phenotype.hpoa

The HPO project provides a comprehensive set of computable definitions of rare diseases in the form of annotations which describe the clinical features (HPO terms) that characterize each disease. Each annotated feature can have metadata including its typical age of onset and the frequency. Ror instance, the HPO lists the frequency of Protrusio acetabuli in persons with Marfan syndrome as 113/146 based on a published clinical study (PMID:26339165).

Field	Item	Required	Example
1	Database ID	Yes	MIM:154700, ORPHA:558 or MONDO:0007947
2	DB_Name	Yes	Achondrogenesis, type IB
3	Qualifier	No	NOT or empty
4	HPO_ID	Yes	HP:0002487
5	DB_Reference	Yes	OMIM:154700 or PMID:15517394
6	Evidence	Yes	IEA or PCS
7	Onset	No	HP:0003577
8	Frequency	No	HP:0003577 or 12/45 or 22%
9	Sex	No	MALE or FEMALE
10	Modifier	No	HP:0025257
11	Aspect	Yes	‘P’ or ‘C’ or ‘I’ or ‘M’
12	BiocurationBy	Yes	HPO:skoehler[YYYY-MM-DD]

The file contains 12 tab-separated fields, some of which can be left empty. The ‘Modifier’ and ‘BiocurationBy’ fields can contain multiple items separated by semicolons. For instance, to indicate that a disease is characterized by a skin rash (HP:0000988) that is Recurrent (HP:0031796) and Triggered by cold (HP:0025206) one would annotate HP:0031796;HP:0025206 in the Modifier column. Many annotations go through multiple stages of biocuration. In this case, the individual biocuration events are also added as a semicolon-separated list.