ArticleDatabase : the journal of biological databases and curation2012
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.
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 11 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
11 citing papers in PubMed.
- Using deep learning to identify translational research in genomic medicine beyond bench to bedside.Database : the journal of biological databases and curation · 2019Article
- Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach.Database : the journal of biological databases and curation · 2018Article
- Assisting document triage for human kinome curation via machine learning.Database : the journal of biological databases and curation · 2018Article
- Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.Database : the journal of biological databases and curation · 2016Article
- Animal-Free Chemical Safety Assessment.Frontiers in pharmacology · 2016Review
- Identifying named entities from PubMed for enriching semantic categories.BMC bioinformatics · 2015Article
- Scaling drug indication curation through crowdsourcing.Database : the journal of biological databases and curation · 2015Article
- DNorm: disease name normalization with pairwise learning to rank.Bioinformatics (Oxford, England) · 2013Article
- CoIN: a network analysis for document triage.Database : the journal of biological databases and curation · 2013Article
- Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.Database : the journal of biological databases and curation · 2013Article
- Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts.Database : the journal of biological databases and curation · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.
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.