Ontology-Based Search of Genomic Metadata

Abstract

The Encyclopedia of DNA Elements (ENCODE) is a huge and still expanding public repository of more than 4,000 experiments and 25,000 data files, assembled by a large international consortium since 2007; unknown biological knowledge can be extracted from these huge and largely unexplored data, leading to data-driven genomic, transcriptomic, and epigenomic discoveries. Yet, search of relevant datasets for knowledge discovery is limitedly supported: metadata describing ENCODE datasets are quite simple and incomplete, and not described by a coherent underlying ontology. Here, we show how to overcome this limitation, by adopting an ENCODE metadata searching approach which uses high-quality ontological knowledge and state-of-the-art indexing technologies. Specifically, we developed S.O.S. GeM (http://www.bioinformatics.deib.polimi.it/SOSGeM/), a system supporting effective semantic search and retrieval of ENCODE datasets. First, we constructed a Semantic Knowledge Base by starting with concepts extracted from ENCODE metadata, matched to and expanded on biomedical ontologies integrated in the well-established Unified Medical Language System. We prove that this inference method is sound and complete. Then, we leveraged the Semantic Knowledge Base to semantically search ENCODE data from arbitrary biologists' queries. This allows correctly finding more datasets than those extracted by a purely syntactic search, as supported by the other available systems. We empirically show the relevance of found datasets to the biologists' queries.

GenoSurf: metadata driven semantic search system for integrated genomic datasets

“…The data management backend has been produced in the last 2 years, capitalizing on several previous years of experience in the use of bio-ontologies for specific research projects (e.g. SOS-GeM (41) and GPKB (42)). The repository currently integrates about 40 million metadata items from five sources, described by 39 attributes over eight connected tables of the core schema and enriched with terms from eight different ontologies, which have been reduced to the same knowledge schema.…”

Semantic concept schema of the linear mixed model of experimental observations

“…This information is necessary to properly construct the statistical model and interpret the obtained estimates in terms of the variable names, units, etc., and to exploit the ontological knowledge for experimental metadata-based semantic search (e.g. 44 ) to further improve the data discoverability.…”

Aplicação de Tecnologias da Web Semântica em Motores de Busca na Internet

“…A derivação de novos conhecimentos por meio do processo de inferência é um dos benefícios da representação de informações por meio de ontologias. Fernández et al (2016) utilizaram ontologias para gerar uma base de metadados semânticos a partir de metadados e registros médicos do repositório Encyclopedia of DNA elements (ENCODE). Com o intuito de complementar as informações, os autores propuseram a aplicação de técnicas de inferência sobre as informações na base semântica.…”

“…Uma das principais motivações dos autores (Fernández et al, 2016) é que, apesar de fornecer informações de alta qualidade, o suporte para busca e recuperação de informações no repositório ENCODE -baseado estritamente na sintaxe dos termos de busca -é insuficiente. Nesse contexto, os autores buscaram melhorar a recuperação nesta base por meio do uso de ontologias e da anotação semântica dos metadados da coleção no repositório ENCONDE.…”