Table 2. Tools and applications using HPO.
| Tool | Reference |
|---|---|
| Phenotype-driven differential diagnosis | |
| Phenomizer | (70) |
| BOQA | (71) |
| FACE2GENE | (72) |
| Phenolyzer | (73) |
| Phenotype-driven exome/genome analysis | |
| Exomiser | (35,74) |
| PhenIX | (32) |
| Phevor | (36) |
| PhenoVar | (75) |
| eXtasy | (76) |
| OMIMExplorer | (77) |
| Phen-Gen | (78) |
| Geno2MP | (21) |
| Genomiser | (79) |
| SimReg | (50) |
| ontologySimilarity | * |
| Functional and network analysis | |
| TopGene/ToppFunn | (80) |
| WebGestalt | (81) |
| SUPERFAMILY | (82) |
| GREAT | (83) |
| Random walk on heterogeneous network | (84) |
| PANDA | (85) |
| PREDICT | (86) |
| Clinical data management and analysis | |
| Phenotips | (15) |
| Patient Archive | (2) |
| GENESIS (GEM.app) | (87) |
| Cross-species phenotype analysis | |
| PhenoDigm | (88) |
| MouseFinder | (89) |
| Monarch | (2,53) |
| PhenomeNet | (90) |
| UberPheno | (56) |
| MORPHIN | (91) |
| PhenogramViz | (92) |
| Phenotype knowledge resources and databases | |
| Orphanet | (3) |
| MalaCards | (93) |
| NIH genetic testing registry | (94) |
| OMIM | (95) |
| dcGO | (96) |
| ClinVar | (97) |
| GeneSetDB | (98) |
| MSeqDR | (99) |
| DIDA (digenic diseases database) | (100) |
| Genetic and Rare Diseases (GARD) Information Center | (101) |
| Visualization | |
| PhenoStacks | (102) |
| PhenoBlocks | (103) |
| DECIPHER (phenogram) | (63) |
| phenogrid | (2) |
| ontologyPlot | * |
*Greene, D., Richardson, S. and Turro, E. OntologyX: a suite of R packages for working with ontological data, under review.