BioTAGME: A comprehensive platform for biological knowledge network analysis

This Network was built through BioTAGME, a system that combines TAGME, an entity-annotation framework based on Wikipedia corpus with a network-based inference methodology (i.e., DT-Hybrid). BioTAGME exploits several Biological Ontologies as "ground truth" of significant bio-entities, such as DisGeNET, DrugBank, STRING and many more. We Deployed BioTAGME on PubMed, where the aim was on extracting biological entities and their relations from titles and abstracts. Biological entities are the nodes of our graph, while edges are the relations between them. Edges are of three categories: Literature edges: interactions derived from publications. STRING: protein-protein associations stored in the STRING database. BioTAGME: interactions predicted by our tool.

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Personal Data Attributes

Description: Personal Data related Information

Field Value
Anonymised No
ChildrenData No
Cross Border Authorised Yes
Data Protection Impact Assessment No
Ethics Committee Approval No
General Data Yes
Informed Consent Template No
Non Personal Data Explanation This Network was built through BioTAGME, a system that combines TAGME, an entity-annotation framework based on Wikipedia corpus with a network-based inference methodology (i.e., DT-Hybrid).BioTAGME exploits several Biological Ontologies as "ground truth" of significant bio-entities, such as DisGeNET, DrugBank, STRING and many more. We Deployed BioTAGME on PubMed, where the aim was on extracting biological entities and their relations from titles and abstracts.Biological entities are the nodes of our graph, while edges are the relations between them.Edges are of three categories:Literature edges: interactions derived from publications.STRING: protein-protein associations stored in the STRING database.BioTAGME: interactions predicted by our tool.
Personal Data No
Personal data was manifestly made public by the data subject No
Sensitive Data No
Additional Info
Field Value
Accessibility Both
Accessibility Mode Download
Availability On-Line
Basic rights Download
Creation Date 2022-03-03
Creator Ferragina, Paolo, paolo.ferragina@unipi.it, orcid.org/0000-0003-1353-360X
Dataset Citation Antonio Di Maria, Salvatore Alaimo, Lorenzo Bellomo, Fabrizio Billeci, Paolo Ferragina, Alfredo Ferro, & Alfredo Pulvirenti. (2022). BioTAGME: A comprehensive platform for biological knowledge network analysis (1.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6325345
Dataset Re-Use Safeguards None
Field/Scope of use Any use
Group Network Medicine
Language eng, English
License term 2022-03-03 /2024-01-01
Manifestation Type Original
Processing Degree Primary
Retention Period 2022-03-03 /2024-01-01
Sublicense rights No
Territory of use World Wide
Thematic Cluster Social Network Analysis [SNA]
Thematic Cluster Text and Social Media Mining [TSMM]
system:type Dataset
Management Info
Field Value
Author Pellungrini Roberto
Maintainer Pellungrini Roberto
Version 1
Last Updated 19 March 2022, 09:51 (CET)
Created 18 March 2022, 11:34 (CET)