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PathoPhenoDB

PathoPhenoDB is a biological database. The database connects pathogens to their phenotypes using multiple databases such as NCBI, Human Disease Ontology Human Phenotype Ontology, Mammalian Phenotype Ontology, PubChem, SIDER and CARD. Pathogen-disease associations were gathered mainly through the CDC and the List of Infectious Diseases page on Wikipedia. The manner by which they assigned taxonomy was semi-automatic. When mapped against NCBI Taxonomy, if the pathogen was not an exact match, it was then mapped to the parent class. PathoPhenoDB employs NPMI in order to filter pairs based on their co-occurrence statistics.

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Jun 5, 2026
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PathoPhenoDB is a biological database.1 The database connects pathogens to their phenotypes using multiple databases such as NCBI, Human Disease Ontology2 Human Phenotype Ontology,3 Mammalian Phenotype Ontology,4 PubChem, SIDER5 and CARD.6 Pathogen-disease associations were gathered mainly through the CDC and the List of Infectious Diseases page on Wikipedia. The manner by which they assigned taxonomy was semi-automatic. When mapped against NCBI Taxonomy, if the pathogen was not an exact match, it was then mapped to the parent class. PathoPhenoDB employs NPMI7 in order to filter pairs based on their co-occurrence statistics.

See also

See also

References

References

  1. Kafkas, Şenay; Abdelhakim, Marwa; Hashish, Yasmeen; Kulmanov, Maxat; Abdellatif, Marwa; Schofield, Paul N.; Hoehndorf, Robert (2019-06-03). "PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research". Scientific Data. 6 (1): 79. Bibcode:2019NatSD...6...79K. doi:10.1038/s41597-019-0090-x. ISSN 2052-4463. PMC 6546783. PMID 31160594.
  2. Schriml, Lynn M.; Parkinson, Helen; Vasant, Drashtti; Malone, James; Binder, Janos X.; Mungall, Christopher J.; Fu, Gang; Bolton, Evan; Mitraka, Elvira (2015-01-28). "Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data". Nucleic Acids Research. 43 (D1): D1071–D1078. doi:10.1093/nar/gku1011. ISSN 0305-1048. PMC 4383880. PMID 25348409.
  3. Robinson, Peter N.; Köhler, Sebastian; Bauer, Sebastian; Seelow, Dominik; Horn, Denise; Mundlos, Stefan (2008-11-17). "The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease". The American Journal of Human Genetics. 83 (5): 610–615. doi:10.1016/j.ajhg.2008.09.017. ISSN 0002-9297. PMC 2668030. PMID 18950739.
  4. Richardson, Joel E.; Kadin, James A.; Bult, Carol J.; Blake, Judith A.; Eppig, Janan T. (2015-01-28). "The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease". Nucleic Acids Research. 43 (D1): D726–D736. doi:10.1093/nar/gku967. ISSN 0305-1048. PMC 4384027. PMID 25348401.
  5. Bork, Peer; Jensen, Lars Juhl; Letunic, Ivica; Kuhn, Michael (2016-01-04). "The SIDER database of drugs and side effects". Nucleic Acids Research. 44 (D1): D1075–D1079. doi:10.1093/nar/gkv1075. ISSN 0305-1048. PMC 4702794. PMID 26481350.
  6. McArthur, Andrew G.; Wright, Gerard D.; Brinkman, Fiona S. L.; Johnson, Timothy A.; Pawlowski, Andrew C.; Westman, Erin L.; Sardar, Daim; Elsayegh, Tariq; Frye, Jonathan G. (2017-01-04). "CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database". Nucleic Acids Research. 45 (D1): D566–D573. doi:10.1093/nar/gkw1004. ISSN 0305-1048. PMC 5210516. PMID 27789705.
  7. Church, Kenneth Ward; Hanks, Patrick (March 1990). "Word Association Norms, Mutual Information, and Lexicography". Comput. Linguist. 16 (1): 22–29. ISSN 0891-2017.