v1 Data Sources
Full Documentation: Release v1.0.0
Rationale: The ontologies and data sources used in this release were initially selected because they were used in a recent knowledge graph constructed by Robert Hoehndorf's lab. We extended this work to include data from the Comparative Toxicogenomics Database to allow for the incorporation of additional chemical-entity relations.
Release: 2018; https://zenodo.org/record/2529950 ontology download
Citations:
Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. May 2000;25(1):25-9. [abstract|full text]
The Gene Ontology Consortium. The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. Jan 2019;47(D1):D330-D338. [abstract|full text]
Release: 2018 ontology download
Citation:
Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, et al. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Research. (2018) doi: 10.1093/nar/gky1105
Annotation Files:
- Disease-Phenotype relations:
ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt - Gene-Phenotype relations:
ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt
Release: 2018 ontology download
Citation:
Schriml, L. M., Mitraka, E., Munro, J., Tauber, B., Schor, M., Nickle, L., Felix, V., Jeng, L., Bearer, C., Lichenstein, R., Bisordi, K., Campion, N., Hyman, B., Kurland, D., Oates, C.P., Kibbey, S., Sreekumar, P., Le, C., Giglio, M. Greene, C. (2018). Human Disease Ontology 2018 update: classification, content and workflow expansion. Nucleic acids research, 47(D1), D955–D962. doi:10.1093/nar/gky1032 PMID:30407550
Release: 2018
Citations:
Curated [chemical–gene interactions|chemical–disease|gene–disease] data were retrieved from the Comparative Toxicogenomics Database (CTD), MDI Biological Laboratory, Salisbury Cove, Maine, and NC State University, Raleigh, North Carolina. World Wide Web (URL: http://ctdbase.org/).
Davis AP, Grondin CJ, Johnson RJ, Sciaky D, McMorran R, Wiegers J, Wiegers TC, Mattingly CJ The Comparative Toxicogenomics Database: update 2019. Nucleic Acids Res. 2018 Sep 24.
Files:
- Chemical-Gene relations:
CTD_chem_gene_ixns.tsv.gz - Chemical-Pathway relations:
CTD_chem_pathways_enriched.tsv.gz - Chemical-Disease relations:
CTD_chemicals_diseases.tsv.gz - Gene-Pathway relations:
CTD_genes_pathways.tsv.gz
Release: 2018
Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M. The reactome pathway knowledgebase. Nucleic acids research. 2017 Nov 14;46(D1):D649-55.
Files:
- Pathway-GO relations:
gene_association.reactome
Release: 2018
Citation
The UniProt Consortium, UniProt: a worldwide hub of protein knowledge, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D506–D515, https://doi.org/10.1093/nar/gky1049
Release: 2018
Citation:
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 2015 Jan; 43:D447-52.PubMed.
Files:
- Gene-Gene relations:
9606.protein.links.v10.5.txt.gz - String-Entrez relations:
entrez_mappings/entrez_gene_id.vs.string.v10.28042015.tsv
This project is licensed under Apache License 2.0 - see the LICENSE.md file for details. If you intend to use any of the information on this Wiki, please provide the appropriate attribution by citing this repository:
@software{callahan_tj_2019_3830982,
author = {Callahan, TJ and
William A. Baumgartner Jr and
Ignacio J. Tripodi and
Adrianne L. Stefanski and
Jordan M. Wyrwa and
Lawrence Hunter},
title = {PheKnowLator},
month = mar,
year = 2019,
note = {{Newer version of the v1.0.0 release that includes output data generated by this code.}},
publisher = {Zenodo},
version = {v.1.0.0},
doi = {10.5281/zenodo.3830982},
url = {https://doi.org/10.5281/zenodo.3830982}
}