Last modified 2025-10-13

Create, Edit, or Delete Metadata

At a Glance

If metadata fields are not provided in SLIMS, the Allen Institute's laboratory information management system, you can create your own samples, cohorts, or subjects. This document explains how to create, edit, or delete metadata, and includes example files for you to use.

Create Metadata

Most of the metadata in HISE is referenced from lab data in SLIMS. This tight coupling between SLIMS and HISE reduces human error to ensure accurate tracking of samples and lab resources. Sometimes, however, partners need to reference samples that exist outside of SLIMS. To track them, the direct cohort metadata ingest process lets you create your own cohorts, sample, subject, and specimen metadata values.

Before you can create your own metadata values, the HISE Support team must first configure the project. It designates the file type for demographic ingest and defines the demographics scheme. You suppy a map to associate the fields in your CSV file with the metadata fields in HISE, as shown in Table 1. The map should also include the expected date format for fields that require one.

TABLE 1
Variable in CSV	Field	Date format if applicable
birthYear	subject.birthYear	yyyy
cohortGuid	cohort.cohortGuid
cohortDescription	cohort.cohortDescription
daysSinceFirstVisit	sample.daysSinceFirstVisit
ethnicity	subject.ethnicity
race	subject.race
sampleKitGuid	sample.sampleKitGuid
biologicalSex	subject.biologicalSex
specimenGuid	specimen.specimenGuid
subjectGuid	subject.subjectGuid

To format the CSV file correctly, it's helpful to understand how the metadata fields relate to one another at various levels and in various groups, as shown in Table 2.

TABLE 2
Level	Name	Description	Examples
1	Cohort	Serves as an umbrella for all other metadata fields. This is the highest-level grouping, beneath which all subjects and samples are grouped together by cohort. Each cohort has many related subjects and samples. The cohort (either a new one added by CSV or one that already exists in HISE) must be defined before you create subjects within the cohort. These two cohort columns are the only required fields.	cohort cohortDescription
2	Subject	Subject fields represent the next level of granularity among the groupings. A single subject must be in a single cohort, but multiple samples or specimens might be associated with it. HISE accommodates nonhuman metadata as well as human metadata. Subject fields for nonhuman species include `genotype`, `mouseId`, `ageAtEnrollment`, `sacrificeDate`, and `strain`.	subjectGuid birthYear ageAtEnrollment ethnicity race sex genotype mouseId sacrificeDate strain
3	Sample	The third-highest category includes sampleKitGuids and sample metadata. The relationship between sample and specimen is one to many. In other words, a single sample can be associatd with multiple specimens. However, a single sample is associated with only one subject. Sample fields for nonhuman species include `batchId`, `diseaseState`, and `notes`.	batchId sampleKitGuid daysSinceFirstVisit visitDetails visitName diseaseState notes
4	Specimen	The most granular metadata fields are those related to specimens, including `specimenGuid`. A single subject or sample can have multiple associated specimen fields. A specimen field is not an umbrella for any other field or group. Specimen fields for nonhuman species include `panelId`, `specimenType`, `specimenSource`, and `specimenTissueSubtype`.	specimenGuid panelId specimenType specimenSource specimenTissueSubtype totalViableCellCount

The CSV file shown in Table 3 (Demographics_example.csv) creates a new cohort with associated subject, sample, and specimen metadata:

A cohort with the name "Cohort A" and the description "Good Cohort."
A subject within Cohort A with the subject GUID "subjectA" and the following subject characteristics:
- Birth year: 1999
- Ethnicity: Other
- Race: Other
- Sex: Male
A sample from subjectA with the sample kit GUID "sampleAA" and the following sample characteristics:
- Days since first visit: 0
- Visit details: Tired
- Visit name: firstVisit
A specimen within sampleAA with the specimen GUID "specimenA" and a total cell count of 9000.

TABLE 3

cohort

cohortDescription

subjectGuid

sampleKitGuid

birthYear

daysSinceFirstVisit

ethnicity

race

sex

specimenGuid

totalCellCount

visitDetails

visitName

Cohort A

Good Cohort

Cohort A

subjectA

1999

other

male

subjectA

sampleAA

tired

firstVisit

sampleAA

specimenA

9000

After you supply the necessary map, we create a watchfolder and share the link with you. You can then upload your CSV file and begin to create new metadata fields.

The headers and date format in the file you upload must match the information you send to Support. Otherwise, errors will occur, and you'll be unable to create new values.

Edit Metadata

To edit a subject, sample, or specimen metadata field you created, set up a CSV as in the attached example file (edit_demographics_example.csv). For sampleAA within subjectAA, the file changes values for fields like sex, birthYear, and daySinceFirstVisit.

To make any edits, define the cohort, subjectGuid, or sampleKitGuid. Then assign the metadata fields you want to change.

Delete Metadata

HISE lets you soft-delete a cohort, subject, sample, or specimen. These deletions cascade to the fields below. For example, if you delete cohort, the umbrella that covers all other fields, the subjects, samples, and specimen files previously mapped to the deleted cohort are deleted as well. To request soft deletion of a field at any level, contact Support.

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