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, it can be validated with validate_upload.py, or if you only have an individual TSV, use validate_tsv.py. Examples of both good and bad uploads, and the validation messages they produce, are available.

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.

Imaging mass spectrometry

• 3D Imaging Mass Cytometry

• Imaging Mass Cytometry

• MALDI-IMS / SIMS-IMS / NanoDESI / DESI

• MIBI

Imaging assays

• AF

• CODEX / CODEX2

• Cell DIVE / cell-dive

• Light Sheet

• MxIF

• PAS microscopy

• seqFISH

Other TSVs

• antibodies

• contributors

• donor

• sample

• sample-block

• sample-section

• sample-suspension

Clinical imaging modalities

• Body CT

• MRI

• Micro CT

• OCT

• Ultrasound

Sequence assays

• SNARE-seq2 / sciATACseq / snATACseq

• Slide-seq

• WGS

• bulk RNA

• bulkATACseq

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

Mass spectrometry

• CE-MS

• GC-MS

• LC-MS / MS / LC-MS Bottom-Up / MS Bottom-Up / LC-MS Top-Down / MS Top-Down