Evidence map›Paper›PMID 25070993›Full record

ArticleDatabase : the journal of biological databases and curation2014

BC4GO: a full-text corpus for the BioCreative IV GO task.

Kimberly Van Auken, Mary L Schaeffer, Peter McQuilton, Stanley J F Laulederkind, Donghui Li, Shur-Jen Wang, G Thomas Hayman, Susan Tweedie, Cecilia N Arighi, James Done and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.

0numbers the graph read from it
0cells of the map it votes in
24citing 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

24 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Review
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Automatic gene annotation using GO terms from cellular component domain.BMC medical informatics and decision making · 2018
    Article
  14. Article
  15. Article
  16. Semantic annotation in biomedicine: the current landscape.Journal of biomedical semantics · 2017
    Review
  17. Article
  18. Article
  19. Review
  20. Review
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

15 authors.

Kimberly Van AukenWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Mary L SchaefferWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Peter McQuiltonWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Stanley J F LaulederkindWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Donghui LiWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Shur-Jen WangWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
G Thomas HaymanWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Susan TweedieWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Cecilia N ArighiWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
James DoneWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Hans-Michael MüllerWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Paul W SternbergWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USAWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Yuqing MaoWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Chih-Hsuan WeiWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.
Zhiyong LuWormBase, Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, USDA-ARS Plant Genetics Research Unit and Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA, FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, Rat Genome Database, Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA, TAIR, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA, Center for Bioinformatics and Computational Biology, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA, Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA, National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA zhiyong.lu@nih.gov.

Funding

Resource ProjectU41HG002273 · NHGRI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI CHERRY, J. MICHAEL, MUNGALL, CHRISTOPHER J · 2012 to 2021
$34.7M
WormBase: a core data resource for C. elegans and other nematodesU41HG002223 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI KERSEY, PAUL, SCHEDL, TIM · 2013 to 2017
$20.5M
WormBase: a core data resource for C. elegans and other nematodesU24HG002223 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI TIM SCHEDL, PAUL Warren STERNBERG · 2018 to 2026
$18.9M
Named Entity Recognition and Relationship Extraction in BiomedicineZIALM091813 · NLM · NATIONAL LIBRARY OF MEDICINE · PI LU, ZHIYONG · 2013 to 2022
$13.4M
Textpresso: information retrieval and extraction system for biological literatureR01HG004090 · NHGRI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI MULLER, HANS-MICHAEL · 2006 to 2012
$2.1M
Biocreative Conference GrantR13GM109648 · NIGMS · UNIVERSITY OF COLORADO DENVER · PI ARIGHI, CECILIA NOEMI, COHEN, KEVIN B. · 2014 to 2016
$36k
Intramural NIH HHSMedical Research Council G1000968NHGRI NIH HHS HG002223NHGRI NIH HHS HG002273NHGRI NIH HHS HG004090NHGRI NIH HHS U24 HG002223NHGRI NIH HHS U41 HG002273NIGMS NIH HHS R13 GM109648
6 · The paper itself

Abstract

Gene function curation via Gene Ontology (GO) annotation is a common task among Model Organism Database groups. Owing to its manual nature, this task is considered one of the bottlenecks in literature curation. There have been many previous attempts at automatic identification of GO terms and supporting information from full text. However, few systems have delivered an accuracy that is comparable with humans. One recognized challenge in developing such systems is the lack of marked sentence-level evidence text that provides the basis for making GO annotations. We aim to create a corpus that includes the GO evidence text along with the three core elements of GO annotations: (i) a gene or gene product, (ii) a GO term and (iii) a GO evidence code. To ensure our results are consistent with real-life GO data, we recruited eight professional GO curators and asked them to follow their routine GO annotation protocols. Our annotators marked up more than 5000 text passages in 200 articles for 1356 distinct GO terms. For evidence sentence selection, the inter-annotator agreement (IAA) results are 9.3% (strict) and 42.7% (relaxed) in F1-measures. For GO term selection, the IAAs are 47% (strict) and 62.9% (hierarchical). Our corpus analysis further shows that abstracts contain ∼ 10% of relevant evidence sentences and 30% distinct GO terms, while the Results/Experiment section has nearly 60% relevant sentences and >70% GO terms. Further, of those evidence sentences found in abstracts, less than one-third contain enough experimental detail to fulfill the three core criteria of a GO annotation. This result demonstrates the need of using full-text articles for text mining GO annotations. Through its use at the BioCreative IV GO (BC4GO) task, we expect our corpus to become a valuable resource for the BioNLP research community. Database URL: http://www.biocreative.org/resources/corpora/bc-iv-go-task-corpus/.

Indexed as

Databases, GeneticMolecular Sequence AnnotationSoftwareVocabulary, ControlledComputational BiologyData MiningHumans

Identifiers

PMID25070993
PMCPMC4112614

What OpenQuestion holds

Textmetadata
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.