Permissible Values
- Some fields will only accept certain values from a list of controlled terminology that is provided in the permissible values column of the dictionary tables. Values must match the dictionary spelling exactly, but can be submitted case-insensitive.
- Other fields must meet a regular expression for their value.
patient
| Field | Permissible values |
|---|---|
| patient_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| sex | female, male, other, Not provided, Not collected |
| history | This field accepts a detailed description string of up to 1000 characters, comprising letters, digits, spaces, parentheses, and specific symbols (+.', |
| ethnicity | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| ethnicity_assessment_method | self-assessed, genetic, Not provided, Not collected |
| initial_diagnosis | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| age_at_initial_diagnosis | This field accepts age values (in 'months' as well). |
patient_sample
| Field | Permissible values |
|---|---|
| patient_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| sample_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| collection_date | This field accepts a collection date in the format 'MMM YYYY' (e.g., Jan 2023). |
| collection_event | This field accepts string such as 'collection event ' followed by a numeric value eg. 'collection event 1'. |
| months_since_collection_1 | This field accepts numeric values, including integers, ranges, or 'All'. |
| age_in_years_at_collection | This field accepts age values (in 'months' as well). |
| diagnosis | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| tumour_type | primary, metastatic, recurrent, refractory, pre-malignant, Not provided, Not collected |
| primary_site | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| collection_site | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| stage | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| staging_system | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| grade | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| grading_system | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| virology_status | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| sharable | yes, no, Not provided, Not collected |
| treatment_naive_at_collection | yes, no, Not provided, Not collected |
| treated_at_collection | yes, no, Not provided, Not collected |
| treated_prior_to_collection | yes, no, Not provided, Not collected |
| model_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
sharing
| Field | Permissible values |
|---|---|
| model_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| accessibility | academia, industry, academia and industry |
| europdx_access_modality | transnational access, collaboration only, Not applicable |
| This field accepts an email address or multiple separated by comma (,). | |
| name | This field accepts a contact name or multiple separated by comma (,). |
| form_url | This field accepts a URL starting with 'http://' or 'https://'. |
| database_url | This field accepts a URL starting with 'http://' or 'https://'. |
pdx_model
| Field | Permissible values |
|---|---|
| model_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| engraftment_type | heterotopic, orthotopic, Not provided, Not collected |
| host_strain_name | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| host_strain_nomenclature | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| engraftment_site | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| sample_type | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| sample_state | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| passage_number | This field accepts numeric values, including integers, ranges, or 'All'. |
| publications | This field accepts a PubMed ID (PMID) in the format 'PMID: [ID], ' with optional whitespace. |
model_validation
| Field | Permissible values |
|---|---|
| model_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| validation_technique | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| description | This field accepts a detailed description string of up to 1000 characters, comprising letters, digits, spaces, parentheses, and specific symbols (+.',<>%:;_/-&). |
| passages_tested | This field accepts numeric values, including integers, ranges, or 'All'. |
| validation_host_strain_nomenclature | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
cell_model
| Field | Permissible values |
|---|---|
| model_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| name | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| type | organoid, CRC, 3-D: other, 2D: other, cell line, Not provided, Not collected |
| growth_properties | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| parent_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| origin_patient_sample_id | This field accepts a URL-safe string of characters, including letters, digits, spaces, slashes, periods, underscores, and |
| comments | This field accepts a detailed description string of up to 1000 characters, comprising letters, digits, spaces, parentheses, and specific symbols (+.',<>%:;_/-&). |
| supplier | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| external_ids | This field accepts a free text string of up to 250 characters, including letters, digits, spaces, parentheses, and specific symbols (.',<%>:;_/-&). |
| publications | This field accepts a PubMed ID (PMID) in the format 'PMID: [ID], ' with optional whitespace. |