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.

See also
Antimicrobial Resistance databases

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" (https://ww
w.ncbi.nlm.nih.gov/pmc/articles/PMC6546783). Scientific Data. 6 (1): 79.
Bibcode:2019NatSD...6...79K (https://ui.adsabs.harvard.edu/abs/2019NatSD...6...79K).
doi:10.1038/s41597-019-0090-x (https://doi.org/10.1038%2Fs41597-019-0090-x).
ISSN 2052-4463 (https://www.worldcat.org/issn/2052-4463). PMC 6546783 (https://www.ncb
i.nlm.nih.gov/pmc/articles/PMC6546783). PMID 31160594 (https://pubmed.ncbi.nlm.nih.gov/
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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PM
C4383880). Nucleic Acids Research. 43 (D1): D1071–D1078. doi:10.1093/nar/gku1011 (htt
ps://doi.org/10.1093%2Fnar%2Fgku1011). ISSN 0305-1048 (https://www.worldcat.org/issn/0
305-1048). PMC 4383880 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383880).
PMID 25348409 (https://pubmed.ncbi.nlm.nih.gov/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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668
030). The American Journal of Human Genetics. 83 (5): 610–615.
doi:10.1016/j.ajhg.2008.09.017 (https://doi.org/10.1016%2Fj.ajhg.2008.09.017). ISSN 0002-
9297 (https://www.worldcat.org/issn/0002-9297). PMC 2668030 (https://www.ncbi.nlm.nih.go
v/pmc/articles/PMC2668030). PMID 18950739 (https://pubmed.ncbi.nlm.nih.gov/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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384027). Nucleic
Acids Research. 43 (D1): D726–D736. doi:10.1093/nar/gku967 (https://doi.org/10.1093%2F
nar%2Fgku967). ISSN 0305-1048 (https://www.worldcat.org/issn/0305-1048).
PMC 4384027 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384027). PMID 25348401
(https://pubmed.ncbi.nlm.nih.gov/25348401).
 5. Bork, Peer; Jensen, Lars Juhl; Letunic, Ivica; Kuhn, Michael (2016-01-04). "The SIDER
database of drugs and side effects" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC470279
4). Nucleic Acids Research. 44 (D1): D1075–D1079. doi:10.1093/nar/gkv1075 (https://doi.or
g/10.1093%2Fnar%2Fgkv1075). ISSN 0305-1048 (https://www.worldcat.org/issn/0305-104
8). PMC 4702794 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702794).
PMID 26481350 (https://pubmed.ncbi.nlm.nih.gov/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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210516).
Nucleic Acids Research. 45 (D1): D566–D573. doi:10.1093/nar/gkw1004 (https://doi.org/10.
1093%2Fnar%2Fgkw1004). ISSN 0305-1048 (https://www.worldcat.org/issn/0305-1048).
PMC 5210516 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210516). PMID 27789705
(https://pubmed.ncbi.nlm.nih.gov/27789705).
7. Church, Kenneth Ward; Hanks, Patrick (March 1990). "Word Association Norms, Mutual
Information, and Lexicography" (http://dl.acm.org/citation.cfm?id=89086.89095). Comput.
Linguist. 16 (1): 22–29. ISSN 0891-2017 (https://www.worldcat.org/issn/0891-2017).

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