Use Specified Metadata Models (Tutorial)

At a Glance

A metadata model is a schema or data dictionary that defines entity-related attributes. HISE supports metadata models for nonhuman species, including mice. These models allow HISE to accommodate diverse research subjects while maintaining the system's core functionality and data organization.

	Abbreviations Key
AIFI	Allen Institute for Immunology	HISE	Humman Immune System Explorer
BMiF	bone marrow insterstitial fluid	MERSCOPE	multiplexed error robust scope
BMMC	bone marrow mononuclear cells	OCT	optimal cutting temperature
CyTOF	cytometry by time of flight	PBMC	peripheral blood mononuclear cells
FFPE	formalin-fixed, parrafin-embedded	PFA	paraformaldehyde
GUID	globally unique identifier	SLIMS	simple laboratory information system (Agilent)

Support for Cells and Nonhuman Species

Description

When scientists work with nonhuman metadata, HISE determines the object of study (mice, for example). Then it pulls in the correct cohort, subject, and sample references from SLIMS, and the server returns the data to be displayed in those fields.

To future-proof HISE, we've designed metadata models to ingest, display, and filter data in a dynamic, species-agnostic way that allows you to create your own data dictionary. You can now designate and define the metadata that's most relevant and useful to your project.

Subject Metadata

In the HISE UI, the Subject field now includes nonhuman subjects. We chose mice as a proof of concept. Therefore, you can see the nonhuman subjects only if you select mice as the object of study. In other words, a project can have only one object of study, and the resulting fields displayed are tied to the core metadata for that selection.

Mouse metadata is listed in the following box. You can use these fields, or designate and define your own, to create a targeted search query (see the instructions in Advanced Search for Cells or Nonhuman Metadata).

To see the Mice section, select a mouse-related project, and then navigate to Data Processing > Subject.

Mouse Metadata
Mouse ID	Sacrifice Date	Notes
Partner Subject GUID	Strain	Cohort
Date of Birth	Genotype	Last Modified

Sample Metadata

To accommodate cell studies and nonhuman species research, HISE includes three specimen fields: Specimen Type, Specimen Source, and Specimen Tissue Subtype. A sample can include multiple tissues as separate specimens. The specimen fields are used to distinguish these specimens from one another (for example, to distinguish skin tissue from tumor cells and bone marrow).The new fields and the available filters for each are shown in the following table. To see them in HISE, navigate to RESEARCH > Data Availability Dashboard, and click the arrow next to Batch ID.

Field	Available Filters
Specimen Type	BMiF, BMMC, Cells, CyTOF, Fixed cells, PBMC, Plasma, Purified Cells, Sample Pool, Serum, Sputum, Supernatant, Tempus Tube, Tissue - Disaggregated, Tissue - Intact, Whole Blood
Specimen Source	Lung Lobe 1, Lung Lobe 3, test, lymphNode
Specimen Tissue Subtype	10x Visium CytAssist slide, 10x Xenium slide FFPE, FFPE block, FFPE scroll, FFPE slide, Fresh - OCT block, Fresh - OCT scroll, MERSCOPE slide - FFPE, PFA - OCT slide, Tissue - media, Tissue - no media, pending, test

Advanced Search for Cells or Nonhuman Metadata

Instructions

The sample metadata specimen fields and the subject fields for mouse metadata are visible and searchable in the Query Builder. To get there, use the following instructions.

1. Navigate to HISE, and use your organizational email address to sign in.

2. From the top navigation menu, click RESEARCH, and choose Advanced Search from the drop-down list.