yes | 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 | yes | Reference version | GencodeV27; Ensembl 87 |
Information about the protocol.
Location: type/protocol/protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| type | The type of protocol. | object | no | See module process_type_ontology | Protocol type | sample enrichment |
Information about the sequencing protocol.
Location: type/protocol/sequencing/sequencing_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| instrument_manufacturer_model | The manufacturer and model of the sequencer. | object | yes | See module instrument_ontology | Instrument manufacturer and model | ||
| local_machine_name | Local name for the particular machine used for sequencing. | string | no | Local machine name | Machine1; HSMA-20 | ||
| paired_end | Whether the sequenced molecule was sequenced from both ends. | boolean | yes | Paired end | Should be one of: yes, or no. | ||
| method | The general method for sequencing. | object | yes | See module sequencing_ontology | Sequencing method | ||
| 10x | Fields specific for 10x experiments. | object | no | See module 10x | 10x-specific |
Information about how a sequencing library was prepared.
Location: type/protocol/sequencing/library_preparation_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| cell_barcode | Information about cell identifier barcodes. | object | no | See module barcode | Cell barcode | ||
| spatial_barcode | Information about spatial barcodes. | object | no | See module barcode | Spatial barcode | ||
| input_nucleic_acid_molecule | Starting nucleic acid molecule isolated for sequencing. | object | yes | See module biological_macromolecule_ontology | Input nucleic acid molecule | ||
| nucleic_acid_source | Source cells or organelles from which nucleic acid molecules were collected. | string | yes | 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 | yes | See module library_construction_ontology | Library construction method | ||
| library_construction_kit | Name of kit used to construct the sequencing library. | object | no | See module purchased_reagents | Library construction kit | ||
| nucleic_acid_conversion_kit | Name of kit used to convert RNA to DNA for sequencing. | object | no | See module purchased_reagents | Nucleic acid conversion kit | ||
| end_bias | The type of tag or end bias the library has. | string | yes | 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. | |
| primer | Primer used for cDNA synthesis from RNA. | string | no | Primer | poly-dT, random | Should be one of: poly-dT, or random. | |
| strand | Library strandedness. | string | yes | Strand | first, second, unstranded, not provided | Should be one of: first, second, unstranded, or not provided. | |
| spike_in_kit | Information about a spike-in kit. | object | no | See module purchased_reagents | Spike-in kit | ||
| spike_in_dilution | Dilution of spike-in. | integer | no | Spike-in dilution | 100 | ||
| umi_barcode | Information about unique molecular identifier (UMI) barcodes. | object | no | See module barcode | UMI barcode | ||
| library_preamplification_method | The method used to amplify RNA prior to adaptor ligation. | object | no | See module library_amplification_ontology | Library pre-amplification method | ||
| cdna_library_amplification_method | The method used to amplify cDNA library prior to sequencing. | object | no | See module library_amplification_ontology | cDNA library amplification method | ||
| nominal_length | Average (insert) size of the fragments being sequenced. | integer | no | Nominal length | 250 | ||
| nominal_sdev | Standard deviation of the (insert) size of the fragments being sequenced. | integer | no | Nominal standard deviation | 30 |
Information about the analysis protocol.
Location: type/protocol/analysis/analysis_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| type | The type of protocol. | object | yes | See module process_type_ontology | Protocol type | ||
| computational_method | A URI to a versioned workflow and versioned execution environment in a GA4GH-compliant repository. | string | no | Computational method | SmartSeq2SingleCell; 10x | ||
| matrix | Information related to protocols that output a matrix. | object | no | See module matrix | Matrix | ||
| alignment_software | Name of alignment software used to map FASTQ files to reference genome. | string | no | Alignment software | Cellranger; kallisto bustools; GSNAP; STAR | ||
| alignment_software_version | Version of alignment software used to map FASTQ files to reference genome. | string | no | Alignment software version | v2.0.1; 2.4.2a; v0.45.2 | ||
| gene_annotation_version | The Ensembl release version accession number or NCBI RefSeq assembly version used for gene annotation. | string | no | Gene annotation version | v110; GCF_000001405.40; GCF_000001635.27 |
Information about how cultured cells are developed into cell aggregates.
Location: type/protocol/biomaterial_collection/aggregate_generation_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| formation_method | Method used to form cell aggregates. | string | yes | Aggregate formation method | rocking; suspension cultures; hanging drops; spinner flasks | ||
| cell_uniformity | Description of the cell aggregates uniformity after formation. | string | no | Aggregate cell uniformity | Mostly homogenous embryoid bodies of variable cell numbers; Low-homogeneity in morphology and size |
Information about how a biomaterial is enriched for a feature or characteristic of interest.
Location: type/protocol/biomaterial_collection/enrichment_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| method | The method by which enrichment was achieved. | object | yes | See module process_type_ontology | Enrichment method | ||
| markers | A list of markers used to enrich for or against certain cells. | string | no | Markers | CD4+ CD8-; HLA-G+ | ||
| minimum_size | Minimum cell or organelle size passing selection, in microns. | number | no | Minimum size selected | 70 | ||
| maximum_size | Maximum cell or organelle size passing selection, in microns. | number | no | Maximum size selected | 90 |
Information about the dissociation protocol used to separate individual cells or nuclei.
Location: type/protocol/biomaterial_collection/dissociation_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| method | How cells or organelles were dissociated. | object | yes | See module process_type_ontology | Dissociation method | ||
| reagents | A list of purchased reagents used in this protocol. | array | no | See module purchased_reagents | Protocol reagents |
Information about how a biomaterial is treated to become an induced pluripotent stem cell.
Location: type/protocol/biomaterial_collection/ipsc_induction_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| method | Induction method applied to primary cell culture to induce pluripotent stem cell generation. | string | yes | 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. | |
| reprogramming_factors | Reprogramming factors added to primary cell culture to induce pluripotency. | string | no | Reprogramming factors | POU5F1; SOX2; KLF4; c-MYC | ||
| ipsc_induction_kit | Kit used to induce pluripotent stem cell generation. | object | no | See module purchased_reagents | Induction kit | ||
| pluripotency_test | Description of how pluripotency was tested in induced pluripotent stem cells. | string | no | Pluripotency test | Teratoma formation; PluriTest; Rt-PCR | ||
| percent_pluripotency | Percent of iPSCs that passed the pluripotency test. | number | no | Percent pluripotency | 97.2 | ||
| pluripotency_vector_removed | Whether a viral vector was removed after induction. | string | no | Pluripotent vector removed | yes, no, unknown | Should be one of: yes, no, or unknown. | |
| reagents | Additional purchased reagents used in this protocol. | array | no | See module purchased_reagents | Additional reagents |
Information about the biomaterial collection protocol.
Location: type/protocol/biomaterial_collection/collection_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| method | Method used to collect the biomaterial. | object | yes | See module process_type_ontology | Collection method | ||
| reagents | A list of purchased reagents used in this protocol. | array | no | See module purchased_reagents | Protocol reagents |
Information about how a cell is differentiated to a desired cell type or organoid.
Location: type/protocol/biomaterial_collection/differentiation_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| method | Method applied to cell culture to induce a specific differentiation response. | string | yes | Differentiation method | Embryoid Body; Monolayer; Inductive Co-Culture | ||
| media | Culture media used to induce a specific differentiation response. | string | no | Differentiation media | RPMI 1640 + B27; Neurobasal Media; StemPro-34 Serum-Free Medium | ||
| small_molecules | Small molecules added to stem cell medium to induce a specific differentiation response. | string | no | Small molecules | Retinoic Acid; CHIR99021 (GSK-inhibitor); Activin A; BMP4 | ||
| target_cell_yield | Percent of target cells obtained after directed differentiation of origin cell. | number | no | Percent target cell yield | 95 | ||
| reagents | A list of purchased reagents used in the differentiation protocol. | array | no | See module purchased_reagents | Differentiation reagents | ||
| target_pathway | Targeted pathway for specific differentiation response. | string | no | Target pathway | Wnt pathway; Hedgehog signaling pathway | ||
| validation_method | Method used to validate origin cell successfully differentiated to target cell. | string | no | Differentiation validation method | Pancreatic Cell DTZ Detection Assay; qPCR; Flow Cytometry; Immunocytochemistry Staining | ||
| validation_result | Result confirming successful differentiation to target cell type. | string | no | Validation result | CD103 Positive; Nestin Positive; HCN4 Positive; CD11C Negative |
Information about how cells are subjected to a treatment or stimulus, such as an immune activator or a drug.
Location: type/protocol/biomaterial_collection/treatment_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| method | Method applied to cell culture to induce a specific treatment response. | array | yes | See module treatment_method_ontology | Treatment method | ||
| media | Culture media used to induce a specific treatment response. | string | no | Treatment media | RPMI 1640; Complete Medium | ||
| reagents | A list of purchased reagents used in the treatment protocol. | array | no | See module purchased_reagents | Treatment reagents | ||
| target_pathway | Targeted pathway for specific treatment response. | array | no | See module target_pathway_ontology | Target pathway | insulin signalling pathway; immune cell activation; chemokine signalling pathway. |
Information about the preparation protocol of the imaged specimen used in an imaging experiment.
Location: type/protocol/imaging/imaging_preparation_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| fresh_slicing_method | The method by which fresh tissue was sliced. | string | no | Fresh slicing method | vibrotome | ||
| imaged_slice_thickness | Thickness of the imaged slice in micrometres. | number | no | Imaged slice thickness | 10 | ||
| final_slicing_method | The method by which the final slice was obtained. | string | no | Final slicing method | cryosectioning | ||
| post_resection_interval | Length of time between surgical resection and fresh slicing of tissue. | number | no | Time between resection and fresh slicing | 5 | ||
| post_resection_interval_unit | The unit of time in which the post resection interval is expressed. | object | no | See module time_unit_ontology | Post resection interval time unit | day | |
| pre_final_slice_preservation_method | Tissue preservation method used prior to final slicing. | object | no | See module preservation_storage | Pre-final slice preservation method | freezing | |
| post_final_slicing_interval | Length of time between secondary slicing and hybridization. | number | no | Post final slicing interval | 7 | ||
| post_final_slicing_interval_unit | The unit of time in which the post final slicing interval is expressed. | object | no | See module time_unit_ontology | Post final slicing interval time unit | day | |
| fiducial_marker | Fiducial markers for the alignment of images taken across multiple rounds of imaging. | string | no | Fiducial marker | beads | ||
| expansion_factor | Factor by which the imaged tissue was expanded in one dimension. | number | no | Expansion factor | 3 | ||
| permeabilisation_time | The permeabilisation time in time units that the tissue was exposed to. | number | no | Permeabilisation time | 12 | ||
| permeabilisation_time_unit | The unit in which permeabilisation time is expressed. | object | no | See module time_unit_ontology | Permeabilisation time unit |
Information about the imaging protocol.
Location: type/protocol/imaging/imaging_protocol.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | protocol | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| protocol_core | Core protocol-level information. | object | yes | See core protocol_core | Protocol core | ||
| microscope_setup_description | Description of the microscope setup. | string | no | Microscope setup description | Motorized stage (SCAN IM 112 x 74, Marzhauser), sCMOS camera (Zyla 4.2; Andor), 60x, Plan-Apo, 1.3 NA, silicone oil objective (UPLSAPO60XS2; Olympus). | ||
| microscopy_technique | The type of microscopy. | object | yes | See module microscopy_ontology | Microscopy technique | ||
| magnification | Magnification of the objective used for imaging. | string | yes | Magnification | 60x; 100x | ||
| numerical_aperture | Numerical aperture of the objective. | number | no | Numerical aperture | 1.3; 0.75 | ||
| immersion_medium_type | Immersion medium used for imaging. | string | no | Immersion medium | oil; air | ||
| immersion_medium_refractive_index | Refractive index of the immersion medium used for imaging. | number | no | Refractive index of the immersion medium | 1.5; 1 | ||
| pixel_size | Pixel size in nanometers. | number | no | Pixel size | 109 | ||
| number_of_tiles | Number of XY tiles in the experiment. | integer | no | Number of tiles | 2000 | ||
| tile_size_y | Y size of the tile in micrometers. | number | no | Tile size Y | 100 | ||
| tile_size_x | X size of the tile in micrometers. | number | no | Tile size X | 100 | ||
| z_stack_step_size | Z-stack step size in nanometers. | number | no | Z stack step size | 200 | ||
| number_of_z_steps | Number of steps in a Z stack. | integer | no | Number of Z steps | 40 | ||
| overlapping_tiles | Whether tiles were collected with overlap. | string | no | Overlapping tiles | yes, no | Should be one of: yes, or no. | |
| channel | Information about each channel used in the imaging protocol. | array | no | See module channel | Channel | ||
| probe | Information about each probe in the imaging experiment. | array | no | See module probe | Probe |
A project entity contains information about the overall project.
Location: type/project/project.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | project | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| project_core | Core project-level information. | object | yes | See core project_core | Project core | ||
| contributors | People contributing to any aspect of the project. | array | no | See module contact | Contributors | ||
| supplementary_links | External link(s) pointing to code, supplementary data files, or analysis files associated with the project which will not be uploaded. | array | no | Supplementary link(s) | https://github.com/czbiohub/tabula-muris; http://celltag.org/ | ||
| publications | Publications resulting from this project. | array | no | See module publication | Publications | ||
| hca_bionetworks | HCA Bionetworks and Atlases the project is associated with | array | no | See module hca_bionetwork | HCA Bionetwork(s) | ||
| insdc_project_accessions | An International Nucleotide Sequence Database Collaboration (INSDC) project accession. | array | no | INSDC project accession | SRP000000 | ||
| ega_accessions | A list of accessions referring to EGA (European Genome-Phenome Archive) datasets or studies. | array | no | EGA Study/Dataset Accession(s) | EGAS00000000001; EGAD00000000002 | ||
| dbgap_accessions | A list of database of Genotypes and Phenotypes (dbGaP) study accessions. | array | no | dbGaP Study Accession(s) | phs001997.v1.p1; phs001836 | ||
| geo_series_accessions | A Gene Expression Omnibus (GEO) series accession. | array | no | GEO series accession | GSE00000 | ||
| array_express_accessions | An ArrayExpress accession. | array | no | ArrayExpress accession | E-AAAA-00 | ||
| insdc_study_accessions | An International Nucleotide Sequence Database Collaboration (INSDC) study accession. | array | no | INSDC study accession | PRJNA000000 | ||
| biostudies_accessions | A BioStudies study accession. | array | no | BioStudies accession | S-EXMP1; S-HCAS33 | ||
| funders | Funding source(s) supporting the project. | array | yes | See module funder | Funding source(s) | ||
| estimated_cell_count | An estimated number of cells in this project | integer | no | Estimated cell count | 10000; 2100000 |
Information about the specimen that was collected from the donor organism.
Location: type/biomaterial/specimen_from_organism.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | biomaterial | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| biomaterial_core | Core biomaterial-level information. | object | yes | See core biomaterial_core | Biomaterial core | ||
| genus_species | The scientific binomial name for the species of the specimen. | array | no | See module species_ontology | Genus species | ||
| organ | The organ that the biomaterial came from. | object | yes | See module organ_ontology | Organ | ||
| organ_parts | A term for a specific part of the organ that the biomaterial came from. | array | no | See module organ_part_ontology | Organ part | ||
| diseases | Short description of known disease(s) of the specimen. | array | no | See module disease_ontology | Known disease(s) | ||
| adjacent_diseases | Short description of the disease(s) adjacent to the specimen's collection site (e.g. breast cancer). | array | no | See module disease_ontology | Adjacent disease(s) | ||
| state_of_specimen | State of the specimen at the time of collection. | object | no | See module state_of_specimen | State of specimen | ||
| preservation_storage | Information about how a specimen was preserved and/or stored over a period of time. | object | no | See module preservation_storage | Preservation/Storage | ||
| collection_time | When the biomaterial was collected. | string | no | Time of collection | 2016-01-21T00:00:00Z; 2016-03 | ||
| purchased_specimen | Information about a purchased specimen. | object | no | See module purchased_reagents | Purchased specimen |
Information about the suspension of cells or nuclei derived from the collected or cultured specimen.
Location: type/biomaterial/cell_suspension.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | biomaterial | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| biomaterial_core | Core biomaterial-level information. | object | yes | See core biomaterial_core | Biomaterial core | ||
| cell_morphology | Features relating to the morphology of cells in a biomaterial. | object | no | See module cell_morphology | Cell morphology | ||
| growth_conditions | Features relating to the growth and/or maintenance of a biomaterial. | object | no | See module growth_conditions | Growth conditions | ||
| genus_species | The scientific binomial name for the species of the suspension. | array | no | See module species_ontology | Genus species | ||
| selected_cell_types | The cell type(s) selected to be present in the suspension. | array | no | See module cell_type_ontology | Selected cell type(s) | ||
| estimated_cell_count | Estimated number of cells in the suspension. | integer | no | Estimated cell count | 1; 2100 | ||
| plate_based_sequencing | Fields specific for plate-based sequencing experiments. | object | no | See module plate_based_sequencing | Plate-based sequencing |
Information about the cell line or cell culture biomaterial.
Location: type/biomaterial/cell_line.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | biomaterial | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| biomaterial_core | Core biomaterial-level information. | object | yes | See core biomaterial_core | Biomaterial core | ||
| supplier | The supplier of the cell line. | string | no | Supplier | HipSci; ATCC | ||
| catalog_number | The supplier catalogue number for the cell line. | string | no | Catalog number | 77650057 | ||
| lot_number | The supplier lot or batch number for the cell line. | string | no | Lot/batch number | 24.10.14 | ||
| catalog_url | The supplier catalogue URL for the cell line. | string | no | Catalog URL | www.phe-culturecollections.org.uk/products/celllines/ipsc/detail.jsp?refId=77650057&collection=ecacc_ipsc | ||
| cell_cycle | The cell cycle phase if the cell line is synchronized growing cells or the phase is known. | object | no | See module cell_cycle_ontology | Cell cycle | ||
| type | The type of cell line. | string | yes | 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 | yes | See module organ_ontology | Organ model | ||
| cell_morphology | Features relating to the morphology of the cells. | object | no | See module cell_morphology | Cell morphology | ||
| growth_conditions | Features relating to the growth and/or maintenance of the cell lines. | object | no | See module growth_conditions | Growth conditions | ||
| confluency | The percent a plate surface is covered by cells. | number | no | Percent confluency | 60 | ||
| cell_type | The cell type that the cell line represents. | object | no | See module cell_type_ontology | Cell type | ||
| karyotype | The karyotype of the cell line. | string | no | Karyotype | sex chromosome complement of XY; del(2) (q11) | ||
| tissue | The tissue that the cell line was derived from. | object | no | See module organ_part_ontology | Tissue | ||
| date_established | Date when the cell line was established. | string | no | Date established | 2017-03-19; 2002/03; 1995 | ||
| disease | Short description of any disease association to the cell type. | object | no | See module disease_ontology | Disease | ||
| genus_species | The scientific binomial name for the species of the cell line. | array | no | See module species_ontology | Genus species | ||
| publication | A publication that cites the cell line creation. | object | no | See module publication | Publication |
Information about a tissue specimen after it has been sectioned and prepared for imaging.
Location: type/biomaterial/imaged_specimen.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | biomaterial | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| biomaterial_core | Core biomaterial-level information. | object | yes | See core biomaterial_core | Biomaterial core | ||
| overview_images | List of filenames of photographs of specimen. | array | no | Gross image | my_image_file.jpg; overview_image.tiff | ||
| slice_thickness | Thickness of the imaged slice in micrometres. | number | yes | Imaged slice thickness | 14 | ||
| internal_anatomical_structures | Internal (landmark) structures visible in the overview image that are informative about the broader anatomical context/location of the sample. | array | no | See module organ_part_ontology | Internal tissue structures |
Information about the donor from which a specimen was collected.
Location: type/biomaterial/donor_organism.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | biomaterial | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| biomaterial_core | Core biomaterial-level information. | object | yes | See core biomaterial_core | Biomaterial core | ||
| human_specific | Fields specific to human (homo sapiens) organisms. | object | no | See module human_specific | Human-specific | ||
| mouse_specific | Fields specific to mouse (mus musculus) organisms. | object | no | See module mouse_specific | Mouse-specific | ||
| genus_species | The scientific binomial name for the species of the organism. | array | no | See module species_ontology | Genus species | ||
| sex | The biological sex of the organism. | string | yes | 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 | yes | Alive at collection | yes, no, unknown, not applicable | Should be one of: yes, no, not applicable, or unknown. | |
| organism_age | Age of organism in Age units measured since birth. | string | no | Age | 20; 45-65 | ||
| organism_age_unit | The unit in which Age is expressed. | object | no | See module time_unit_ontology | Age unit | ||
| development_stage | A classification of the developmental stage of the organism. | object | yes | See module development_stage_ontology | Development stage | ||
| diseases | Short description of known disease(s) of the organism. | array | no | See module disease_ontology | Known disease(s) | ||
| death | Information about conditions of death of the organism. | object | no | See module death | Death conditions | ||
| familial_relationships | Information about other organisms related to this organism. | array | no | See module familial_relationship | Familial relationship | ||
| medical_history | Information about the medical history of the organism. | object | no | See module medical_history | Medical history | ||
| gestational_age | Gestational age of pregnancy in Gestational age units measured from the last menstrual period. | string | no | Gestational age | 22; 8-9 | ||
| gestational_age_unit | The unit in which Gestational age is expressed. | object | no | See module time_unit_ontology | Gestational age unit | ||
| height | Height of organism in Height unit. | string | no | Height | 160; 120-140 | ||
| height_unit | The unit in which Height is expressed. | object | no | See module length_unit_ontology | Height unit | ||
| weight | Weight of organism in Weight unit. | string | no | Weight | 60; 40-60 | ||
| weight_unit | The unit in which Weight is expressed. | object | no | See module mass_unit_ontology | Weight unit | ||
| organ_donor | Whether biomaterial was collected after extraction for organ transplantation. | boolean | no | Organ donor | yes; no |
Information about an organoid biomaterial.
Location: type/biomaterial/organoid.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | biomaterial | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| biomaterial_core | Core biomaterial-level information. | object | yes | See core biomaterial_core | Biomaterial core | ||
| genus_species | The scientific binomial name for the species of the organoid. | array | no | See module species_ontology | Genus species | ||
| model_organ | Organ for which this organoid is a model system. | object | yes | See module organ_ontology | Organ model | ||
| model_organ_part | Organ part for which this organoid is a model system. | object | no | See module organ_part_ontology | Organ part model | ||
| age | Age of the organoid in Organoid age unit measured from when cell aggregates started differentiating to desired organoid model. | number | no | Organoid age | 55 | ||
| age_unit | The unit in which Organoid age is expressed. | object | no | See module time_unit_ontology | Organoid age unit | ||
| size | Size of the organoid in Organoid size unit. | number | no | Organoid size | 4 | ||
| size_unit | The unit in which the Organoid size is expressed. | object | no | See module length_unit_ontology | Organoid size unit | ||
| morphology | General description of the organoid morphology. | string | no | Organoid morphology | Epithelial monolayer with budding crypt-like domains; Optic cup structure | ||
| embedded_in_matrigel | Whether the organoid is embedded in a matrigel. | boolean | no | Embeddded in matrigel | Should be one of: yes, no. | ||
| growth_environment | Growth environment in which the organoid is grown. | string | no | Growth environment | matrigel; liquid suspension; adherent | ||
| input_aggregate_cell_count | Estimated number of cells per input cell aggregate. | number | no | Input aggregate cell count | 10000 | ||
| stored_oxygen_levels | Percent oxygen level organoid was stored in prior to sequencing. | number | no | Stored oxygen level | 75 |
Information about a process completed in the experiment.
Location: type/process/process.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | process | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| process_core | Core process-level information. | object | yes | See core process_core | Process core | ||
| start_time | Date and time the process started. | string | no | Start time | 2019-01-16T12:00:00Z; 2019/01/16 | ||
| end_time | Date and time the process ended. | string | no | End time | 2019-01-16T12:00:00Z; 2019/01/16 | ||
| length_of_time | Length of time the process took to execute in Length of time unit. | string | no | Length of time | 10; 55-60 | ||
| length_of_time_unit | The unit in which Length of time is expressed. | object | no | See module time_unit_ontology | Length of time unit | ||
| type | The type of process. | object | no | See module process_type_ontology | Process type | ||
| deviation_from_protocol | A deviation from the protocol provided. | string | no | Deviation from protocol | Skipped ACK lysis step; Used 100um filter instead of 40um filter | ||
| insdc_experiment | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | object | no | See module insdc_experiment | INSDC experiment accession |
Information about the analysis process.
Location: type/process/analysis/analysis_process.json
| Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example |
|---|---|---|---|---|---|---|---|
| schema_type | The type of the metadata schema entity. | string | yes | process | |||
| provenance | Provenance information provided by the system. | object | no | See provenance | |||
| process_core | Core process-level information. | object | yes | See core process_core | Process core | ||
| type | The type of process. | object | yes | See module process_type_ontology | Process type | ||
| inputs | Input parameters used in the pipeline run. | array | yes | Input parameters | |||
| tasks | Information about steps in the workflow. | array | yes | Workflow tasks | |||
| timestamp_start_utc | Initial start time of the full pipeline in UTC. | string | yes | Start timestamp (UTC) | 2018-01-21T09:34:27Z | ||
| timestamp_stop_utc | Terminal stop time of the full pipeline in UTC. | string | yes | Stop timestamp (UTC) | 2018-01-21T11:35:01Z | ||
| analysis_run_type | Whether the analysis was run or was copied forward as an optimization. | string | yes | 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 | yes | Reference files |