Cell line

Information about the cell line or cell culture biomaterial.

Properties

Catalog numbercell_line.catalog_number (string) The supplier catalogue number for the cell line. For example "77650057".

Catalog URLcell_line.catalog_url (string) The supplier catalogue URL for the cell line. For example "www.phe-culturecollections.org.uk/products/celllines/ipsc/detail.jsp?refId=77650057&collection=ecacc_ipsc".

Percent confluencycell_line.confluency (number) The percent a plate surface is covered by cells. For example "60".

Date establishedcell_line.date_established (string) Date when the cell line was established. For example "2017-03-19", "2002/03" or "1995".

Karyotypecell_line.karyotype (string) The karyotype of the cell line. For example "sex chromosome complement of XY" or "del(2) (q11)".

Lot/batch numbercell_line.lot_number (string) The supplier lot or batch number for the cell line. For example "24.10.14".

Suppliercell_line.supplier (string) The supplier of the cell line. For example "HipSci" or "ATCC".

Cell line typeRequiredcell_line.type (string enum) The type of cell line. Should be one of: "primary", "immortalized", "stem cell", "stem cell-derived", "induced pluripotent" or "synthetic".

Cell cycle ontology IDcell_line.cell_cycle.ontology (string from cell_cycle_ontology) An ontology term identifier in the form prefix:accession. For example "GO:0051321" or "GO:0000080".Graph restriction: Subclasses of GO:0007049, GO:0022403 from obo:hcao or obo:go.

Cell cycle ontology labelcell_line.cell_cycle.ontology_label (string from cell_cycle_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 "meiotic cell cycle" or "mitotic G1 phase".

Cell cycleRequiredcell_line.cell_cycle.text (string from cell_cycle_ontology) The name of a cell cycle of the cells in the specimen. For example "meiotic cell cycle" or "mitotic G1 phase".

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

Cell viability methodcell_line.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_line.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_line.cell_morphology.percent_cell_viability (number from cell_morphology) Percent of cells determined to be viable. For example "98.7".

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

Length unit ontology IDcell_line.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_line.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_line.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 type ontology IDcell_line.cell_type.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_line.cell_type.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_line.cell_type.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".

Disease ontology IDcell_line.disease.ontology (string from disease_ontology) An ontology term identifier in the form prefix:accession. For example "MONDO:0005148", "PATO:0000461" or "HP:0001397".Graph restriction: Subclasses of MONDO:0000001, PATO:0000461, HP:0000118 from obo:mondo or obo:efo or obo:hp including self.

Disease ontology labelcell_line.disease.ontology_label (string from disease_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 "type 2 diabetes mellitus" or "normal".

DiseaseRequiredcell_line.disease.text (string from disease_ontology) The text for the term as the user provides it. For example "type 2 diabetes mellitus" or "normal".

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

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

Organ ontology IDcell_line.model_organ.ontology (string from organ_ontology) An ontology term identifier in the form prefix:accession. For example "UBERON:0000948" or "UBERON:0002405".Graph restriction: Subclasses of UBERON:0000465 from obo:hcao or obo:uberon including self.

Organ ontology labelcell_line.model_organ.ontology_label (string from organ_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 "heart" or "immune system".

OrganRequiredcell_line.model_organ.text (string from organ_ontology) The text for the term as the user provides it. For example "heart" or "immune system".

AuthorsRequiredcell_line.publication.authors (array from publication) A list of authors associated with the publication. For example "Doe JD".

Publication DOIcell_line.publication.doi (string from publication) The publication digital object identifier (doi) of the publication. For example "10.1016/j.cell.2016.07.054".

Official HCA PublicationRequiredcell_line.publication.official_hca_publication (boolean from publication) Has the publication been accepted as an official HCA publication, according to the process described in https://www.humancellatlas.org/publications/ ? For example "yes" or "no".

Publication PMIDcell_line.publication.pmid (integer from publication) The PubMed ID of the publication. For example "27565351".

Publication titleRequiredcell_line.publication.title (string from publication) The title of the publication. For example "Study of single cells in the human body.".

Publication URLcell_line.publication.url (string from publication) A URL for the publication. For example "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5667944/".

Organ part ontology IDcell_line.tissue.ontology (string from organ_part_ontology) An ontology term identifier in the form prefix:accession. For example "UBERON:0002371" or "UBERON:0000006".Graph restriction: Subclasses of UBERON:0000465 from obo:hcao or obo:uberon including self.

Organ part ontology labelcell_line.tissue.ontology_label (string from organ_part_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" or "islet of Langerhans".

Organ partRequiredcell_line.tissue.text (string from organ_part_ontology) The text for the term as the user provides it. For example "bone marrow" or "islet of Langerhans".

HDBR accessioncell_line.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_line.biomaterial_core.biomaterial_description (string from biomaterial_core) A general description of the biomaterial.

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

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

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

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

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

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

Timecourse relevancecell_line.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_line.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".

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

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

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

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

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

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

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

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

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