Repository logo

Linking common human diseases to their phenotypes; development of a resource for human phenomics.

Accepted version



Change log


Kafkas, Şenay 
Althubaiti, Sara 
Gkoutos, Georgios V 
Schofield, Paul N 


BACKGROUND: In recent years a large volume of clinical genomics data has become available due to rapid advances in sequencing technologies. Efficient exploitation of this genomics data requires linkage to patient phenotype profiles. Current resources providing disease-phenotype associations are not comprehensive, and they often do not have broad coverage of the disease terminologies, particularly ICD-10, which is still the primary terminology used in clinical settings. METHODS: We developed two approaches to gather disease-phenotype associations. First, we used a text mining method that utilizes semantic relations in phenotype ontologies, and applies statistical methods to extract associations between diseases in ICD-10 and phenotype ontology classes from the literature. Second, we developed a semi-automatic way to collect ICD-10-phenotype associations from existing resources containing known relationships. RESULTS: We generated four datasets. Two of them are independent datasets linking diseases to their phenotypes based on text mining and semi-automatic strategies. The remaining two datasets are generated from these datasets and cover a subset of ICD-10 classes of common diseases contained in UK Biobank. We extensively validated our text mined and semi-automatically curated datasets by: comparing them against an expert-curated validation dataset containing disease-phenotype associations, measuring their similarity to disease-phenotype associations found in public databases, and assessing how well they could be used to recover gene-disease associations using phenotype similarity. CONCLUSION: We find that our text mining method can produce phenotype annotations of diseases that are correct but often too general to have significant information content, or too specific to accurately reflect the typical manifestations of the sporadic disease. On the other hand, the datasets generated from integrating multiple knowledgebases are more complete (i.e., cover more of the required phenotype annotations for a given disease). We make all data freely available at .



Disease–phenotype associations, Ontologies, Text mining, UK Biobank, Data Mining, Databases, Factual, Humans, Knowledge Bases, Phenomics, Phenotype

Journal Title

J Biomed Semantics

Conference Name

Journal ISSN


Volume Title



Springer Science and Business Media LLC


All rights reserved
King Abdullah University of Science and Technology (KAUST) (OSR-2018-CRG7-3790)
King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) The Alan Turing Institute