NLP-based classification of software tools for metagenomics sequencing data analysis into EDAM semantic annotation

TL;DR

This paper presents a machine learning-based system to classify metagenomics software tools into semantic categories, aiding researchers in selecting appropriate tools for data analysis pipelines.

Contribution

It introduces a novel classification approach using NLP and machine learning to categorize metagenomics tools into EDAM semantic annotations, improving pipeline construction.

Findings

Achieved an AUPRC of 0.85 with Logistic Regression and BioBERT.

Used 224 curated tools with text from abstracts and methods.

Identified optimal features and models for accurate classification.

Abstract

Motivation: The rapid growth of metagenomics sequencing data makes metagenomics increasingly dependent on computational and statistical methods for fast and efficient analysis. Consequently, novel analysis tools for big-data metagenomics are constantly emerging. One of the biggest challenges for researchers occurs in the analysis planning stage: selecting the most suitable metagenomics software tool to gain valuable insights from sequencing data. The building process of data analysis pipelines is often laborious and time-consuming since it requires a deep and critical understanding of how to apply a particular tool to complete a specified metagenomics task. Results: We have addressed this challenge by using machine learning methods to develop a classification system of metagenomics software tools into 13 classes (11 semantic annotations of EDAM and two virus-specific classes) based on the descriptions of the tools. We trained three classifiers (Naive Bayes, Logistic Regression, and Random Forest) using 15 text feature extraction techniques (TF-IDF, GloVe, BERT-based models, and others). The manually curated dataset includes 224 software tools and contains text from the abstract and the methods section of the tools' publications. The best classification performance, with an Area Under the Precision-Recall Curve score of 0.85, is achieved using Logistic regression, BioBERT for text embedding, and text from abstracts only. The proposed system provides accurate and unified identification of metagenomics data analysis tools and tasks, which is a crucial step in the construction of metagenomics data analysis pipelines.