Welcome to GDDP, computational Genetic Disease Diagnosis based on Phenotypes.

It's very easy to query for OMIM diseases based on phenotypes using this application:

  1. Select "Query" from the top navigation bar
  2. Paste or enter the phenotype text
  3. Select the computational method (Method2 is selected by default)
  4. Click Submit
  5. Select "HPO terms" for recognized HPO terms and "OMIM diseases" for ranked OMIM disease list

Statistics of current disease knowledge base:

  • Number of OMIM diseases: 7036
  • Number of HPO Phenotypic Abnormality terms: 7934
  • Last update: 1/23/2017

Enter the phenotype text

Please enter phenotype

Please enter phenotype


Chen J, Xu H, Jegga A, Zhang K, White P, Zhang G. 2018. Novel phenotype-disease matching tool for rare genetic diseases. Genetics in Medicine. [PDF]

Method 1

Method 1: integrated semantic similarity

  • Evaluating similarities between all pairs of phenotype terms.
  • calculating a similarity score to summarize the similarities between all the query terms (Q) and the HPO terms annotated to a target disease D_k.

Method 2

Method 2: weighted overlapping

  • In this method, the phenotypes of a patient (query terms, Q) and HPO terms annotated to diseases (D_k) are first ‘up-induced’ based on HPO tree structure so that if a HPO term is annotated to a patient/disease, all of its ancestors are also annotated to the patient/disease. In order to compare the query terms (Q) with the terms annotated to a disease (D_k), we can construct a weighted 2x2 contingency table that contains the weighted counts of HPO terms shared or not shared between the query terms and the terms annotated to a disease. A Fisher’s exact test is then applied to this 2x2 contingency table and the p-value from the test can be used to rank the concordance/discordance between the query terms and the phenotypes of a disease.