Tissue Sample Block Metadata Attributes

The attributes shown here have been colleced for tissue Block data, available from the HuBMAP Search and Entity APIs at Sample.metadata.<attribute>.
These attributes are harmonized across all versions of the tissue Block metadata specifications. See the latest version of the tissue Block Metadata Specifications for the schema and directory structure needed when ingesting Segmentation Mask metadata.

* indicates a required field

Attribute	Description	Allowable Values
source_id *	The unique identifier from HuBMAP or SenNet for the source (parent data) from which the sample was derived. Example: HBM122.EFGH.789
sample_id *	The unique HuBMAP or SenNet identifier assigned to the sample by the ingest portal. Example: HBM743.CKJW.876
lab_id	An identifier assigned by the data provider to reference an external metadata record for the dataset. The external record may be maintained independently and can support dataset traceability and provenance tracking. Leave this field empty if no such identifier exists.
preparation_protocol_doi *	The DOI for the protocols.io page that details the assay or the procedures used for sample procurement and preparation. For example, in the case of an imaging assay, the protocol may start with tissue section staining and end with the generation of an OME-TIFF file. The documented protocol should also include any image processing steps involved in producing the final OME-TIFF. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1
source_storage_duration_value *	The length of time the sample was stored prior to processing it. For assays performed on tissue sections, this refers to how long the tissue section (e.g., slide) was stored before the assay began (e.g., imaging). For assays performed on suspensions, such as sequencing, it refers to how long the suspension was stored before library construction started. Example: 12
source_storage_duration_unit *	The unit of measurement used to specify the source storage duration value. Example: hour	`day` `hour` `minute` `month` `year`
tissue_weight_value	The weight of a tissue block or the piece of tissue used in a suspension. This information is crucial for calculating the percentage of the parent block that was utilized in the suspension preparation. If the weight is not applicable or unknown, this field may be left blank. Example: 100
tissue_weight_unit	The unit of measurement for the tissue weight value. If no tissue weight is specified, this field may be left blank. Example: g	`g` `kg` `mg` `ug`
volume_value	The volume of the object in question. Example: 102
volume_unit	The unit of measurement for the volume value. If no volume measurement is specified, this field may be left blank. Example: mm^3	`cm^3` `ml` `mm^3` `um^3`
pathology_distance_value	The distance from which the surgical sample was obtained relative to the pathology site. If this information is not applicable, this field may be left blank. Example: 100
pathology_distance_unit	The unit of measurement for the pathology distance value. If no distance measurement is applicable, this field may be left blank. Example: mm	`cm` `mm`
preparation_medium *	The medium used during the sample preparation process. If no specific medium was utilized, enter “None”. If medium was not recorded, enter “Unknown”. Example: Fresh frozen CMC	`1X fixation & permeabilization buffer` `2% PFA/2.5% Glutaraldehyde` `Allprotect tissue reagent (ALL)` `Alpha-MEM` `Biops buffer` `Bouin's` `CLARITY hydrogel` `DMEM` `Ethanol` `Fixed frozen OCT (Cytofix/Cytoperm)` `Fixed frozen OCT (Formalin, sucrose protected)` `Fixed frozen OCT (PFA, sucrose protected)` `Fresh frozen CMC` `Fresh frozen gelatin` `Fresh frozen OCT` `Growth media` `HPMC-PVP` `HTK Solution` `Inflated (Agarose)` `Inflated (OCT)` `Lysis buffer` `MACS tissue storage solution` `Methanol` `Modified Davidson's Fixative` `NBF (Neutral Buffered Formalin)` `None` `PAXgene tissue kit (PXT)` `PBS` `Perfadex Plus` `PFA (Paraformaldehyde)` `PLP (Periodate-Lysine-Paraformaldehyde)` `RNAlater` `Trumps fixative` `Unknown` `UW Solution` `UWS Solution`
preparation_condition *	The condition under which the sample preparation took place, such as whether the sample was placed on dry ice during the process. If preparation condition was not recorded, enter “Unknown”. Example: Frozen on dry ice	`Frozen at -20 degrees celsius` `Frozen in liquid nitrogen` `Frozen in liquid nitrogen vapor` `Frozen on dry ice` `Frozen on ice` `Incubated at 37 degrees celsius` `Stored in ambient temperature` `Stored in refrigerator` `Stored on wet ice` `Unknown`
processing_time_value	The duration for which the tissue was handled prior to its initial preservation. Example: 120
processing_time_unit	The unit of measurement for the processing time value. If processing time is not specified, this field may be left blank. Example: minute	`day` `hour` `minute`
storage_medium *	The medium used to preserve the sample. If no specific medium was utilized, enter “None”. If medium was not recorded, enter “Unknown”. Example: FFPE (Paraffin embedded)	`1X quench buffer` `2% PFA/2.5% Glutaraldehyde` `Allprotect tissue reagent (ALL)` `CMC` `Concentrated quench buffer` `Cryo-EM` `DMSO (no serum)` `DMSO (serum)` `Ethanol` `FFPE (Paraffin embedded)` `Formic acid in water` `Gelatin` `HPMC-PVP` `MACS tissue storage solution` `Methanol` `NBF (Neutral Buffered Formalin)` `None` `Nuclease-free water` `OCT` `PAXgene tissue kit (PXT)` `PBS` `PFA (Paraformaldehyde)` `RNAlater` `Tris-EDTA` `Unknown` `Water`
storage_method *	The method used to store the sample after preparation and prior to performing the assay. If no specific storage method was utilized, enter “None”. If storage method was not recorded, enter “Unknown”. Example: Frozen in dry ice	`Frozen at -20 degrees celsius` `Frozen at -80 degrees celsius` `Frozen in liquid nitrogen` `Frozen in liquid nitrogen vapor` `Frozen on dry ice` `Frozen on ice` `Incubated at 37 degrees celsius` `None` `Stored in ambient temperature` `Stored in desiccator` `Stored in refrigerator` `Unknown`
quality_criteria	The quality criteria used to assess the sample, which may include metrics such as RIN (e.g., RIN: 8.7) or visual inspection parameters for suspensions prior to cell lysis. These criteria can be captured at a high level with general terms like “OK” or “not OK” or with more specific descriptors such as “debris” “clump” or “low clump”. Example: RIN: 8.7, low clump, no visible debris
histological_report	The key variables in the histopathological report that are crucial for assessing the tissue, including the absence of necrosis, comments on tissue composition, descriptions of significant pathology, and high-level assessments of inflammation or fibrosis. Example: No necrosis observed; tissue composed predominantly of hepatocytes with mild portal inflammation and minimal fibrosis
notes	Miscellaneous details about the sample that are not captured in the existing metadata fields. Example: Sample was stored at 4°C for 48 hours prior to processing due to equipment maintenance delay
metadata_schema_id *	The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9