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The HPO Browser has a separate page for every term in the HPO. The following page, for instance, is for the root term: http://www.human-phenotype-ontology.org/hpoweb?id=HP:0000118.
PhenExplorer: The PhenExplorer has been superceded by the new HPO browser, which has all the functionalities of PhenExplorer and has additional features such as Excel-Exports
The Phenomizer is available at http://compbio.charite.de/phenomizer.
It is a web-based application for clinical diagnostics in human genetics using semantic similarity searches in ontologies Köhler et al., AJHG, October 2009. The Manual for the Phenomizer can be found here. Note, that since the initial publication The Phenomizer has been update to the latest HPO ontology and annotation data. Of course, we also updated the p-values, meaning that the example from the publication (Table 1) is not exactly reproducible anymore. Sorry, for any inconvenience.
You may also try a new beta-prototype (Orphamizer) using a different algorithm and a different set of diseases and phenotype-associations. (See http://compbio.charite.de/phenomizer_orphanet)
Please have a look at PhenIX and Exomiser.
PhenogramViz helps to visually explore gene-to-phenotype relations in CNVs. It also prioritzes pathogenic CNVs.