Metadata Dictionary
patient (patient)
The collection of descriptors associated with patient information for data submission to CancerModels.org.
| Field & Description | Attributes | Type | Permissible Values | Notes |
|---|---|---|---|---|
| patient_id Unique anonymous/de-identified ID for the patient from the provider. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| sex Sex of the patient. | Required | TEXT | Any of the following:
| Any of the following values: ['male', 'female', 'other', 'not collected', 'not provided'] |
| history Cancer relevant comorbidity or environmental exposure. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| ethnicity Patient Ethnic group. Can be derived from self-assessment or genetic analysis. | TEXT | Values must meet the regular expression: | #/fields/format/NCIT | |
| ethnicity_assessment_method Patient Ethnic group assessment method. | TEXT | Any of the following:
| Any of the following: ['self-assessed', 'genetic', 'not provided', 'not collected'] | |
| initial_diagnosis Diagnosis of the patient when first diagnosed at age_at_initial_diagnosis - this can be different than the diagnosis at the time of collection which is collected in the sample section. | TEXT | Values must meet the regular expression: | #/fields/format/NCIT | |
| age_at_initial_diagnosis This is the age of first diagnostic. Can be prior to the age at which the tissue sample was collected for implant. | TEXT | Values must meet the regular expression: | #/fields/format/AGE | |
| age_category Age category at time of sampling. | TEXT | Any of the following:
| Any of the following values: ['adult', 'pediatric', 'fetus', 'not collected', 'not provided'] | |
| smoking_status Patient's smoking history | TEXT | Values must meet the regular expression: | Any of the following values: ['current smoker', 'ex-smoker', 'non-smoker', or 'never smoked'; followed by free text] | |
| alcohol_status Alcohol intake of the patient, self-reported | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] | |
| alcohol_frequency The average number of days per week on which the patient consumes alcohol, self-reported. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| family_history_of_cancer If a first-degree relative of the patient has been diagnosed with a cancer of the same or different type. | TEXT | Values must meet the regular expression: | #/fields/format/Free |
patient sample (patient_sample)
The collection of descriptors associated with clinical information of the tumor sample for data submission to CancerModels.org.
| Field & Description | Attributes | Type | Permissible Values | Notes |
|---|---|---|---|---|
| patient_id Unique anonymous/de-identified ID for the patient from the provider. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| sample_id Unique ID of the patient tumour sample used to generate cancer models. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| collection_date Date of collections. Important for understanding the time relationship between models generated for the same patient. | TEXT | Values must meet the regular expression: | MMM YYYY | |
| collection_event Collection event corresponding to each time a patient was sampled to generate a cancer model, subsequent collection events are incremented by 1. | TEXT | Values must meet the regular expression: | collection event + 'event number' | |
| months_since_collection_1 The time difference between the 1st collection event and the current one (in months). | TEXT | Values must meet the regular expression: | Numeric. The collection event 1 should be 0, collection event 2 should be 6 if 6 months have elapase between collection 1 and collection 2 and collection event 3 should be 9 if 9 months have elapsed between collection 1 and collection 3. | |
| age_in_years_at_collection Patient age at collection. | Required | TEXT | Values must meet the regular expression: | #/fields/format/AGE |
| diagnosis Diagnosis at time of collection of the patient tumour used in the cancer model | Required | TEXT | Values must meet the regular expression: | #/fields/format/NCIT |
| tumour_type Collected tumour type. | Required | TEXT | Any of the following:
| #/fields/format/NCIT |
| primary_site Site of the primary tumor where primary cancer is originating from (may not correspond to the site of the current tissue sample). | Required | TEXT | Values must meet the regular expression: | #/fields/format/NCIT |
| collection_site Site of collection of the tissue sample (can be different than the primary site if tumour type is metastatic). | Required | TEXT | Values must meet the regular expression: | #/fields/format/NCIT |
| collection_method Method of collection of the tissue sample | TEXT | Values must meet the regular expression: | Any of the following: Biopsy, surgical resection, blood draw, free text | |
| stage Stage of the patient at the time of collection. | TEXT | Values must meet the regular expression: | Should be in the format of the stage classification. | |
| staging_system Stage classification system used to describe the stage, add the version if available. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| grade The implanted tumour grade value. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| grading_system Grade classification corresponding used to describe the stage, add the version if available. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| virology_status Positive virology status at the time of collection. Any relevant virology information which can influence cancer like EBV, HIV, HPV status. | TEXT | Values must meet the regular expression: | #/fields/format/NCIT | |
| gene_mutation_status Outcome of mutational status tests for the following genes: BRAF, PIK3CA, PTEN, KRAS. | TEXT | Values must meet the regular expression: | HGNC Symbols | |
| sharable Is patient treatement information avalaible and sharable? If yes fill out following treatment columns: treatment_naive_at_collection, treated_at_collection, treated_prior_to_collection. | Required | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] |
| treatment_naive_at_collection Was the patient treatment naive at the time of collection? This includes the patient being treated at the time of tumour sample collection and if the patient was treated prior to the tumour sample collection. The value will be 'yes' if either treated_at_collection or treated_prior_to_collection are 'yes'. | Required | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] |
| treated_at_collection Was the patient being treated for cancer at the time of tumour sample collection. This includes any of the following: radiotherapy, chemotherapy, targeted therapy, homorno-therapy. | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] | |
| treated_prior_to_collection Was the patient treated for cancer prior to the time of tumour sample collection. This includes any of the following: radiotherapy, chemotherapy, targeted therapy, homorno-therapy. | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] | |
| response_to_treatment Patient’s response to treatment. | TEXT | Values must meet the regular expression: | RECIST criteria: CR, PR, PD, SD | |
| model_id Unique identifier for all the cancer models derived from the same tissue sample. Needs to be unique. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
sharing (sharing)
The collection of descriptors associated with model data sharability for data submission to CancerModels.org.
| Field & Description | Attributes | Type | Permissible Values | Notes |
|---|---|---|---|---|
| model_id Unique identifier for all the cancer models derived from the same tissue sample. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| accessibility Define any limitation of access of the model per type of users like academia, industry, academia and industry, or national limitation if needed (e.g. no specific consent for sequencing). | Required | TEXT | Any of the following:
| Any of the following: ['academia', 'industry', 'academia and industry'] |
| europdx_access_modality If part of EUROPDX consortium fill this in. Designates a model is accessible for transnational access through the EDIReX infrastructure, or only on a collaborative basis (i.e. upon approval of the proposed project by the owner of the model) | TEXT | Any of the following:
| Any of the following: ['transnational access', 'collaboration only', 'not provided'] | |
| date_submitted Please add the date of submission to the resource | TEXT | Values must meet the regular expression: | DD/MM/YYYY | |
| model_availability Model availability status, i.e. if the model is still available to purchase. | TEXT | Any of the following:
| Any of the following: ['available','NA', 'discontinued'] | |
| email Contact email for any requests from users about models. If multiple, include as comma separated list. | Required | TEXT | Values must meet the regular expression: | Email address |
| name Contact person (should match that included in email column). | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| form_url If the center has a contact form rather than a contact email include the link here. | TEXT | Values must meet the regular expression: | URL | |
| database_url If the institution has a public database and wants that link to be shared, include it here. | TEXT | Values must meet the regular expression: | URL |
pdx model (pdx_model)
The collection of descriptors associated with PDX models for data submission to CancerModels.org
| Field & Description | Attributes | Type | Permissible Values | Notes |
|---|---|---|---|---|
| model_id Unique identifier for all the cancer models derived from the same tissue sample. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| host_strain_name Host mouse strain name (e.g. NOD-SCID, NSG, etc). | Required | TEXT | Values must meet the regular expression: | Mouse strain name |
| host_strain_nomenclature The full nomenclature form of the host mouse strain name. | Required | TEXT | Values must meet the regular expression: | Use most precise nomenclature where possible. |
| engraftment_site Organ or anatomical site used for the PDX tumour engraftment (e.g. mammary fat pad, Right flank). | Required | TEXT | Values must meet the regular expression: | Use anatomical graft site, not collected, or not provided. |
| engraftment_type PDX Engraftment Type: Orthotopic if the tumour was engrafted at a corresponding anatomical site (e.g. patient tumour of primary site breast was grafted in mouse mammary fat pad). If grafted subcuteanously use hererotopic. | Required | TEXT | Any of the following:
| Any of the following: ['heterotopic', 'orthotopic', 'not collected', 'not provided']. |
| sample_type Description of the type of material grafted into the mouse. (e.g. tissue fragments, cell suspension). | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| sample_state PDX Engraftment material state (e.g. fresh or frozen). If other please describe. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| passage_number Passage number: When different host strains, or PDX Engraftment Site or PDX Engraftment Type or PDX Engraftment Material were used during the PDX line generation, please add passage - add rows per model as needed. We assume that passage 0 corresponds to first engraftment - if not the case please indicate what passage 0 correspond to. passage number- add rows if columns D,E,F, G changes - if no change and always same D,E,F,G add 'all' as passage value to specify the conditions are the same in all passages. | Required | TEXT | Values must meet the regular expression: | Numeric or all. |
| publications If model has been part of a published study include PubMed IDs separated by commas. | TEXT | Values must meet the regular expression: | #/fields/format/PMID | |
| supplier Please provide the supplier brief acronym or name followed by a colon and thel number or name use to reference the model. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| supplier_type Model supplier type - commercial, academic, other. | Required | TEXT | Any of the following:
| Any of the following: ['commercial', 'academic', 'other'] |
| catalog_number Catalogue number of model, if commercial. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| vendor_link Link to purchasable cell model, if commercial. | TEXT | Values must meet the regular expression: | URL | |
| external_ids Depmap accession, Cellusaurus accession or another id. Please place in comma separated list. | TEXT | Values must meet the regular expression: | #/fields/format/Free |
model validation (model_validation)
The collection of descriptors associated with cancer model validation techniques for data submission to CancerModels.org
| Field & Description | Attributes | Type | Permissible Values | Notes |
|---|---|---|---|---|
| model_id Unique identifier for all the cancer models derived from the same tissue sample. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| validation_technique Any technique used to validate PDX against their original patient tumour, including fingerprinting, histology, immunohistochemistry. | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| description Short description of what was compared and what was the result: (e.g. high, good, moderate concordance between xenograft, 'model validated against histological features of same diagnosis' or 'not determined') - It needs to be clear if the model is validated or not. | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| passages_tested Provide a list of all passages where validation was performed. Passage 0 correspond to first engraftment (if this is not the case please define how passages are numbered). | Required | TEXT | Values must meet the regular expression: | A list of numbers separated by commas. |
| validation_host_strain_nomenclature Validation host mouse strain, following mouse strain nomenclature from MGI JAX. | TEXT | Values must meet the regular expression: | Full host strain name, not collected, or not provided | |
| morphological_features If model type is 3D: Organoid or cell lines, Morphological features of the model. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| SNP_analysis Was SNP analysis done on the model? | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] | |
| STR_analysis Was STR analysis done on the model? | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] | |
| tumour_status Gene expression validation of established model. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| model_purity Presence of tumour vs stroma or normal cells. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| comments Comments about the model that cannot be expressed by other fields. | TEXT | Values must meet the regular expression: | #/fields/format/Free |
cell model (cell_model)
The collection of descriptors associated with cell and organoid models for data submission to CancerModels.org
| Field & Description | Attributes | Type | Permissible Values | Notes |
|---|---|---|---|---|
| model_id Unique identifier for all the cancer models derived from the same tissue sample. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| model_name Most common name associated with the model. Please use the CCLE name if available. | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| model_name_aliases Additional model names, if known. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| type Type of organoid or cell model. | Required | TEXT | Any of the following:
| One of the following: ['organoid', 'CRC', '3-D: other', '2D: other', 'cell line']. |
| parent_id Please add the model Id of the model used to generate the model. If the model was not in this set, please refer to it by external id. | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC | |
| origin_patient_sample_id Unique ID of the patient tumour sample used to generate the model. | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC | |
| growth_properties Observed growth properties of the related model. | Required | TEXT | Values must meet the regular expression: | One of the following: ['embedded 3d culture', 'adherent', 'mix of adherent and suspension', 'suspension']. |
| media_id Unique identifier for each media formulation (Catalogue number). | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| growth_media Base media formulation the model was grown in. | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| plate_coating Coating on plate model was grown in. | Required | TEXT | Any of the following:
| Any of the following values: ['laminin', 'matrigel', 'collagen', 'none'] |
| other_plate_coating Other coating on plate model was grown in (not mentioned above). | Required | TEXT | Any of the following:
| Any of the following values: ['peg-based hydrogel', 'none'] |
| passage_number Passage number at time of sequencing/screening. | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
| contaminated Is there contamination present in the model. | Required | TEXT | Any of the following:
| Any of the following: ['yes', 'no', 'not provided', 'not collected'] |
| contamination_details What are the details of the contamination. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| supplements Additional supplements the model was grown with. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| drug Additional drug/compounds the model was grown with. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| drug_concentration Concentration of Additional drug/compounds the model was grown with. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| publications If the model has been part of a published study include PubMed IDs separated by commas. | TEXT | Values must meet the regular expression: | #/fields/format/PMID | |
| supplier Please provide the supplier brief acronym or name followed by a colon and thel number or name use to reference the model. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| supplier_type Model supplier type - commercial, academic, other. | Required | TEXT | Any of the following:
| Any of the following: ['commercial', 'academic', 'other'] |
| catalog_number Catalogue number of model, if commercial. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| vendor_link Link to purchasable cell model, if commercial. | TEXT | Values must meet the regular expression: | URL | |
| rrid Cellosaurus ID | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| external_ids Depmap accession, Cellusaurus accession or another id. Please place in comma separated list. | TEXT | Values must meet the regular expression: | #/fields/format/Free | |
| comments Add crucial comments about the model that cannot be expressed by other fields. | Required | TEXT | Values must meet the regular expression: | #/fields/format/Free |
preclinical images (preclinical_images)
The collection of descriptors associated with model data sharability for data submission to CancerModels.org.
| Field & Description | Attributes | Type | Permissible Values | Notes |
|---|---|---|---|---|
| model_id Unique identifier for all the cancer models derived from the same tissue sample. | Required | TEXT | Values must meet the regular expression: | #/fields/format/ALPHANUMERIC |
| passage_number Passage number: When different host strains, or PDX Engraftment Site or PDX Engraftment Type or PDX Engraftment Material were used during the PDX line generation, please add passage - add rows per model as needed. We assume that passage 0 corresponds to first engraftment - if not the case please indicate what passage 0 correspond to. passage number- add rows if columns D,E,F, G changes - if no change and always same D,E,F,G add 'all' as passage value to specify the conditions are the same in all passages. | Required | TEXT | Values must meet the regular expression: | Numeric or all. |
| engraftment_site Organ or anatomical site used for the PDX tumour engraftment (e.g. mammary fat pad, Right flank). | Required | TEXT | Values must meet the regular expression: | Use anatomical graft site, not collected, or not provided. |
| treatment treatment name, can be surgery, radotherapy, drug name or drug combination (radiotherapy, chemotherapy, targeted therapy, homornal therapy) | Required | TEXT | Values must meet the regular expression: | list drugs or conpounds or surgery or radiotherapy, drug/treatment type needs to be separated by '+' if several |
| modality PET, MRI, CT, BLI, etc | Required | TEXT | Any of the following:
| Any of the following: PET, MR, CT, BLI, etc |
| contrast_sequence_used Contrast or sequence used for image generation | Required | TEXT | Values must meet the regular expression: | free alphanumerical and and -_~. |
| number_of_images Number of images available for the contrast/sequence used | Required | TEXT | Values must meet the regular expression: | Numeric. |
| project_id Preclinical imaging project id | Required | TEXT | Values must meet the regular expression: | free alphanumerical and and -_~. |
| project_url Project link | TEXT | Values must meet the regular expression: | URL |