Text mining
PhenoteFX can also help to annotate patients one at a time starting from clinical vignettes (short descriptions). In the following example, we use the description of individual 1 from
For this example, we will use data from Wieczorek D, et al. (2010) A specific mutation in the distant sonic hedgehog (SHH) cis-regulator (ZRS) causes Werner mesomelic syndrome (WMS) while complete ZRS duplications underlie Haas type polysyndactyly and preaxial polydactyly (PPD) with or without triphalangeal thumb. Hum Mutat 31:81-9
To perform text mining, click the Add to cohort button.
Now, paste the relevant text into the dialog that appears, click the Analyze button.
Confirm the relevant findings by adding a check mark (or drag and drop to the exluded findings list below). Here, we
have also used the browser to add the term Tonic pupil HP:0012074 <https://hpo.jax.org/app/browse/term/HP:0012074>_,
which the text mining algorithm did not pick up.
Finally, click on Add selected terms to get the final list of terms for the current individual.
When you are satisfied with the terms, click on the Confirm & close button.
One or multiple individuals
Text mining can be used for one patient or for a cohort of patients. If you use it for a cohort of
patients, then click on the Add to cohort button for each patient until you are done.
Finalizing text mining
To transfer the text mined results to the main PhenoteFX application, click on the Finish button.
Adjusting results
To add more information or edit a line, you can right click on many of the fields (Onset, Frequency, Sex, Pub, Evidence). For instance, here we have right-clicked on a frequency and could change the frequency.
