ArticleDatabase : the journal of biological databases and curation2012
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.
Article in Database : the journal of biological databases and curation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed.
- Integrating graph convolutional networks with large language models for structured biomedical material knowledge representation.Regenerative biomaterials · 2025Article
- Classifying domain-specific text documents containing ambiguous keywords.Database : the journal of biological databases and curation · 2021Article
- A behind-the-scenes tour of the IEDB curation process: an optimized process empirically integrating automation and human curation efforts.Immunology · 2020Article
- Identification of most influential co-occurring gene suites for gastrointestinal cancer using biomedical literature mining and graph-based influence maximization.BMC medical informatics and decision making · 2020Article
- BioConceptVec: Creating and evaluating literature-based biomedical concept embeddings on a large scale.PLoS computational biology · 2020Article
- PubTator central: automated concept annotation for biomedical full text articles.Nucleic acids research · 2019Article
- LitSense: making sense of biomedical literature at sentence level.Nucleic acids research · 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
- An effective biomedical document classification scheme in support of biocuration: addressing class imbalance.Database : the journal of biological databases and curation · 2019Article
- Constructing a database for the relations between CNV and human genetic diseases via systematic text mining.BMC bioinformatics · 2018Article
- Annotation and detection of drug effects in text for pharmacovigilance.Journal of cheminformatics · 2018Article
- Scaling up data curation using deep learning: An application to literature triage in genomic variation resources.PLoS computational biology · 2018Article
- Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.BMC bioinformatics · 2018Article
- Assisting document triage for human kinome curation via machine learning.Database : the journal of biological databases and curation · 2018Article
- BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics.Database : the journal of biological databases and curation · 2018Article
- Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.Journal of integrative bioinformatics · 2017Review
- MeSH Now: automatic MeSH indexing at PubMed scale via learning to rank.Journal of biomedical semantics · 2017Article
- DIGNiFI: Discovering causative genes for orphan diseases using protein-protein interaction networks.BMC systems biology · 2017Article
- The Immune Epitope Database: How Data Are Entered and Retrieved.Journal of immunology 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
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Manual curation of data from the biomedical literature is a rate-limiting factor for many expert curated databases. Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature curation systems such as those used by the expert curated databases. To close this gap and better understand all aspects of literature curation, we invited submissions of written descriptions of curation workflows from expert curated databases for the BioCreative 2012 Workshop Track II. We received seven qualified contributions, primarily from model organism databases. Based on these descriptions, we identified commonalities and differences across the workflows, the common ontologies and controlled vocabularies used and the current and desired uses of text mining for biocuration. Compared to a survey done in 2009, our 2012 results show that many more databases are now using text mining in parts of their curation workflows. In addition, the workshop participants identified text-mining aids for finding gene names and symbols (gene indexing), prioritization of documents for curation (document triage) and ontology concept assignment as those most desired by the biocurators. DATABASE URL: http://www.biocreative.org/tasks/bc-workshop-2012/workflow/.
Indexed as
Identifiers
What OpenQuestion holds
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.