Well-defined schemas ensure that HuBMAP data and metadata are reusable. If you are starting work on a new assay type, review the guidelines for directory schemas. If you have an upload prepared, follow the instructions in the Metadata Validation Workflow document to validate your upload.

Assay types and their schemas are linked below.

• An Excel file listing all the schemas and their fields is available.
• For more information, see the ingest-validation-tools repo.

Organ

• Organ

Sample

• Sample

• Sample Block

• Sample Section

• Sample Suspension

Clinical Imaging Modalities

• Body CT

• MRI

• Micro CT

• OCT

• Ultrasound

Fluorescence In Situ Hybridization (FISH)

• MERFISH

• seqFISH

Histology

• Histology

• PAS microscopy

Imaging Mass Spectrometry (IMS)

• 3D Imaging Mass Cytometry

• DESI

• Imaging Mass Cytometry

• MALDI

• Multiplex Ion Beam Imaging

• NanoDESI

• SIMS

Mass Spectrometry

• CE-MS

• GC-MS

• LC-MS

Multiplex Fluorescence Based Experiment (MxFBE)

• CODEX

• Cell DIVE

• CyCIF

• MxIF

• PhenoCycler

Sequence Assays

• 10x Multiome

• ATACseq (bulk) / bulkATACseq

• RNAseq (GeoMx)

• RNAseq (Visium)

• RNAseq (bulk) / bulk-RNA

• SNARE-seq2 / sciATACseq / snATACseq / scATAC-seq

• Slide-seq

• WGS

• scRNAseq-10xGenomics-v2 / scRNAseq-10xGenomics-v3 / snRNAseq-10xGenomics-v2 / snRNAseq-10xGenomics-v3 / scRNAseq / sciRNAseq / snRNAseq / SNARE2-RNAseq / scRNA-seq

Single-cycle Fluorescence Microscopy (SFM)

• Auto-fluorescence / AF

• Confocal

• Enhanced Stimulated Raman Spectroscopy (SRS)

• Light Sheet

• Second Harmonic Generation

• Thick Section Multiphoton MxIF

Spatial Transcriptomics

• CosMx

• DBiT

• GeoMx (RNA) / GeoMx (protein) / GeoMx

• HiFi-Slide

• Molecular Cartography

• Visium

• Xenium

Other TSVs

• Publication

• antibodies

• contributors