DigitalPathology

HTAN Digital Pathology Data Model Schema for Phase 2

CoreFileAttributes

Universal attributes that apply to all file-based data in HTAN

Attribute	Type	Required	Description
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseImagingAttributes

Base attributes shared across all imaging modules (Digital Pathology, Multiplex Microscopy, etc.)

Attribute	Type	Required	Description
EXPERIMENTAL_STRATEGY_AND_DATA_SUBTYPES	ExperimentalStrategyAndDataSubtypes	Yes	What is the experimental strategy used for the study (or what type of data subtypes exist in the study)? Per RFC, the only valid value for imaging data types is “Pathological”.
DE_IDENTIFICATION_METHOD_TYPE	DeIdentificationMethodType	Yes	De-identification Method Type
DE_IDENTIFICATION_METHOD_DESCRIPTION	string	Conditional: Required when DE_IDENTIFICATION_METHOD_TYPE is not ‘Not Applicable’	Required when DE_IDENTIFICATION_METHOD_TYPE is not ‘Not Applicable’
DE_IDENTIFICATION_SOFTWARE	string	No	Software that was used to de-identify the images (if used)
LICENSE	License	Yes	Official or legal permission to do or own a specified thing. Per RFC, the only valid value is “CC BY 4.0”.
IMAGE_MODALITY	ImageModality	Yes	The method in which the images are generated.
IMAGING_EQUIPMENT_MANUFACTURER	string	Yes	Producer of the imaging equipment that was used to generate the digital image
IMAGING_EQUIPMENT_MODEL	string	No	The words used to describe the specific model of the instrument used to carry out an imaging experiment
IMAGING_SOFTWARE	string	No	The name of the software package that was used to capture, generate, and process the image
CITATION_OR_DOI	string	Yes	Raw Data Protocol or Digital Object Identifier Text; Publication and/or digital object identifier of the publication for open access studies. Must be a valid URL (http or https).
IMAGING_PROTOCOL	string	No	A rule which guides how an activity should be performed. Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol. Must be a valid URL (http or https).
STAINING_METHOD	StainingMethod	Yes	Any of the various methods that use a dye, reagent, or other material for producing coloration in tissues or microorganisms for microscopic examination
OBJECTIVE	string	Yes	The manufacturer and or model number for the optical element that gathers light from an object being observed and focuses the light rays from it to produce a real image of the object
NOMINAL_MAGNIFICATION	integer	Yes	The magnification of the lens as specified by the manufacturer - i.e. ‘60’ is a 60X lens. Integer value >= 0 (no units)
IMMERSION	ImmersionMedium	No	Immersion medium. Each objective is designed for a specific immersion medium, which is marked on the objective. The main types of immersion media are air, oil, and water.
LENS_NUMERICAL_APERTURE	float	No	The numerical aperture of the lens. Floating point value > 0.
PASSED_QC	boolean	Yes	Confirm that the image has passed internal quality control checks
QC_COMMENT	string	Yes	Comments related to quality control checks
SPECIES	Species	Yes	NCBI Taxonomy ID. Per RFC, the only valid value is “9606 (Homo sapiens)”.
HAS_SLIDE_LABEL	boolean	Yes	Does the image contain a slide label
SLIDE_LABEL_REDACTED	boolean	Conditional: Required when HAS_SLIDE_LABEL is true	Required when HAS_SLIDE_LABEL is true
DE_IDENTIFIED	boolean	Yes	Confirm that any HIPAA identifiers are redacted, masked, or not present in the slide label and that any dates or strings present in internal metadata does not represent PHI
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

DigitalPathologyData

Container for digital pathology imaging data

Attribute	Type	Required	Description
FILE_FORMAT	string	Yes	Format of the imaging file. Must be compatible with Bio-Formats or OpenSlide Python. OME-TIFF files use extensions .ome.tif, .ome.tiff, .ome.tf2, .ome.tf8, or .ome.btf. NDPIS (Hamamatsu) use .ndpi.
FILENAME	string	Yes	Name of the file. Must end with an extension matching the FILE_FORMAT (.ome.tif, .ome.tiff, .ome.tf2, .ome.tf8, .ome.btf for ome-tiff; .tiff or .tif for tiff; .qptiff for qptiff; .svs for svs; .ndpi for ndpi)
HAS_ANNOTATIONS	boolean	Yes	Does the image contain annotations
ANNOTATION_TYPE	AnnotationType	Conditional: Required when HAS_ANNOTATIONS is true	Required when HAS_ANNOTATIONS is true
EXPERIMENTAL_STRATEGY_AND_DATA_SUBTYPES	ExperimentalStrategyAndDataSubtypes	Yes	What is the experimental strategy used for the study (or what type of data subtypes exist in the study)? Per RFC, the only valid value for imaging data types is “Pathological”.
DE_IDENTIFICATION_METHOD_TYPE	DeIdentificationMethodType	Yes	De-identification Method Type
DE_IDENTIFICATION_METHOD_DESCRIPTION	string	No	Required when DE_IDENTIFICATION_METHOD_TYPE is not ‘Not Applicable’
DE_IDENTIFICATION_SOFTWARE	string	No	Software that was used to de-identify the images (if used)
LICENSE	License	Yes	Official or legal permission to do or own a specified thing. Per RFC, the only valid value is “CC BY 4.0”.
IMAGE_MODALITY	ImageModality	Yes	The method in which the images are generated.
IMAGING_EQUIPMENT_MANUFACTURER	string	Yes	Producer of the imaging equipment that was used to generate the digital image
IMAGING_EQUIPMENT_MODEL	string	No	The words used to describe the specific model of the instrument used to carry out an imaging experiment
IMAGING_SOFTWARE	string	No	The name of the software package that was used to capture, generate, and process the image
CITATION_OR_DOI	string	Yes	Raw Data Protocol or Digital Object Identifier Text; Publication and/or digital object identifier of the publication for open access studies. Must be a valid URL (http or https).
IMAGING_PROTOCOL	string	No	A rule which guides how an activity should be performed. Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol. Must be a valid URL (http or https).
STAINING_METHOD	StainingMethod	Yes	Any of the various methods that use a dye, reagent, or other material for producing coloration in tissues or microorganisms for microscopic examination
OBJECTIVE	string	Yes	The manufacturer and or model number for the optical element that gathers light from an object being observed and focuses the light rays from it to produce a real image of the object
NOMINAL_MAGNIFICATION	integer	Yes	The magnification of the lens as specified by the manufacturer - i.e. ‘60’ is a 60X lens. Integer value >= 0 (no units)
IMMERSION	ImmersionMedium	No	Immersion medium. Each objective is designed for a specific immersion medium, which is marked on the objective. The main types of immersion media are air, oil, and water.
LENS_NUMERICAL_APERTURE	float	No	The numerical aperture of the lens. Floating point value > 0.
PASSED_QC	boolean	Yes	Confirm that the image has passed internal quality control checks
QC_COMMENT	string	Yes	Comments related to quality control checks
SPECIES	Species	Yes	NCBI Taxonomy ID. Per RFC, the only valid value is “9606 (Homo sapiens)”.
HAS_SLIDE_LABEL	boolean	Yes	Does the image contain a slide label
SLIDE_LABEL_REDACTED	boolean	No	Required when HAS_SLIDE_LABEL is true
DE_IDENTIFIED	boolean	Yes	Confirm that any HIPAA identifiers are redacted, masked, or not present in the slide label and that any dates or strings present in internal metadata does not represent PHI
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

Enums

AnnotationType

Value	Description
Artifact	Artifact annotation
Cell	Cell annotation
Nucleus	Nucleus annotation
ROI	Region of Interest annotation
Tissue	Tissue annotation

DeIdentificationMethodType

Value	Description
Automatic	Automatic de-identification method
Manual	Manual de-identification method
Not Applicable	De-identification not applicable
Semiautomatic	Semi-automatic de-identification method

ExperimentalStrategyAndDataSubtypes

Value	Description
Pathological	Pathological experimental strategy and data subtype

ImageModality

Value	Description
SM	Slide Microscopy

ImmersionMedium

Value	Description
Air	Air immersion medium
Glycerol	Glycerol immersion medium
Oil	Oil immersion medium
Other	Other immersion medium
Water	Water immersion medium

License

Value	Description
CC BY 4.0	Creative Commons Attribution 4.0 International License

Species

Value	Description
9606 (Homo sapiens)	NCBI Taxonomy ID for Homo sapiens

StainingMethod

Value	Description
CODEX	CODEX staining method
CyCIF	Cyclic Immunofluorescence staining method
ExSeq	Expansion Sequencing staining method
GeoMX-DSP	GeoMX Digital Spatial Profiling staining method
H&E	Hematoxylin and Eosin staining method
IHC	Immunohistochemistry staining method
IMC	Imaging Mass Cytometry staining method
MERFISH	Multiplexed Error-Robust Fluorescence In Situ Hybridization staining method
MIBI	Multiplexed Ion Beam Imaging staining method
MxIF	Multiplexed Immunofluorescence staining method
Not Applicable	Staining not applicable
SABER	Signal Amplification By Exchange Reaction staining method
mIHC	Multiplexed Immunohistochemistry staining method
t-CyCIF	Tissue Cyclic Immunofluorescence staining method