Biomedical Text Mining and Ontologies

Tagger: BeCalm API for rapid named entity recognition

The paper implements a BeCalm API for efficient and stable named entity recognition in biomedical text, supporting multiple document sources and handling large volumes of abstracts quickly.

EXTRACT 2.0: text-mining-assisted interactive annotation of biomedical named entities and ontology terms

The paper describes an updated text-mining tool, EXTRACT 2.0, designed to assist in the interactive annotation of biomedical named entities and ontology terms, improving usability and curation efficiency.

WikiGenomes: an open Web application for community consumption and curation of gene annotation data in Wikidata.

WikiGenomes provides a web platform for community curation of gene annotations in Wikidata, addressing the lack of resources for comprehensive genomic data curation.

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

The paper assesses the sustainability of expert curation in UniProtKB/Swiss-Prot by analyzing literature triage and curatorial workload.

Measuring the importance of annotation granularity to the detection of semantic similarity between phenotype profiles

This study evaluates how varying levels of annotation granularity affect semantic similarity metrics in phenotype profiles, finding that coarse annotations may suffice for detecting significant similarity.

Binary Relation Extraction from Biomedical Literature using Dependency Trees and SVMs

This paper presents a binary relation extraction system using dependency tree features and SVMs, showing improved performance over co-occurrence and rule-based methods.

Semi-Automated Identification of Ontological Labels in the Biomedical Literature with goldi

The paper introduces goldi, an R package for identifying ontological terms in text, using word matching and an acceptance function.