Clinical_Metadata_Template
VEOIBD Clinical Metadata Template [Source]
| Key | Key Description | Type | Valid Values | DependsOn | Required | Source | Module |
|---|---|---|---|---|---|---|---|
| participant_role | participant role | STRING | ibd,non_ibd,mother,father,sibling,second_degree | True | https://ncithesaurus.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&version=22.07d&code=C71384 | Clinical | |
| sex | biological sex | STRING | male,female | True | https://ncithesaurus.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&version=22.07d&code=C28421&ns=ncit | Clinical | |
| gi_phenotype | GI phenotype | STRING | CD,UC,IBDU,CTL,other | True | Sage Bionetworks | Clinical | |
| immunodeficiency | immunodeficiency diagnosis | STRING | no,yes,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&version=22.07d&code=C39725&ns=ncit | Clinical | |
| autoimmune | autoimmune diagonsis | STRING | no,yes,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C2889 | Clinical | |
| disease_activity_location | disease activity location | STRING | L1,L2,L3,L4,E1,E2,E3,E4 | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C117884 | Clinical | |
| upper_disease_type | upper disease type | STRING | L4A,L4B | False | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8743432/ | Clinical | |
| disease_activity_behavior | disease activity behavior | STRING | never_severe,ever_severe,nonstricturing_nonpenetrating,stricturing,penetrating,penetrating_and_stricturing,unknown | False | Sage Bionetworks | Clinical | |
| growth_delay | growth delay | STRING | no,yes,unknown | False | https://hpo.jax.org/app/browse/term/HP:0001510 | Clinical | |
| perianal_involvement | perianal involvment | STRING | no,yes,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C99148 | Clinical | |
| extraintestinal_manifestations | history of extra intestinal manifestations | STRING | no,yes,unknown | False | Clinical | ||
| gi_surgeries | GI surguries | STRING | no,yes,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C15330 | Clinical | |
| ibd_history | family history of ibd | STRING | no,yes,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C3138 | Clinical | |
| consanguinity | history of consagunity | STRING | no,yes,unknown | False | https://thesaurus.cancer.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C189764 | Clinical | |
| race | race | STRING | white,black,asian,native_american,pacific_islander,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C17049 | Clinical | |
| ethnicity | ethnicity | STRING | hispanic,not_hispanic,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C16564 | Clinical | |
| jewish_origin | jewish ancestry | STRING | no,yes,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C86561 | Clinical | |
| breastfed | history of breast feeding | STRING | no,yes,unknown | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&ns=ncit&code=C25596 | Clinical | |
| site | site identifier (BCH = Boston, LMU = Munich, HSC = Toronto) | STRING | BCH,LMU,HSC | True | Sage Bionetworks | Clinical | |
| external_share | Per ICF, data can be shared externally with scientific research community | STRING | no,yes,unknown | False | 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 | ||
| family_id | family identifier | STRING | True | Sage Bionetworks | Clinical | ||
| age_at_diagnosis | age at diagnosis in years | NUM | False | https://ncithesaurus.nci.nih.gov/ncitbrowser/pages/concept_details.jsf?dictionary=NCI_Thesaurus&version=22.07d&code=C156420&ns=ncit | Clinical | ||
| 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 | ||
| Component | Category of metadata; provide the same one for all items/rows. | True | https://w3id.org/biolink/vocab/category |