Tier 1 Metadata

Dataset

Field	Description
Study PI Required string (multivalued)	Description Example Sarah,A,Teichmann Source HCA BioNetworks AnnData Location
Batch Condition string (multivalued)	Description Allowed Values Example ["patient", "seqBatch"] Source CELLxGENE Schema BioNetworks AnnData Location
Default Embedding string	Description Source CELLxGENE Schema BioNetworks AnnData Location
Sequencing Platform string	Description Allowed Values Example EFO:0008563 Rationale Source HCA BioNetworks AnnData Location
Assay Ontology Term ID Required string	Description Allowed Values Example EFO:0009922 Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Reference Genome Required string	Description Allowed Values Example GRCh38 GRCh37 Rationale Source HCA BioNetworks AnnData Location
Alignment Software Required string	Description Example cell ranger 3.0.1 kallisto bustools GSNAP Rationale Source HCA BioNetworks AnnData Location
Intron Inclusion string	Description Allowed Values Example yes no Rationale Source HCA BioNetworks AnnData Location
Sequenced Fragment Required string	Description Allowed Values Example 3 prime tag full length Rationale Source HCA BioNetworks AnnData Location
Gene Annotation Version Required string	Description Allowed Values Example v110 GCF_000001405.40 Rationale Source HCA BioNetworks AnnData Location
Comments string	Description Source HCA BioNetworks AnnData Location
Protocol URL string	Description Example https://www.biorxiv.org/conte nt/early/2017/09/24/193219 Rationale Source HCA BioNetworks AnnData Location
Title Required string	Description Example Cells of the adult human heart collection is "All — Cells of the adult human heart" Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Ambient Count Correction Required string	Description Example none soupx cellbender Source HCA BioNetworks AnnData Location
Doublet Detection Required string	Description Example none doublet_finder manual Source HCA BioNetworks AnnData Location
Embedding Required numpy.ndarray	Description Allowed Values Example X_tSNE X_UMAP Source CELLxGENE Schema BioNetworks AnnData Location

Donor

Field	Description
Donor ID Required string	Description Allowed Values Example CR_donor_1 MM_donor_1 LR_donor_2 Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Organism Ontology Term ID Required string	Description Allowed Values Example NCBITaxon:9606 NCBITaxon:10090 Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Manner of Death Required string	Description Allowed Values Example 1 2 3 4 0 unknown not applicable Rationale Source HCA BioNetworks AnnData Location
Sex Ontology Term ID Required string	Description Allowed Values Example PATO:0000383 for female, PATO:0000384 for male Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Self Reported Ethnicity Ontology Term ID Required string (multivalued)	Description Allowed Values Example unknown HANCESTRO:0008 Rationale Source HCA BioNetworks AnnData Location

Sample

Field	Description
Sample ID Required string	Description Example SC24 SC25 SC28 Rationale Source HCA BioNetworks AnnData Location
Tissue Ontology Term ID Required string	Description Allowed Values Example UBERON:0001828 UBERON:0000966 Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Tissue Free Text string	Description Example terminal ileum Rationale Source HCA BioNetworks AnnData Location
Sample Source Required string	Description Allowed Values Example surgical donor postmortem donor Rationale Source HCA BioNetworks AnnData Location
Sample Collection Method Required string	Description Allowed Values Example biopsy brush surgical resection Rationale Source HCA BioNetworks AnnData Location
Tissue Type Required string	Description Allowed Values Example tissue organoid cell culture Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Sampled Site Condition Required string	Description Allowed Values Example healthy diseased adjacent Rationale Source HCA BioNetworks AnnData Location
Disease Ontology Term ID Required string	Description Allowed Values Example MONDO:0005385 PATO:0000461 Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Sample Preservation Method Required string	Description Allowed Values Example fresh frozen at -70C Rationale Source HCA BioNetworks AnnData Location
Suspension Type Required string	Description Allowed Values Example cell nucleus na Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Is Primary Data Required string	Description Allowed Values Example true false Rationale Source HCA BioNetworks AnnData Location
Development Stage Ontology Term ID Required string	Description Allowed Values Example HsapDv:0000237 unknown Rationale Source CELLxGENE Schema BioNetworks AnnData Location
Radial Tissue Term Required string	Description Allowed Values Example EPI LP MUSC SUB MLN PP Source HCA BioNetworks AnnData Location
Cell Enrichment Required string	Description Allowed Values Example CL:0000057+ na Rationale Source HCA BioNetworks AnnData Location
Sample Collection Year string	Description Example 2018 Rationale Source HCA BioNetworks AnnData Location
Sample Collection Site string	Description Allowed Values Example AIDA_site_1 AIDA_site_2 Rationale Source HCA BioNetworks AnnData Location
Sample Collection Relative Time Point string	Description Example sampleX_day1 Rationale Source HCA BioNetworks AnnData Location
Cell Number Loaded integer	Description Example 5000 4000 Rationale Source HCA BioNetworks AnnData Location
Cell Viability Percentage decimal	Description Example 88 95 93.5 Rationale Source HCA BioNetworks AnnData Location
Institute Required string	Description Example EMBL-EBI Genome Institute of Singapore Rationale Source HCA BioNetworks AnnData Location
Author Batch Notes string	Description Example Batch run by different personnel on different days Rationale Source HCA BioNetworks AnnData Location

Library

Field	Description
Library ID Required string	Description Example A24 NK_healthy_001 Rationale Source HCA BioNetworks AnnData Location
Library ID Repository string	Description Example GSM1684095 Rationale Source HCA BioNetworks AnnData Location
Library Preparation Batch Required string	Description Example batch01 batch02 Rationale Source HCA BioNetworks AnnData Location
Library Sequencing Run Required string	Description Example run1 NV0087 Rationale Source HCA BioNetworks AnnData Location

Cell

Field	Description
Author Cell Type string	Description Example Goblet cell microglia Rationale Source HCA BioNetworks AnnData Location
Cell Type Ontology Term ID Required string	Description Allowed Values Example CL:0001204 Rationale Source HCA BioNetworks AnnData Location

Feature

Field	Description
Feature ID Required string	Description Source CELLxGENE Schema BioNetworks AnnData Location
Feature is Filtered Required boolean	Description Source CELLxGENE Schema BioNetworks AnnData Location

Matrix Layers

Field	Description
Matrix Layer Required oneOf(numpy.ndarray, scipy.sparse.csr_matrix)	Description Allowed Values Source CELLxGENE Schema BioNetworks AnnData Location