PathoPhenoDB

PathoPhenoDB is a biological database.{{Cite journal|last1=Kafkas|first1=Şenay|last2=Abdelhakim|first2=Marwa|last3=Hashish|first3=Yasmeen|last4=Kulmanov|first4=Maxat|last5=Abdellatif|first5=Marwa|last6=Schofield|first6=Paul N.|last7=Hoehndorf|first7=Robert|date=2019-06-03|title=PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research|journal=Scientific Data|volume=6|issue=1|pages=79|doi=10.1038/s41597-019-0090-x|issn=2052-4463|pmid=31160594|pmc=6546783|bibcode=2019NatSD...6...79K}} The database connects pathogens to their phenotypes using multiple databases such as NCBI, Human Disease Ontology{{Cite journal|last1=Schriml|first1=Lynn M.|last2=Parkinson|first2=Helen|last3=Vasant|first3=Drashtti|last4=Malone|first4=James|last5=Binder|first5=Janos X.|last6=Mungall|first6=Christopher J.|last7=Fu|first7=Gang|last8=Bolton|first8=Evan|last9=Mitraka|first9=Elvira|date=2015-01-28|title=Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data|journal=Nucleic Acids Research|volume=43|issue=D1|pages=D1071–D1078|doi=10.1093/nar/gku1011|pmid=25348409|issn=0305-1048|pmc=4383880}} Human Phenotype Ontology,{{Cite journal|last1=Robinson|first1=Peter N.|last2=Köhler|first2=Sebastian|last3=Bauer|first3=Sebastian|last4=Seelow|first4=Dominik|last5=Horn|first5=Denise|last6=Mundlos|first6=Stefan|date=2008-11-17|title=The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease|journal=The American Journal of Human Genetics|volume=83|issue=5|pages=610–615|doi=10.1016/j.ajhg.2008.09.017|pmid=18950739|issn=0002-9297|pmc=2668030}} Mammalian Phenotype Ontology,{{Cite journal|last1=Richardson|first1=Joel E.|last2=Kadin|first2=James A.|last3=Bult|first3=Carol J.|last4=Blake|first4=Judith A.|last5=Eppig|first5=Janan T.|date=2015-01-28|title=The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease|journal=Nucleic Acids Research|volume=43|issue=D1|pages=D726–D736|doi=10.1093/nar/gku967|pmid=25348401|pmc=4384027|issn=0305-1048}} PubChem, SIDER{{Cite journal|last1=Bork|first1=Peer|last2=Jensen|first2=Lars Juhl|last3=Letunic|first3=Ivica|last4=Kuhn|first4=Michael|date=2016-01-04|title=The SIDER database of drugs and side effects|journal=Nucleic Acids Research|volume=44|issue=D1|pages=D1075–D1079|doi=10.1093/nar/gkv1075|pmid=26481350|pmc=4702794|issn=0305-1048|doi-access=free}} and CARD.{{Cite journal|last1=McArthur|first1=Andrew G.|last2=Wright|first2=Gerard D.|last3=Brinkman|first3=Fiona S. L.|last4=Johnson|first4=Timothy A.|last5=Pawlowski|first5=Andrew C.|last6=Westman|first6=Erin L.|last7=Sardar|first7=Daim|last8=Elsayegh|first8=Tariq|last9=Frye|first9=Jonathan G.|date=2017-01-04|title=CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database|journal=Nucleic Acids Research|volume=45|issue=D1|pages=D566–D573|doi=10.1093/nar/gkw1004|pmid=27789705|pmc=5210516|issn=0305-1048|doi-access=free}} 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{{Cite journal|last1=Church|first1=Kenneth Ward|last2=Hanks|first2=Patrick|date=March 1990|title=Word Association Norms, Mutual Information, and Lexicography|url=http://dl.acm.org/citation.cfm?id=89086.89095|journal=Comput. Linguist.|volume=16|issue=1|pages=22–29|issn=0891-2017}} in order to filter pairs based on their co-occurrence statistics.