The Budding Masters of Text-Mining and OMICS Tools
Photo: © Mye-InfoBank
The participants of this excellent training school have learnt the basics of several bioinformatic tools for text mining, analysis and visualization. The main tools that were presented were:
- UniReD1, a text mining tool that creates clusters of proteins with a potential functional association based on high quality and manually annotated proteins from UniProtKB/Swiss-Prot.
- BioTextQuest2, which combines the discovery of significant terms in article clusters with knowledge annotation offering interactive user-friendly visualization. The platform generates tag-cloud-based illustrations of terms semantically annotated according to biological entities. The users can simultaneously compare terms and documents of each cluster, thus facilitating the association of concepts and the generation of hypotheses.
- FLAME3, a web tool that uses interactive UpSet plots for the functional and literature enrichment analysis of multiple lists. This platform can analyze genes/proteins for related articles, gene ontologies, pathways, annotations, regulatory motifs, domains, diseases, and phenotypes, and can also generate protein-protein interactions derived from the platform STRING.
- Arena3Dweb, an interactive visualization tool with a multilayer approach. It can integrate information from other platforms, such as STRING and Cytoscape, and allows the visualization of multi-layered graphs in 3D space.
- Theodosiou T et al. UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. NAR Genom Bioinform. 2020. doi: 10.1093/nargab/lqaa005.
- Papanikolaou N et al. BioTextQuest+: A knowledge integration platform for literature mining and concept discovery. Bioinformatics, 2014. doi: 10.1093/bioinformatics/btu524.
- Thanati F et al. Biology (Basel). 2021. doi: 10.3390/biology10070665.
Hosts: Concepción Marañón Lizana and Jordi Muntane Relat
Trainers: Ioannis Iliopoulos, Georgios Pavlopoulos, Theodosios Theodosiou, Ismini Baltsavia and Costas Bouyioukos
Location: Centro Pfizer – Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), P. T. Ciencias de la Salud, Avda. de la Ilustración 114, 18016 Granada, Spain