Workshop details

The vast amount of scientific literature available in the publication databases poses as a new challenge for researchers. In order to keep up with the new published contents, and also the extraction of knowledge from them, a new technology has emerged: Text-mining. In this workshop, we will present the main aspects of text-mining applied to the reconstruction of biological interactions, from the identification of scientific literature sources towards the curated reconstructions of co-occurrence analysis using ad hoc software.

Learning objectives

• Familiarize with the common text-mining tools applied to biological information extraction.

• Understand how text preprocessing can facilitate knowledge extraction using text-mining;

• Discover some applications of text-mining in Biology;

• Explore the MeSH database and how perform a PubMed search using MeSH terms;

• Learn how to rank the scientific literature according to a user-selected topic;

• Create a co-occurrence network using the software PESCADOR.

Syllabus

• Introduction to text-mining analysis;

• Major techniques applied to text-mining;

• Text-mining challenges applications;

• Biology user perspective text-mining applications;

• Text preprocessing approaches;

• Text-mining based protein-protein interactions;

• Mutation extraction from literature;

• Translational research applications of text-mining;

• Literature ranking;

• The MeSH database;

• MeSH-oriented PubMed searches;

• MedLine Ranker;

• Co-occurrence analysis: PESCADOR

Format

• Zoom live webinar: 1h live webinar with pre-recorded presentation split in two sessions of 30min each with a break of 5min between them. Attendees are welcome to join asynchronous live group discussion (Q&A) with the speaker on Discord during and after the scheduled session.

• General discussion session: 1h Q&A recurrent pre-dated session booked for attendees of multiple slots of this workshop.

• Recorded presentation: Attendees registering using a Google e-mail account, will have private access to the recorded webinars.

• Certificate: all attendees checking-in and out of both 30min sessions will be entitled to receive a certificate of participation (PDF/PNG) that can be shared on your social media with credentials (QR-code) that can be verified on our website, with an option (extra fee) to register as a NFT asset with an unique address on the Ethereum blockchain.