Cell suspension

Cell morphologycell_suspension.cell_morphology.cell_morphology (string from cell_morphology) General description of the morphology of cells. For example "adherent cells" or "form single layer colonies".

Cell sizecell_suspension.cell_morphology.cell_size (string from cell_morphology) Size of cells in Cell size unit. For example "15" or "20-30".

Cell viability methodcell_suspension.cell_morphology.cell_viability_method (string from cell_morphology) The method by which cell viability was determined. For example "Fluorescein diacetate hydrolysis" or "ATP test".

Cell viability resultcell_suspension.cell_morphology.cell_viability_result (string enum from cell_morphology) Result of the cell viability test. Should be one of: "pass" or "fail".

Percent cell viabilitycell_suspension.cell_morphology.percent_cell_viability (number from cell_morphology) Percent of cells determined to be viable. For example "98.7".

Percent necrotic cellscell_suspension.cell_morphology.percent_necrosis (number from cell_morphology) Percent of cells identified to be necrotic. For example "10".

Cell suspension>Cell morphology>Cell size unit (length_unit_ontology object) The unit in which the Cell size is expressed.

Length unit ontology IDcell_suspension.cell_morphology.cell_size_unit.ontology (string from length_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000017" or "UO:0000008".Graph restriction: Subclasses of UO:0000001 from obo:efo or obo:uo.

Length unit ontology labelcell_suspension.cell_morphology.cell_size_unit.ontology_label (string from length_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "micrometer" or "meter".

Length unitRequiredcell_suspension.cell_morphology.cell_size_unit.text (string from length_unit_ontology) The name of a length unit being used. For example "micrometer" or "meter".

Cell suspension>Genus species (species_ontology array) The scientific binomial name for the species of the suspension.

Species ontology IDcell_suspension.genus_species.ontology (string from species_ontology) An ontology term identifier in the form prefix:accession. For example "NCBITaxon:9606" or "NCBITaxon:10090".Graph restriction: Subclasses of OBI:0100026, NCBITaxon:2759 from obo:efo or obo:NCBITaxon.

Species ontology labelcell_suspension.genus_species.ontology_label (string from species_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "Homo sapiens" or "Mus musculus".

SpeciesRequiredcell_suspension.genus_species.text (string from species_ontology) The name of the species to which the organism belongs. For example "Homo sapiens" or "Mus musculus".

Cell suspension>Growth conditions (growth_conditions object) Features relating to the growth and/or maintenance of a biomaterial.

Culture environmentcell_suspension.growth_conditions.culture_environment (string from growth_conditions) Cell culture environment in which cells are grown. For example "Adherent cell culture" or "Suspension cell culture".

Drug treatmentcell_suspension.growth_conditions.drug_treatment (string from growth_conditions) Description of drugs added to the growth medium. For example "100 ug/mL ampicillin" or "15 ug/mL tetracycline".

Feeder layer typecell_suspension.growth_conditions.feeder_layer_type (string enum from growth_conditions) Type of feeder layer cells on which biomaterial was grown. Should be one of: "feeder-free", "feeder-dependent, JK1 feeder cells", "feeder-dependent, SNL 76/7 feeder cells", "feeder-dependent, human marrow stromal cells", "feeder-dependent, bovine embryonic fibroblast cells", "feeder-dependent, mouse embryonic fibroblast cells", "feeder-dependent, mouse fibroblast STO cells", "feeder-dependent, mouse bone marrow stromal cells", "feeder-dependent, mouse yolk sac-derived endothelial cells", "feeder-dependent, human foreskin fibroblast cells", "feeder-dependent, human newborn fibroblast cells", "feeder-dependent, human fetal lung fibroblast cells", "feeder-dependent, human uterine endometrial cells", "feeder-dependent, human breast parenchymal cells", "feeder-dependent, human embryonic fibroblast cells", "feeder-dependent, human adipose stromal cells", "feeder-dependent, human amniotic epithelial cells", "feeder-dependent, human placental fibroblast cells", "feeder-dependent, human umbilical cord stromal cells", "feeder-dependent, human fetal muscle cells", "feeder-dependent, human fetal skin cells", "feeder-dependent, human fetal liver stromal cells", "feeder-dependent, human fallopian tubal epithelial cells" or "feeder-dependent, human amniotic mesenchymal cells".

Growth mediumcell_suspension.growth_conditions.growth_medium (string from growth_conditions) The solid, liquid, or semi-solid medium used to support growth. For example "human placental cord serum" or "RPMI 1640 + 2mM Glutamine + 10-20% FBS".

Mycoplasma testing methodcell_suspension.growth_conditions.mycoplasma_testing_method (string enum from growth_conditions) The method by which the biomaterial was tested for mycoplasma contamination. Should be one of: "Direct DNA stain", "Indirect DNA stain", "Broth and agar culture", "PCR", "Nested PCR", "ELISA", "Autoradiography", "Immunostaining", "Cell-based assay" or "Microbiological assay".

Mycoplasma testing resultscell_suspension.growth_conditions.mycoplasma_testing_results (string enum from growth_conditions) Whether the biomaterial passed or failed the mycoplasma test. Should be one of: "pass" or "fail".

Passage numbercell_suspension.growth_conditions.passage_number (integer from growth_conditions) The number of passages that the biomaterial has been through. For example "22".

Cell suspension>Plate-based sequencing (plate_based_sequencing object) Fields specific for plate-based sequencing experiments.

Plate labelRequiredcell_suspension.plate_based_sequencing.plate_label (string from plate_based_sequencing) A label or name for the plate on which the well is located. For example "2217".

Well labelcell_suspension.plate_based_sequencing.well_label (string from plate_based_sequencing) A label or name for the well in which the cell is located. For example "A1".

Well qualitycell_suspension.plate_based_sequencing.well_quality (string enum from plate_based_sequencing) Quality of well if imaged before sequencing. Should be one of: "OK", "control, 2-cell well", "control, empty well" or "low quality cell".

Cell suspension>Selected cell type(s) (cell_type_ontology array) The cell type(s) selected to be present in the suspension.

Cell type ontology IDcell_suspension.selected_cell_types.ontology (string from cell_type_ontology) An ontology term identifier in the form prefix:accession. For example "CL:1001610" or "CL:0000746".Graph restriction: Subclasses of CL:0000003 from obo:hcao or obo:cl.

Cell type ontology labelcell_suspension.selected_cell_types.ontology_label (string from cell_type_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "bone marrow hematopoietic cell" or "cardiac muscle cell".

Cell typeRequiredcell_suspension.selected_cell_types.text (string from cell_type_ontology) The name of a cell type supplied by a user. For example "bone marrow hematopoietic cell" or "cardiac muscle cell".

Cell suspension>Biomaterial coreRequired (biomaterial_core object) Core biomaterial-level information.

HDBR accessioncell_suspension.biomaterial_core.HDBR_accession (string from biomaterial_core) A Human Developmental Biology Resource (HDBR) sample accession. For example "34526" or "14758, 2, liver".

Biomaterial descriptioncell_suspension.biomaterial_core.biomaterial_description (string from biomaterial_core) A general description of the biomaterial.

Biomaterial IDRequiredcell_suspension.biomaterial_core.biomaterial_id (string from biomaterial_core) A unique ID for the biomaterial.

Biomaterial namecell_suspension.biomaterial_core.biomaterial_name (string from biomaterial_core) A short, descriptive name for the biomaterial that need not be unique.

BioSamples accessioncell_suspension.biomaterial_core.biosamples_accession (string from biomaterial_core) A BioSamples accession. For example "SAMN00000000".

Genotypecell_suspension.biomaterial_core.genotype (string from biomaterial_core) Genotype of the biomaterial. For example "DRB1 0401 protective allele" or "HLA-B*3901 allele".

INSDC sample accessioncell_suspension.biomaterial_core.insdc_sample_accession (string from biomaterial_core) An International Nucleotide Sequence Database Collaboration (INSDC) sample accession. For example "SRS0000000".

NCBI taxon IDRequiredcell_suspension.biomaterial_core.ncbi_taxon_id (array from biomaterial_core) A taxonomy ID (taxonID) from NCBI. For example "9606".

Supplementary filescell_suspension.biomaterial_core.supplementary_files (array from biomaterial_core) A list of filenames of biomaterial-level supplementary files. For example "sample_site_image.jpg".

Cell suspension>Biomaterial core>Timecourse (timecourse object) Information relating to a timecourse associated with this biomaterial.

Timecourse relevancecell_suspension.biomaterial_core.timecourse.relevance (string from timecourse) Relevance of the Timecourse value/unit to the experiment. For example "Collection after tumor cells injected into the mammary gland" or "Time tissue underwent liberase digestion".

Timecourse valueRequiredcell_suspension.biomaterial_core.timecourse.value (string from timecourse) The numerical value in Timecourse unit associated with a time interval used in the experiment. For example "2" or "5.5-10.5".

Cell suspension>Biomaterial core>Timecourse>Timecourse unitRequired (time_unit_ontology object) The unit in which the Timecourse value is expressed.

Time unit ontology IDcell_suspension.biomaterial_core.timecourse.unit.ontology (string from time_unit_ontology) An ontology term identifier in the form prefix:accession. For example "UO:0000010" or "UO:0000034".Graph restriction: Subclasses of UO:0000003, UO:0000149 from obo:efo or obo:uo.

Time unit ontology labelcell_suspension.biomaterial_core.timecourse.unit.ontology_label (string from time_unit_ontology) The preferred label for the ontology term referred to in the ontology field. This may differ from the user-supplied value in the text field. For example "second" or "week".

Time unitRequiredcell_suspension.biomaterial_core.timecourse.unit.text (string from time_unit_ontology) The name of a time unit being used. For example "second" or "week".

Cell suspension>provenance (provenance object) Provenance information provided by the system.

Accessioncell_suspension.provenance.accession (string from provenance) A unique accession for this entity, provided by the broker.

Document IDRequiredcell_suspension.provenance.document_id (string from provenance) Identifier for document.

Schema major versioncell_suspension.provenance.schema_major_version (integer from provenance) The major version number of the schema. For example "4" or "10".

Schema minor versioncell_suspension.provenance.schema_minor_version (integer from provenance) The minor version number of the schema. For example "6" or "15".

Submission dateRequiredcell_suspension.provenance.submission_date (string from provenance) When project was first submitted to database.

Submitter IDcell_suspension.provenance.submitter_id (string from provenance) ID of individual who first submitted project.

Update datecell_suspension.provenance.update_date (string from provenance) When project was last updated.

Updater IDcell_suspension.provenance.updater_id (string from provenance) ID of individual who last updated project.