Adding annotations
The PhenoteFX app requires each annotation to have a citation from PubMed. Therefore, the first thing to do is to grab the pubmed id from the article you are curating.
For this example, we will use data from Klopocki E, et al. (2008_) A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome. J Med Genet. 45:370-5.
The corresponding ID that PhenoteFX expects is PMID:18178630 (no space in between PMID: and the number, but PhenoteFX will automatically remove spaces when you paste the id into the dialog).
Paste the PMID into the source field, as shown above.
Now we can add the first annotation. In this case, we will add the mode of inheritance as
Autosomal dominant inheritance HP:0000006. Note that if
we type some letters into the HPO Term field, PhenoteFX will autocomplete the term if it can.
If you hit the enter button, the term will be chosen. Then click on the Add annotation button.
This adds the annotation to the curation file. The PMID is now stored as the default value and does not need to be changed unless you want to switch to a new citation.
We can see the clinical features to annotate in Table 1 of
PMID:18178630. For instance, 11 of 12 affected
individuals had
Triphalangeal thumb HP:0001199.
We can enter the frequency data as follows (and click the Add annotation button to enter the annotation).
Note that in this case, the context of the article implies that if a + is not shown inthe table, the individual
did not have the feature in question. This may not always be the case and the curator should read the article to be
able to accurately curate the data.
We continue entering features in this way. The table states that five individuals had syndactly. However, the text
states that individuals in the family had cutaneous/osseous syndactyly of fingers III–V or IV/V. We do not have further
details, and we typically curate with as much detail as possible given the data in the original publication. To search
for a more detailed syndactyly term, we can use the HPO ontology browser on the top right of PhenoteFX.
From this, we choose the term Finger syndactyly HP:0006101.
The above figure shows the appearance of PhenoteFX after we have entered several annotations. When we are finished, we can use the Save or Save and Close items in the File menu to save our work - see filemenu.