arschat
commented
3 weeks ago | Reed et al. | values | |
|---|---|---|
| sample_id | freetext | |
| donor_id | freetext | |
| BCN_donor_id | freetext | |
| sample_type | Organoid LP sorted; Organoid unsorted; Supernatant unsorted; Supernatant live-sorted | |
| replicate | numeric | |
| processing_date | date | |
| dissociated_cells | numeric | |
| dissociation_minutes | numeric | |
| X10X_library_notes | freetext | |
| surgery_type | contralateral; reduction_mammoplasty; prophylactic_mastectomy | |
| brca_testing | boolean/unknown | |
| brca_status | BRCA1; assume_WT; unknown; BRCA2; WT | |
| brca_notes | family_history; tested; sister_has_variant_of_BRCA2; variant_of_unknown_significance; family_history_referred_for_test | |
| tissue_condition | Contralateral BRCA1; Mammoplasty WT; Mastectomy BRCA1; Mastectomy unknown; Mastectomy BRCA2; Mastectomy WT | |
| risk_status | Contralateral-BR1; AR; HR-BR1; HR-unk; HR-BR2 | |
| donor_age | numeric | |
| parity | numeric/unknown | |
| parity_notes | freetext (0_in_database_could_not_confirm; 3_children_one_set_of_twins; 1_in_database_could_not_confirm ) | |
| Approximate_age_at_each_last_pregnancy | array numeric | |
| Approximate_time_since_last_pregnancy.months. | numeric | |
| Body_mass_index | numeric | |
| Ethnicity | White-British; NA; Other_ethnic_group-Not_stated; White-Any_other_background; Other_ethnic_group-Any_other_ethnic_group; Black_or_Black_British-Any_other_Black_background; Asian_or_Asian_British-Bangladeshi; Asian_or_Asian_British-Any_other_Asian_background; White-Irish | |
| Smoking_status | NA; Never; Present; Past | |
| Alcohol_consumption_levels | NA; Socially; Moderate; None; High; Low | |
| Age_at_first_menstruation | numeric | |
| Menopause_status | Pre; Post; Post_(surgically_induced); Peri/Post; NA | |
| oral_contraceptive_pill_usage | Past; NA; Never; Past_(Present_possible); No | |
| other_hormonal_contraceptive_usage | NA; Past; Present; None_recorded | |
| type_of_other_hormonal_contraceptive | NA; Mirenacoil; Depo-Provera; Cerezette; Desogestrel_pill; Desogestrel; Progesterone_only_injection_and_implant | |
| Hormone_replacement_therapy_usage | Never; Present_; NA; Present; Past | |
| other_hormonal_medication | NA; Present; Past; None_recorded | |
| type_of_other_hormonal_medication | NA; Tamoxifen; Carbimazole; Thyroxine; Levothyroxine; Dianette | |
| Previous_breast_cancer_diagnosis | No; Yes; NA | |
| previous_BC_notes | NA; previous_IDC_in_left_ER+_Her2-; left_DCIS_right_ADH; incidental_finding_IDC_and_HG_DCIS_right_breast; Papilloma_in_right_breast | |
| Previous_other_cancer_diagnosis | NA; Chronic_Myeloid_Leukaemia; Stage_2c_High_grade_serous_Ovarian_Cancer |
Here is the discussion about the definition of the Tier 2 metadata for the breast bionetwork.
It has been decided that for the Breast Atlas v1 HCA will use the already published atlas (Reed et al. 2024) that already has some metadata that could be considered tier 2 (in terms of being biological metadata).
We have to map with existing dcp and tier 2 fields and see which we need to create. Before we proceed with action however, we have to discuss with them cause it is possible that they will add more metadata for tier 2.
spreadsheet with paper's metadata.