PathoPhenoDB

PathoPhenoDB is a biological database.^[1] The database connects pathogens to their phenotypes using multiple databases such as NCBI, Human Disease Ontology^[2] Human Phenotype Ontology,^[3] Mammalian Phenotype Ontology,^[4] PubChem, SIDER^[5] 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 NPMI^[7] in order to filter pairs based on their co-occurrence statistics.

References

^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ 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.
^ Church, Kenneth Ward; Hanks, Patrick (March 1990). "Word Association Norms, Mutual Information, and Lexicography". Comput. Linguist. 16 (1): 22–29. ISSN 0891-2017.

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[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.

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See also

References