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PathoPhenoDB: linking human pathogens to their disease phenotypes in support of infectious disease research

https://doi.org/10.1101/489971
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/wsbm.44openalex-snapshot
The mammalian phenotype ontology: enabling robust annotation and comparative analysis
inferredcites →https://doi.org/10.1007/s00335-012-9404-4openalex-snapshot
Computational tools for comparative phenomics: the role and promise of ontologies
inferredcites →https://doi.org/10.1016/bs.mim.2015.06.004openalex-snapshot
Next-Generation Sequencing for Pathogen Detection and Identification
inferredcites →https://doi.org/10.1016/j.ajhg.2008.09.017openalex-snapshot
The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease
inferredcites →https://doi.org/10.1016/j.jbiotec.2016.12.022openalex-snapshot
Application of next generation sequencing in clinical microbiology and infection prevention
inferredcites →https://doi.org/10.1016/s0140-6736(17)32152-9openalex-snapshot
Global, regional, and national age-sex specific mortality for 264 causes of death, 1980–2016: a systematic analysis for the Global Burden of Disease Study 2016
inferredcites →https://doi.org/10.1038/nprot.2017.066openalex-snapshot
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
inferredcites →https://doi.org/10.1038/sdata.2016.18openalex-snapshot
The FAIR Guiding Principles for scientific data management and stewardship
inferredcites →https://doi.org/10.1038/srep10888openalex-snapshot
Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases
inferredcites →https://doi.org/10.1056/nejmra1615014openalex-snapshot
Classification, Ontology, and Precision Medicine
inferredcites →https://doi.org/10.1093/bib/bbv011openalex-snapshot
The role of ontologies in biological and biomedical research: a functional perspective
inferredcites →https://doi.org/10.1093/bioinformatics/btt613openalex-snapshot
Mouse model phenotypes provide information about human drug targets
inferredcites →https://doi.org/10.1093/bioinformatics/bty559openalex-snapshot
Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes
inferredcites →https://doi.org/10.1093/bioinformatics/bty605openalex-snapshot
Ontology-based validation and identification of regulatory phenotypes
inferredcites →https://doi.org/10.1093/bioinformatics/bty933openalex-snapshot
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
inferredcites →https://doi.org/10.1093/cid/cit626openalex-snapshot
Better Tests, Better Care: Improved Diagnostics for Infectious Diseases
inferredcites →https://doi.org/10.1093/nar/gkn794openalex-snapshot
VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus–host interaction networks
inferredcites →https://doi.org/10.1093/nar/gkr1178openalex-snapshot
The NCBI Taxonomy database
inferredcites →https://doi.org/10.1093/nar/gkr538openalex-snapshot
PhenomeNET: a whole-phenome approach to disease gene discovery
inferredcites →https://doi.org/10.1093/nar/gku1011openalex-snapshot
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
inferredcites →https://doi.org/10.1093/nar/gku967openalex-snapshot
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease
inferredcites →https://doi.org/10.1093/nar/gkv1075openalex-snapshot
The SIDER database of drugs and side effects
inferredcites →https://doi.org/10.1093/nar/gkw1004openalex-snapshot
CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
inferredcites →https://doi.org/10.1126/scitranslmed.3010272openalex-snapshot
Phenomics and the Interpretation of Personal Genomes
inferredcites →https://doi.org/10.1186/2041-1480-5-14openalex-snapshot
The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery
inferredcites →https://doi.org/10.1186/2049-9957-3-21openalex-snapshot
Global burden, distribution, and interventions for infectious diseases of poverty
inferredcites →https://doi.org/10.1186/gb-2010-11-1-r2openalex-snapshot
Integrating phenotype ontologies across multiple species
inferredcites →https://doi.org/10.1186/s13326-016-0090-0openalex-snapshot
Using AberOWL for fast and scalable reasoning over BioPortal ontologies
inferredcites →https://doi.org/10.1186/s13326-019-0208-2openalex-snapshot
Ontology based mining of pathogen–disease associations from literature
inferredcites →https://doi.org/10.3410/f1000research.2-30.v1openalex-snapshot
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research
inferredcites →https://doi.org/10.48550/arxiv.cmp-lg/9511007openalex-snapshot
Using Information Content to Evaluate Semantic Similarity in a Taxonomy
inferredcites →https://doi.org/10.5281/zenodo.1970275openalex-snapshot
PathoPhenoDB: a database of pathogen-phenotype associations

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/bioinformatics/btab147openalex-snapshot
DeepViral: prediction of novel virus–host interactions from protein sequences and infectious disease phenotypes
inferred← citeshttps://doi.org/10.1101/2020.04.22.055095openalex-snapshot
Prediction of novel virus-host interactions by integrating clinical symptoms and protein sequences
inferred← citeshttps://doi.org/10.1101/508762openalex-snapshot
Phenotypic, functional and taxonomic features predict host-pathogen interactions
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