ArticleDatabase : the journal of biological databases and curation2016
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Article in Database : the journal of biological databases and curation, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed.
- Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity.Database : the journal of biological databases and curation · 2025Article
- Proteostasis networks in aging: novel insights from text-mining approaches.Biogerontology · 2023Article
- Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach.BMC genomics · 2020Article
- TeamTat: a collaborative text annotation tool.Nucleic acids research · 2020Article
- Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm.Journal of cheminformatics · 2019Article
- Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine.Database : the journal of biological databases and curation · 2019Article
- Annotation and detection of drug effects in text for pharmacovigilance.Journal of cheminformatics · 2018Article
- Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.BMC bioinformatics · 2018Article
- Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach.Database : the journal of biological databases and curation · 2018Article
- SPRENO: a BioC module for identifying organism terms in figure captions.Database : the journal of biological databases and curation · 2018Article
- The BioGRID interaction database: 2017 update.Nucleic acids research · 2017Article
- The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.Database : the journal of biological databases and curation · 2017Article
- Text mining and expert curation to develop a database on psychiatric diseases and their genes.Database : the journal of biological databases and curation · 2017Article
- A rule-based named-entity recognition method for knowledge extraction of evidence-based dietary recommendations.PloS one · 2017Article
- Automatic query generation using word embeddings for retrieving passages describing experimental methods.Database : the journal of biological databases and curation · 2017Article
- BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.Database : the journal of biological databases and curation · 2016Article
- Overview of the interactive task in BioCreative V.Database : the journal of biological databases and curation · 2016Article
- PIPE: a protein-protein interaction passage extraction module for BioCreative challenge.Database : the journal of biological databases and curation · 2016Article
- BioC viewer: a web-based tool for displaying and merging annotations in BioC.Database : the journal of biological databases and curation · 2016Article
Corrections and comments
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Authors and funding
35 authors.
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Abstract
BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant system for BioGRID curation. In this paper, we describe the framework of the collaborative BioC task and discuss our findings based on the user survey. This track consisted of eight subtasks including gene/protein/organism named entity recognition, protein-protein/genetic interaction passage identification and annotation visualization. Using BioC as their data-sharing and communication medium, nine teams, world-wide, participated and contributed either new methods or improvements of existing tools to address different subtasks of the BioC track. Results from different teams were shared in BioC and made available to other teams as they addressed different subtasks of the track. In the end, all submitted runs were merged using a machine learning classifier to produce an optimized output. The biocurator assistant system was evaluated by four BioGRID curators in terms of practical usability. The curators' feedback was overall positive and highlighted the user-friendly design and the convenient gene/protein curation tool based on text mining.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-1-bioc/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.