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?¶
- Biobank and Specimen Coordinators – Ensure specimens are consistently tracked from acquisition through distribution to assay cores.
- Pathologists and Histology Staff – Provide accurate morphology, tumor status, and preservation details that inform downstream analysis.
- Research Staff and Lab Managers – Maintain the link between specimens, the individuals/models they were derived from, and the assays performed on them.
- 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 | CDE | 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 | CDE:15100774 | |
| 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 material that forms the biospecimen sample, per NCI caDSR CDE 12445832 (Specimen Material Category). See Biospecimen Type for finer-grained specimen classification (e.g. specific analyte types). | True | string | None | None | View | CRDC_CDE:12445832 | |
| 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 | CDE:14688604, CRDC_CDE:14688604 | |
| Biospecimen Acquisition Method | Records the method of acquisition or source for the specimen under consideration. | False | string | None | None | View | CDE:6626651, CRDC_CDE:15115495 | |
| Biospecimen Incidence Type | Text term describing a change in disease status associated with the collection of this specimen. | False | string | None | None | View | CDE:62997 | |
| 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 | View | CDE:8120269 | |
| Species | The species of origin corresponding to the model, or from which the biospecimen originates. | True | string_list | None | None | View | ||
| Sex | Biological sex associated with the individual, biospecimen donor, or model. | True | string | None | None | View | CDE:7572817, CRDC_CDE:7572817 | |
| 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 | CDE:14473376 | |
| Biospecimen Age at Collection Unit | Unit associated with age at the time the biospecimen was collected. | False | string | None | None | None | ||
| Disease Type | The type of tumor associated with the individual, biospecimen, or model. Multiple values permitted, comma separated. | False | string_list | None | None | View | CDE:13471160 | |
| Primary Site | The UBERON identifier of the organ or part of the body where the disease began, i.e. the primary/original disease site (see https://www.ebi.ac.uk/ols4/ontologies/uberon). Reference-validated, not a fixed list. | False | string | None | ^UBERON:\d+$ | None | CDE:14883047, CRDC_CDE:14883047 | |
| Primary Diagnosis | Text term used to describe the histologic diagnosis of the patient, biospecimen donor, or model (NCI Thesaurus concept name -- reference-validated, not a fixed list; see https://ncithesaurus.nci.nih.gov/). | True | string | None | None | None | CRDC_CDE:14905532 | |
| Site of Origin | The UBERON identifier of the anatomic site of origin of the patient's, biospecimen donor's, or model's malignant disease (see https://www.ebi.ac.uk/ols4/ontologies/uberon). | False | string | None | ^UBERON:\d+$ | None | CDE:14156279, CRDC_CDE:14883072 | |
| Tumor Subtype | The molecular or histologic subtype of the tumor associated with the individual, biospecimen, or model. | False | string_list | None | None | None | ||
| Tumor Grade | Numeric value to express the degree of abnormality of cancer cells, a measure of differentiation and aggressiveness. | False | string | None | None | View | CDE:11325685, CRDC_CDE:11325685 | |
| Known Metastasis Sites | The UBERON identifier(s) of the anatomic site(s) of metastasis associated with the malignant disease of the individual or biospecimen donor (see https://www.ebi.ac.uk/ols4/ontologies/uberon). Provide multiple values as a comma-separated list. | False | string_list | None | ^UBERON:\d+$ | None | CDE:2856440, CRDC_CDE:15114457 | |
| 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 | CDE:11326261, CRDC_CDE:11326261 | |
| 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 | CDE:12922545, CRDC_CDE:12922545 | |
| Biospecimen Preservation Method | Text term that represents the method used to preserve the sample. | False | string | None | None | View | CDE:8028962, CRDC_CDE:8028962 | |
| Biospecimen Preservation Medium | The kind of substance holding another substance in solution or suspension to maintain a specimen in a viable state, such as a fixative compound used to preserve tissues and cells for microscopic study (renamed from 'Fixative' to align with the CRDC required-CDE terminology). | True | string_list | None | None | View | CDE:0065078, CRDC_CDE:16323957 | |
| 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 | The UBERON identifier of the primary disease site of the submitted tumor sample (see https://www.ebi.ac.uk/ols4/ontologies/uberon). Reference-validated, not a fixed list. | False | string | None | ^UBERON:\d+$ | None | CDE:14156279 | |
| Biospecimen Site of Resection or Biopsy | The UBERON identifier of the anatomic site of the resection or biopsy of the patient's malignant disease (see https://www.ebi.ac.uk/ols4/ontologies/uberon). | False | string | None | ^UBERON:\d+$ | None | CDE:14883054, CRDC_CDE:14883054, CRDC_CDE:12083894 | |
| 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 | ||
| Treatment Type | Text term that describes the kind of treatment administered to the individual, biospecimen donor, or model. | False | string_list | None | None | View | CDE:14737565, CRDC_CDE:14737565 | |
| Therapeutic Agent | The name of the individual agent(s) used as part of a treatment regimen or experimental protocol (NCI Thesaurus concept name -- reference-validated, not a fixed list; see https://ncithesaurus.nci.nih.gov/). | False | string_list | None | None | None | CRDC_CDE:14913015 | |
| Treatment Response | Text term that describes the final outcome after a treatment was administered to the individual, biospecimen donor, or model. | False | string | None | None | View | CDE:13383448, CRDC_CDE:13383448, CRDC_CDE:15179918 | |
| Last Known Disease Status | Text term that describes the last known disease status of the individual, biospecimen donor, or model. | False | string | None | None | View | CDE:12447172, CRDC_CDE:12447172 | |
| 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 | ||
| ICD-10-CM Disease Code | An alphanumeric value from the tenth version of the International Classification of Disease (ICD-10-CM) used to identify the diagnosis (e.g. C80.1). Reference-validated against the ICD-10-CM code system, not a fixed list. | False | string | None | ^[A-Z][0-9]{2}(\.[0-9A-Z]{1,4})?-?$ | None | CRDC_CDE:11479873 | |
| Biospecimen Treatment Prior to Specimen Collection Indicator | An indication of whether the administration of therapeutic agents was received before the body specimen was collected. | False | string | None | None | None | CRDC_CDE:15157426 | |
| Biospecimen Aliquot Mass | The quantity in micrograms (mcg, ug) of the aliquots derived from the analyte. | False | number | None | None | None | CRDC_CDE:15745091 | |
| Biospecimen Aliquot Volume | The volume in microliters (uL) of the aliquot(s) derived from the analyte. | False | number | None | None | None | CRDC_CDE:15745088 | |
| Biospecimen Days from Diagnosis to Specimen Collection | The number of days from the date the diagnosis was made to the date a sample was collected. | False | number | None | None | None | CRDC_CDE:11248865 | |
| Biospecimen Days from First Subject Visit to Specimen Collection | The number of days from the date the subject first visited to the date a sample was collected. | False | number | None | None | None | CRDC_CDE:11248874 | |
| Biospecimen Days from First Treatment to Specimen Collection | The number of days from the date the first treatment was administered to the date a sample was collected. | False | number | None | None | None | CRDC_CDE:11250807 | |
| Biospecimen Days from Initial Genomic Sequencing to Specimen Collection | The number of days from the date the initial genomic sequencing was done to the date a sample was collected. | False | number | None | None | None | CRDC_CDE:11251130 | |
| Biospecimen Days from Recurrence to Specimen Collection | The number of days from the date the disease recurrence was identified to the date a sample was collected. | False | number | None | None | None | CRDC_CDE:11251133 | |
| Biospecimen Days from Specimen Collection to Initial Pathologic Diagnosis | The number of days from the date a sample was collected to the date of the initial pathologic diagnosis. | False | number | None | None | None | CRDC_CDE:11253404 | |
| Biospecimen Preservation Temperature | The term which describes the temperature used to maintain the specimen in a viable state. | False | string | None | None | None | CRDC_CDE:16306751 | |
| Biospecimen Taxonomy ID | A label provided by the NCBI Taxonomy Database (https://www.ncbi.nlm.nih.gov/taxonomy/) that uniquely identifies the species or other taxonomic group from which the biospecimen originates (e.g. 9606 for Homo sapiens). Companion formal identifier to Biospecimen Species; reference-validated, not a fixed list. | False | string | None | ^\d+$ | None | CRDC_CDE:10543100 |