Biospecimen_Metadata_Template
VEOIBD Biospecimen Metadata Template [Source]
| Key | Key Description | Type | Valid Values | DependsOn | Required | Source | Module |
|---|---|---|---|---|---|---|---|
| sample_key | rc2 sample key (see RC2 Biopsys and Blood Flowcharts) | STRING | A,B,C,D,E,F,G,H | True | Sage Bionetworks | Biospecimen | |
| sample_type | rc2 sample type | STRING | pax_gene,pbmcs,biopsy,serum,whole_blood,dna,epithelial_organoid,bm_organoid,resected_tissue,plasma,unknown | True | Sage Bionetworks | Biospecimen | |
| site | site identifier (BCH = Boston, LMU = Munich, HSC = Toronto) | STRING | BCH,LMU,HSC | True | Sage Bionetworks | Clinical | |
| 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 | NUM | 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 | True | Clinical | ||
| project | project identifier | STRING | RC2,munich,other,unknown | True | Biospecimen | ||
| inflammation | inflammation status | STRING | inflamed,uninflamed,unknown | False | Biospecimen | ||
| media | type of media | STRING | DMSO,FRZ,FORM,TCM,RNA,ORG | False | Biospecimen | ||
| specimen_area_biopsy | biopsy location | STRING | transverse_colon,terminal_ileum,splenic_flexure,sigmoid_colon,rectum,pouch,left_colon,duodenum,descending_colon,cecum,ascending_colon,right_colon | False | Biospecimen | ||
| type_key | rc2 tissue sample identifier | STRING | PG,PB,BX,SM,WB,DN,EO,BO,RT,PL,UK | True | Biospecimen | ||
| collection_date | date collected (yyyy_mm_dd) | STRING | False | Sage Bionetworks | Biospecimen | ||
| volume | volume in mL | NUM | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C25335 | Biospecimen | ||
| local_id | local identifier (max of 5 digits) | NUM | True | https://docs.google.com/spreadsheets/d/1d8-G1ernDQDLTwMJSrX5EQGnq_afsA0G/edit#gid=110285588 | Clinical | ||
| individual_id | individual identifier | STRING | True | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=21.09d&code=C69256&ns=ncit | Clinical | ||
| 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 | |||||
| sample_id | sample identifier | True | |||||
| sample_num | identifying number of sample collected (unique biopsy count # from same region or unique vial count of blood component) | True | |||||
| vial_label | lable on vial | True | |||||
| Component | Category of metadata; provide the same one for all items/rows. | True | https://w3id.org/biolink/vocab/category |