ArticleBMC systems biology2018
BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources.
Article in BMC systems biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Graph databases in systems biology: a systematic review.Briefings in bioinformatics · 2024Pooled it
- Unlocking biological insights from differentially expressed genes: Concepts, methods, and future perspectives.Journal of advanced research · 2025Review
- ARAX: a graph-based modular reasoning tool for translational biomedicine.Bioinformatics (Oxford, England) · 2023Article
- Graph4Med: a web application and a graph database for visualizing and analyzing medical databases.BMC bioinformatics · 2022Article
- FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank.Database : the journal of biological databases and curation · 2022Article
- Ten simple rules for researchers who want to develop web apps.PLoS computational biology · 2022Article
- CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations.Nucleic acids research · 2021Article
- KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species.Plant biotechnology journal · 2021Article
- An overview of graph databases and their applications in the biomedical domain.Database : the journal of biological databases and curation · 2021Article
- Advantages of using graph databases to explore chromatin conformation capture experiments.BMC bioinformatics · 2021Article
- Exploring Integrative Analysis Using the BioMedical Evidence Graph.JCO clinical cancer informatics · 2020Article
- Structured reviews for data and knowledge-driven research.Database : the journal of biological databases and curation · 2020Article
- GREG-studying transcriptional regulation using integrative graph databases.Database : the journal of biological databases and curation · 2020Article
- 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.International journal of molecular sciences · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSeveral online databases provide a large amount of biomedical data of different biological entities. These resources are typically stored in systems implementing their own data model, user interface and query language. On the other hand, in many bioinformatics scenarios there is often the need to use more than one resource. The availability of a single bioinformatics platform that integrates many biological resources and services is, for those reasons a fundamental issue. DESCRIPTION: Here, we present BioGraph, a web application that allows to query, visualize and analyze biological data belonging to several online available sources. BioGraph is built upon our previously developed graph database called BioGraphDB, that integrates and stores heterogeneous biological resources and make them available by means of a common structure and a unique query language. BioGraph implements state-of-the-art technologies and provides pre-compiled bioinformatics scenarios, as well as the possibility to perform custom queries and obtaining an interactive and dynamic visualization of results.
conclusionWe present a case study about functional analysis of microRNA in breast cancer in order to demonstrate the functionalities of the system. BioGraph is freely available at http://biograph.pa.icar.cnr.it . Source files are available on GitHub at https://github.com/IcarPA-TBlab/BioGraph.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.