Create, Edit, or Delete Metadata
 | Abbreviations Key |
| CSV | comma-separated values |
| HISE | Human Immune System Explorer |
| GUID | globally unique identifier |
| SLIMS | simple laboratory information management system |
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 the accompanying image. The map should also include the expected date format for fields that require one.
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.
| TABLE 1 | |||
| 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 | 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 sampleKitGuid daysSinceFirstVisit visitDetails visitName diseaseState notes |
| 4 | Specimen | The most granular metadata fields are those related to specimens, including Specimen fields for nonhuman species include | specimenGuid panelId specimenType specimenSource specimenTissueSubtype totalViableCellCount |
The CSV file shown in Table 2 (Demographics_example.csv) creates a new cohort with associated subject, sample, and specimen metadata. To add additional subjects, add additional rows
- 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 2 | ||||||||||||
cohort | cohortDescription | subjectGuid | sampleKitGuid | birthYear | daysSinceFirstVisit | ethnicity | race | sex | specimenGuid | totalCellCount | visitDetails | visitName |
Cohort A | Good Cohort | |||||||||||
Cohort A | subjectA | 1999 | other | other | male | |||||||
subjectA | sampleAA | 0 | tired | firstVisit | ||||||||
| sampleAA | specimenA | 9000 |
When you've supplied the necessary map to the support team, 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 sent to the HISE support team. 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 soft-delete a field at any level, click the Support button in the upper-right corner of this page, or email immunology-support@allenimmunology.org with your request.
Related Resources
Use Specified Metadata Models (Tutorial)
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