Working with PhenoteFX

PhenoteFX is designed to add HPO disease annotations to the HPO computational disease models (See for instance, the entry for Marfan syndrome). Annotations can be added one by one using the autocomplete menus or they can

Updating the evidence code for an existing entry

Occasionally, we would like to update an existing annotation. For instance, we would like to add a PubMed citation for an entry that was created by text mining. In this case, we will update the evidence code from IEA (inferred from electronic annotation) to PCS (published clinical study). To do this, right click on the table cell with the evidence code and choose the updated evidence code. You will see a popup menu with the four available evidence codes. Click the desired code to update the code in the table.

PhenoteFX - evidence menu

Updating the citation for an existing entry

The citation (reference) for an HPO annotation is kept in the Pub column. We will sometimes want to update this field. For instance, if an entry was created by text mining, we may have a citation such as “OMIM:154700”, but say we have found a PubMed entry that provides more information. Then, we would like to update the entry to PMID:123, where 123 stands for the PubMed id. For instance, the if the HPO entry for Marfan syndrome shows an annotation for Autosomal dominant inheritance that is referenced to OMIM:154700, this indicates that the assertion was derived from the Online Mendelian Inheritance in Man (OMIM) page for Marfan syndrome. The article at PubMed id PMID:17502658 provides more detail about this assertion, and so we would replace OMIM:154700 with PMID:17502658.

To do so, first right click on the publication entry for the annotation of interest. You will see a field to click on.

PhenoteFX - update publication 1

If you click on the field, a new dialog window will appear with the current publication entry. Replace or edit this entry and click on OK in order to change the publication. If you click on Cancel, the window will close and the entry will not be changed.

PhenoteFX - update publication 2

Updating the Description and Frequency fields

The description and the frequency fields can be updated in the same way as the publication field. Please note that for frequency, one of three valid formats must be used.

  1. An HPO Term ID from the Frequency subontology, e.g., HP:0040280
  2. An expression such as 4/6 (meaning that 4 out of 6 patients with the disease in question were found to have the phenotypic feature denoted by the HPO term).
  3. An expression such as 45% (meaning that 45% of patients with the disease in question were found to have the phenotypic feature denoted by the HPO term).

PhenoteFX currently does not check that the format of the frequency term is correct, but this feature will be added in the future.