What is a Good HPO Term?
New term requests
The simplest way to contribute to the HPO is to make a new term request on our issue tracker on Github. The following text is intended to serve as a guide for anyone who would like to contribute to the HPO project by making new term requests.
Does the term you are looking for already exist?
First, please look at the current HPO and check whether the term is already there. Use the browser on this website.
Is the term you are looking for a synonym of an existing term?
If you do not immediately find the term you are looking for, please look for synonyms. One way of doing this is to go to a likely parent of the term and peruse all of the children to spot a likely synonym. For instance, if you are looking for a term entitled Defect in the atrial septum and do not find it, go to the term Abnormal cardiac atrium morphology (HP:0005120). and look through all of the children. With some luck you will find the term Atrial septal defect (HP:0001631) and recognize that Defect in the atrial septum is listed as a synonym of Atrial septal defect (HP:0001631).
Bundled terms
If you find a description in a publication such as "Sparse eyebrows and eyelashes", note that the description is referring to two separate phenotypic features. The HPO would encode this using two different terms, Sparse eyebrow (HP:0045075) and Sparse eyelashes (HP:0000653). The idea is that one HPO term should refer to an atomic phenotypic abnormality rather than to a collection of abnormalities observed in an individual patient. Please debundle the description and proceed as described above. This is a central tenet of Deep phenotyping.
Anatomy of a good term suggestion
A good term request provides the information shown in Table 1. Please use our GitHub issue tracker, choosing the “New Term” template.
| Item | Example |
|---|---|
| Disease ID | OMIM:265380 |
| Disease Name | Alveolar capillary dysplasia with misalignment of pulmonary veins |
| HPO ID | HP:0001734 |
| HPO Term Name | Annular pancreas |
| Frequency | 2/14 |
| Onset | Congenital onset (use terms from the HPO Onset hierarchy) |
| PMID | PMID:19500772 |
| Comment | Any other information or context |
How to suggest new disease annotations
We welcome suggestions for novel disease annotations (HPOAs) to add to HPO. These can be made by submitting a ticket to the HPO tracker with the information shown in Table 2. Please use our GitHub issue tracker, choosing the “New Annotation” template.
| Item | Example |
|---|---|
| Disease ID | OMIM:265380 |
| Disease Name | Alveolar capillary dysplasia with misalignment of pulmonary veins |
| HPO ID | HP:0001734 |
| HPO Term Name | Annular pancreas |
| Frequency | 2/14 |
| Onset | Congenital onset (use terms from the HPO Onset hierarchy) |
| PMID | PMID:19500772 |
| Comment | Any other information or context |