Model
A Model entry documents a non-human organism (e.g. mouse, zebrafish) or a cell line/organoid used as an experimental stand-in for human disease in MC2 Center-supported research. Model metadata captures how the model was derived or acquired (e.g. patient-derived xenograft, cell line, genetically engineered model), its genotype, and the treatment history applied to it during experiments.
This model outlines the key attributes needed to describe a model system, including its link back to the individual it was derived from (when applicable), so that biospecimens and assay data collected from the model can be traced to both the model itself and its clinical origin.
Why You Should Contribute Model Entries¶
Contributing model entries ensures that experimental findings generated from mouse models, cell lines, organoids, and other model systems can be correctly attributed to a well-documented source, including how faithfully the model represents the original patient disease. This supports reproducibility and allows other researchers to evaluate whether a given model system is appropriate for their own experiments.
Who Should Be Contributing Model Entries?¶
- Model System Core Staff – Document how a model was generated, acquired, and maintained (e.g. PDX, cell line, genetically engineered model).
- Research Staff and Lab Managers – Track treatment and experimental history applied to a model over time.
- Principal Investigators (PIs) – Ensure model provenance and its relationship to the source individual is properly documented.
- Data Managers – Maintain the model-level record that biospecimen entries derived from the model key off of.
Download Template¶
You can download the Model 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 |
|---|---|---|---|---|---|---|---|---|
| Model_id | Unique row identifier, used as a primary key for record updates. This should use the GrantNumber-Mxxx format unless directed otherwise. | True | string | None | ^CA\d{6}-M\d{1,9}$ | None | CDE:12220014 | |
| 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 Age | The age of the model when used for an experiment (mice, zebrafish, etc.) or model source (cell lines, organoids, etc.) | False | number | None | None | None | ||
| Model Age Unit | The unit corresponding to the age provided for this model. | False | string | None | None | None | ||
| Sex | Biological sex associated with the individual, biospecimen donor, or model. | True | string | None | None | View | CDE:7572817, CRDC_CDE:7572817 | |
| 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 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 | |
| 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 | |
| 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 | ||
| Species | The species of origin corresponding to the model, or from which the biospecimen originates. | True | string_list | None | None | View | ||
| Model Type | The general label used to identify the model type. | True | string | None | None | None | ||
| Model Method | The term that describes the general method used to create the model. | False | string | None | None | None | ||
| Model Source | The reference organism from which the model was derived, if applicable. This could be a specific Biospecimen Key, Model Key, mouse type, cell line, or other reference. Provide RRID if available, to link to existing cell line information. Do not use this field to designate an Individual as the source of the model. | False | string | None | None | None | ||
| Model Acquisition Type | The method by which the model was obtained. If applicable, please provide a link to the supplier of the model source. | False | string | None | None | None | ||
| Model Graft Source | If the model is an allograft or xenograft, as indicated by Model Type, please provide a unique identifier associated with the source of the graft material (e.g., RRID, Individual Key, Model Key, Biospecimen Key) | False | string | None | None | None | ||
| Model Genotype | The relevant genotype information associated with the model, including markers, background, etc. | 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 | |
| Days to Treatment | Number of days between the date used for index and the date the treatment started. | False | number | None | None | None | ||
| 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 | |
| Treatment Anatomic Site | The UBERON identifier of the organ or part of the body targeted by a therapeutic procedure (see https://www.ebi.ac.uk/ols4/ontologies/uberon). | False | string | None | ^UBERON:\d+$ | None | CRDC_CDE:14461856 |