Biospecimen

A Biospecimen entry documents a tissue, tumor, fluid, or other physical sample collected from an individual or a model organism/cell line for use in MC² Center-supported research. Biospecimen metadata captures how and when a specimen was acquired, its composition and preservation, and clinically relevant context such as disease type, tumor grade, morphology, and treatment history at the time of collection.

This model outlines the key attributes needed to track a biospecimen from acquisition through processing, including its relationship to a parent individual, model, or another biospecimen (for derived specimens), as well as the pathology and preservation details that downstream assays depend on.

Why You Should Contribute Biospecimen Entries

Contributing biospecimen entries ensures that every downstream dataset (imaging, sequencing, spatial transcriptomics, etc.) can be traced back to a well-documented physical sample. Complete biospecimen metadata makes it possible to reproduce experiments, correctly interpret assay results in their clinical context, and avoid ambiguity when the same specimen is used across multiple studies or assay types.

Who Should Be Contributing Biospecimen Entries?

1. Biobank and Specimen Coordinators – Ensure specimens are consistently tracked from acquisition through distribution to assay cores.
2. Pathologists and Histology Staff – Provide accurate morphology, tumor status, and preservation details that inform downstream analysis.
3. Research Staff and Lab Managers – Maintain the link between specimens, the individuals/models they were derived from, and the assays performed on them.
4. Data Managers – Ensure biospecimen records are complete before associated assay-level data (imaging, sequencing, etc.) is submitted.

Download Template

You can download the Biospecimen entry template, which includes all required fields, to streamline the data entry process.

Full Field Reference

Below is the full field reference table with attributes and their descriptions.

Attribute	Description	Required	Column Type	Format	Regex Pattern	Standard Terms	Examples
Biospecimen_id	Unique row identifier, used as a primary key for record updates. This should terminate in ModelKey-Bxxx or IndividualKey-Bxxx format, unless directed otherwise.	True	string	None	B\d{1,9}$	None
Study Key	The unique Study_id foreign keys associated with the resource, found in the grant Study information. Used to group the resource with other components. Please provide multiple values as a comma-separated list.	False	string	None	None	None
Individual Key	Unique Individual_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separated list.	False	string	None	CA\d{6}-IND\d{1,9}	None
Model Key	Unique Model_id foreign key(s) that link metadata entries as part of the same collection. Please provide multiple values as a comma-separate list.	False	string	None	CA\d{6}-M\d{1,9}	None
Parent Biospecimen Key	Biospecimen Key identifer of a biospecimen from which this sample was derived. Do not use this field to reference the source model or individual.	False	string	None	None	None
Biospecimen Type Category	The general category of this biospecimen.	True	string	None	None	View
Biospecimen Type	The type of biospecimen	False	string	None	None	View
Biospecimen Tumor Status	Normal or Tumor Sample Pathology Indicator	True	string	None	None	View
Biospecimen Acquisition Method	Records the method of acquisition or source for the specimen under consideration	False	string	None	None	View
Biospecimen Incidence Type	Text term describing a change in disease status associated with the collection of this specimen.	False	string	None	None	View
Biospecimen Stain	Any of the various methods that use a dye, reagent, or other material for producing coloration in tissues or microorganisms for microscopic examination.	True	string	None	None	None
Biospecimen Species	The species from which the biospecimen originates	True	string_list	None	None	View
Biospecimen Sex	Biological sex associated with the specimen donor	False	string	None	None	View
Biospecimen Age at Collection	Age at the time the biospecimen was collected. Please provide the unit in field Biospecimen Age at Collection Unit.	False	number	None	None	None
Biospecimen Age at Collection Unit	Unit associated with age at the time the biospecimen was collected.	False	string	None	None	None
Biospecimen Disease Type	The type of tumor associated with the specimen. Multiple values permitted, comma separated.	False	string_list	None	None	View
Biospecimen Primary Site	Primary site in the body associated with the primary diagnosis.	False	string	None	None	View
Biospecimen Primary Diagnosis	Text term used to describe the histologic diagnosis relevant to the model system, as described by the World Health Organization's (WHO) International Classification of Diseases for Oncology (ICD-O).	False	string	None	None	View
Biospecimen Site of Origin	The text term used to describe the anatomic site of origin, of the patient's malignant disease.	False	string	None	None	View
Biospecimen Tumor Subtype	The subtype related to the scientific determination and investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms of tissue growth resulting from uncontrolled cell proliferation.	False	string	None	None	None
Biospecimen Tumor Grade	Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness.	False	string	None	None	View
Biospecimen Known Metastasis Sites	The text term(s) used to describe the anatomic site(s) of metastasis associated with the malignant disease of the individual or model.	False	string_list	None	None	View
Biospecimen Tumor Morphology	Morphology code from the third edition of the International Classification of Diseases for Oncology, published in 2000, and used principally in tumor and cancer registries for coding the site (topography) and the histology (morphology) of neoplasms.	False	string	None	None	View
Biospecimen Composition	The text term used to describe the type(s) of tissue contained in the biospecimen. Multiple values permitted, comma separated.	False	string_list	None	None	View
Biospecimen Preservation Method	Text term that represents the method used to preserve the sample.	False	string	None	None	View
Biospecimen Fixative	The name of the compound that preserves tissues and cells in this sample for microscopic study.	True	string_list	None	None	View
Biospecimen Embedding Medium	The name of the material that infiltrates and supports the specimen and preserves its shape and structure for sectioning and microscopy.	True	string_list	None	None	View
Biospecimen Anatomic Site	Text term that represents the name of the primary disease site of the submitted tumor sample.	False	string	None	None	View
Biospecimen Site of Resection or Biopsy	The text term used to describe the anatomic site of the resection or biopsy of the patient's malignant disease.	False	string	None	None	View
Biospecimen Timepoint Type	Label to identify an event associated with the collection of the biospecimen (e.g. Baseline, End of Treatment, Overall survival, Final). Use Biospecimen Timepoint Offset to indicate the number of post-event days that elapsed before the biospecimen was collected. NO PHI/PII INFORMATION IS ALLOWED.	False	string	None	None	None
Biospecimen Timepoint Offset	The number of days that elapsed before the biospecimen was collected, relative to the event described by Biospecimen Timepoint Type. Floating point values are allowed.	False	number	None	None	None
Biospecimen Collection Site	The health care site at which the biospecimen sample was collected.	False	string	None	None	None
Biospecimen Treatment Type	Text term that describes the kind of treatment administered.	False	string_list	None	None	View
Biospecimen Therapeutic Agent	Text identification of the individual agent(s) used as part of a treatment regimen.	False	string	None	None	View
Biospecimen Treatment Response	Text term that describes the treatment response of a model or patient from which this specimen was derived.	False	string	None	None	View
Biospecimen Last Known Disease Status	Text term that describes the last known status of an individual associated with this specimen.	False	string	None	None	View
Biospecimen BioSample Identifier	BioSample (SAMN) accession number corresponding to the source of this biospecimen.	False	string	None	None	None
Biospecimen Description	A description of the biospecimen.	False	string	None	None	None