Evidence map›Paper›PMID 25619558›Full record

ArticleDatabase : the journal of biological databases and curation2015

OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

Weisong Liu, Stanley J F Laulederkind, G Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R Smith, Jeff De Pons, Melinda R Dwinell, Mary Shimoyama

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. The alliance of genome resources: transforming comparative genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2023
    Review
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Establishing geneJournal of genetics · 2019
    Article
  12. Text mining and expert curation to develop a database on psychiatric diseases and their genes.Database : the journal of biological databases and curation · 2017
    Article
  13. Article
  14. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Weisong LiuHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
Stanley J F LaulederkindHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA slaulederkind@mcw.edu.
G Thomas HaymanHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
Shur-Jen WangHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
Rajni NigamHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
Jennifer R SmithHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
Jeff De PonsHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
Melinda R DwinellHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.
Mary ShimoyamaHuman and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA Human and Molecular Genetics Center, Medical College of Wisconsin, Department of Quantitative Health Sciences, University of Massachusetts Medical School, Department of Physiology, Medical College of Wisconsin and Department of Surgery, Medical College of Wisconsin, 8701 Watertown Plank Rd, Milwaukee, WI 53226-3548, USA.

Funding

RAT GENOME DATABASER01HL064541 · NHLBI · MEDICAL COLLEGE OF WISCONSIN · PI ANNE E. KWITEK · 1999 to 2026
$50.0M
Integration of phenotype data from multiple centers using ontologiesR01HL094271 · NHLBI · MEDICAL COLLEGE OF WISCONSIN · PI DWINELL, MELINDA R · 2010 to 2012
$1.1M
NHLBI NIH HHS HL064541NHLBI NIH HHS HL094271NHLBI NIH HHS HL64541NHLBI NIH HHS R01 HL064541
6 · The paper itself

Abstract

The Rat Genome Database (RGD) is the premier repository of rat genomic, genetic and physiologic data. Converting data from free text in the scientific literature to a structured format is one of the main tasks of all model organism databases. RGD spends considerable effort manually curating gene, Quantitative Trait Locus (QTL) and strain information. The rapidly growing volume of biomedical literature and the active research in the biological natural language processing (bioNLP) community have given RGD the impetus to adopt text-mining tools to improve curation efficiency. Recently, RGD has initiated a project to use OntoMate, an ontology-driven, concept-based literature search engine developed at RGD, as a replacement for the PubMed (http://www.ncbi.nlm.nih.gov/pubmed) search engine in the gene curation workflow. OntoMate tags abstracts with gene names, gene mutations, organism name and most of the 16 ontologies/vocabularies used at RGD. All terms/ entities tagged to an abstract are listed with the abstract in the search results. All listed terms are linked both to data entry boxes and a term browser in the curation tool. OntoMate also provides user-activated filters for species, date and other parameters relevant to the literature search. Using the system for literature search and import has streamlined the process compared to using PubMed. The system was built with a scalable and open architecture, including features specifically designed to accelerate the RGD gene curation process. With the use of bioNLP tools, RGD has added more automation to its curation workflow. Database URL: http://rgd.mcw.edu.

Indexed as

Databases, Nucleic AcidGene OntologyGenomeNatural Language ProcessingAnimalsData MiningPubMedRats

Identifiers

PMID25619558
PMCPMC4305386

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.