Name |
Description |
Publication |
EDAM-annotated ontologies |
A manually curated list of all ontologies in AberOWL annotated by topic, species and NCBI taxonomy |
Rodríguez-García MÁ, Slater L, Boudellioua I, Schofield P, Gkoutos G, Hoehndorf R (2016)Updates to the AberOWL ontology repository (ICBO BioCreative 2016)
|
PhenomeNet Similarity Matrix (Human) |
A matrix of PhenomeNet similarity scores between genes and OMIM IDs using human phenotypes only |
Boudellioua I, Razali RBM, Kulmanov M, Hashush Y, Bajic V, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R (2017) Semantic prioritization of novel causative genomic variants. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1005500
Hoehndorf R, Schofield PN, Gkoutos GV (2011) PhenomeNET: a whole-phenome approach to disease gene discovery. Nuclein Acids Research, https://doi.org/10.1093/nar/gkr538 |
PhenomeNet Similarity Matrix (Mouse) |
A matrix of PhenomeNet similarity scores between genes and OMIM IDs using mouse phenotypes only |
Boudellioua I, Razali RBM, Kulmanov M, Hashush Y, Bajic V, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R (2017) Semantic prioritization of novel causative genomic variants. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1005500
Hoehndorf R, Schofield PN, Gkoutos GV (2011) PhenomeNET: a whole-phenome approach to disease gene discovery. Nuclein Acids Research, https://doi.org/10.1093/nar/gkr538 |
Raw Exomes |
A set of synthetic exomes (VCF File Format) generated using ClinVar variants |
Boudellioua I, Razali RBM, Kulmanov M, Hashush Y, Bajic V, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R (2017) Semantic prioritization of novel causative genomic variants. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1005500 |
Raw Exomes (MAF) |
A set of synthetic exomes (VCF File Format) generated using ClinVar variants, filtered by MAF < 1% |
Boudellioua I, Razali RBM, Kulmanov M, Hashush Y, Bajic V, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R (2017) Semantic prioritization of novel causative genomic variants. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1005500 |
Raw Genomes |
A set of synthetic genomes (VCF File Format) generated using ClinVar variants |
Boudellioua I, Razali RBM, Kulmanov M, Hashush Y, Bajic V, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R (2017) Semantic prioritization of novel causative genomic variants. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1005500 |
Raw Genomes (MAF) |
A set of synthetic genomes (VCF File Format) generated using ClinVar variants, filtered by MAF < 1% |
Boudellioua I, Razali RBM, Kulmanov M, Hashush Y, Bajic V, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R (2017) Semantic prioritization of novel causative genomic variants. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1005500 |
RDF Knowledge Graph of proteins, drugs, diseases, functions and phenotypes |
An RDF dataset containing data on the following semantic types, gene, drug, protein function, disease |
Alshahrani M, Khan MA, Maddouri O, Kinjo AR, Queralt-Rosinach N, Hoehndorf R (2017) Neuro-symbolic representation learning on biological knowledge graphs. Bioinformatics btx275. doi:10.1093/bioinformatics/btx275 |
Knowledge Graph embeddings |
A knowledge graph embeddings containing of the RDF dataset mentioned above |
Alshahrani M, Khan MA, Maddouri O, Kinjo AR, Queralt-Rosinach N, Hoehndorf R (2017) Neuro-symbolic representation learning on biological knowledge graphs. Bioinformatics btx275. doi:10.1093/bioinformatics/btx275 |
Protein-protein interaction network embeddings for uniprot proteins |
Network embeddings generated with knowledge graph representation learning method |
Kulmanov M, Khan MA, Hoehndorf R (2017) DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinformatics, btx624, https://doi.org/10.1093/bioinformatics/btx624 |
Functions of CAFA3 targets |
Protein function predictions for CAFA3 targets by using DeepGO |
Kulmanov M, Khan MA, Hoehndorf R (2017) DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier. Bioinformatics, btx624, https://doi.org/10.1093/bioinformatics/btx624 |
SIDER2DO |
Mapping between indications in SIDER and Disease Ontology |
Hoehndorf R, Schofield PN, Gkoutos GV (2015) Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. Scientific Reports, doi: 10.1038/srep10888 |
Disease Similarity Matrix |
A disease-disease similarity matrix based on phenotype similarity, using Human Disease Ontology to represent diseases |
Hoehndorf R, Schofield PN, Gkoutos GV (2015) Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. Scientific Reports, doi: 10.1038/srep10888 |
Disease-Disease drug similarity |
A file containing pairs of diseases (using Human Disease Ontology) treated with the same drugs |
Hoehndorf R, Schofield PN, Gkoutos GV (2015) Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases. Scientific Reports, doi: 10.1038/srep10888 |