Biospecimen Metadata Template
VEOIBD Biospecimen Metadata Template
| Attribute | Description | Required | Valid Values |
|---|---|---|---|
| collection_age | age at time of collection in years | FALSE | |
| collection_id | collection identifier | TRUE | |
| collection_num | ordinal code assigned to each specimen to distinquish between different collection dates | TRUE | |
| individual_id | A unique identifier for every enrolled individual, formatted as `'site''local_id'_'participant_id'`, e.g., BCH00001_0 | TRUE | |
| inflammation | inflammation status | FALSE | inflamed, uninflamed, unknown |
| local_id | local identifier (max of 5 digits) | TRUE | |
| media | type of media | FALSE | DMSO, FRZ, FORM, TCM, RNA, ORG |
| participant_id | Integer code indicating the participant identity or familial relation to proband. 0 = proband; 1 = control; 2 = mother; 3 = father, ≥ 4 = sibling/secondary family | TRUE | 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 |
| project | project identifier | TRUE | RC2, munich, other, unknown |
| sample_id | Unique sample identifier, formatted as `'individual_id'_'participant_id'_'collection_num'_'type_key'_'sample_num'` | TRUE | |
| sample_key | rc2 sample key (see RC2 Biopsys and Blood Flowcharts) | TRUE | A, B, C, D, E, F, G, H |
| sample_num | identifying number of sample collected (unique biopsy count # from same region or unique vial count of blood component) | TRUE | |
| sample_type | rc2 sample type | TRUE | pax_gene, pbmcs, biopsy, serum, whole_blood, dna, epithelial_organoid, bm_organoid, resected_tissue, plasma, unknown |
| site | site identifier indicating which institute oversaw the enrollment and sample collection of the patient. | TRUE | BCH, LMU, HSC, OXF, MSSM |
| specimen_area_biopsy | biopsy location | FALSE | transverse_colon, terminal_ileum, splenic_flexure, sigmoid_colon, rectum, pouch, left_colon, duodenum, descending_colon, cecum, ascending_colon, right_colon |
| type_key | rc2 tissue sample identifier (PB = PBMCs, BX = biopsy, SM = serum, PG = PAXgene tube, PL = plasma, WB = whole blood, DN = DNA, EO = epithelial organoid, RT = resected tissue, BO = bone marrow organoid, UK = unknown) | TRUE | PG, PB, BX, SM, WB, DN, EO, BO, RT, PL, UK |
| vial_label | lable on vial | TRUE | |
| volume | volume in mL | FALSE |