RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

EC Wood, AK Glen, LG Kvarfordt, F Womack… - BMC …, 2022 - Springer
Background Biomedical translational science is increasingly using computational reasoning
on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome …

BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources

A Messina, A Fiannaca, L La Paglia, M La Rosa… - BMC systems …, 2018 - Springer
Background Several online databases provide a large amount of biomedical data of different
biological entities. These resources are typically stored in systems implementing their own …

GeCoAgent: a conversational agent for empowering genomic data extraction and analysis

P Crovari, S Pidò, P Pinoli, A Bernasconi… - ACM Transactions on …, 2021 - dl.acm.org
With the availability of reliable and low-cost DNA sequencing, human genomics is relevant
to a growing number of end-users, including biologists and clinicians. Typical interactions …

BioGrakn: a knowledge graph-based semantic database for biomedical sciences

A Messina, H Pribadi, J Stichbury, M Bucci… - Complex, Intelligent, and …, 2018 - Springer
The proliferation of biological research data generated and shared openly online is of huge
benefit to the scientific community, but there are often significant challenges to overcome …

Arena-Idb: a platform to build human non-coding RNA interaction networks

V Bonnici, GD Caro, G Constantino, S Liuni, D D'Elia… - BMC …, 2018 - Springer
Background High throughput technologies have provided the scientific community an
unprecedented opportunity for large-scale analysis of genomes. Non-coding RNAs …

Biographbot: a conversational assistant for bioinformatics graph databases

A Messina, A Augello, G Pilato, R Rizzo - Innovative Mobile and Internet …, 2018 - Springer
Chatbots technology allows to easily add a conversational interface to a large set of
applications. In this paper, we show a conversational agent based on ALICE framework …

Integrated DB for bioinformatics: a case study on analysis of functional effect of MiRNA SNPs in cancer

A Fiannaca, L La Paglia, M La Rosa, A Messina… - … Technology in Bio-and …, 2016 - Springer
The era of “big data” arose the need to have computational tools in support of biological
tasks. Many types of bioinformatics tools have been developed for different biological tasks …

A performance evaluation of NoSQL databases to manage proteomics data

C Messaoudi, R Fissoune… - International Journal of …, 2018 - inderscienceonline.com
NoSQL databases have recently been introduced as alternatives to traditional relational
database management systems because of their capabilities in terms of storing data and …

Construction and visualization of dynamic biological networks: benchmarking the Neo4j graph database

L Wiese, C Wangmo, L Steuernagel, AO Schmitt… - Data Integration in the …, 2019 - Springer
Genome analysis is a major precondition for future advances in the life sciences. The
complex organization of genome data and the interactions between genomic components …

A terpenoid metabolic network modelled as graph database

WMCD Silva, DJ Vilar, DDS Souza… - … Journal of Data …, 2017 - inderscienceonline.com
Terpenoids are involved in interactions such as signalling for communication intra/inter
species, signalling molecules to attract pollinating insects, and defence against herbivores …