Evidence map›Paper›PMID 25122463›Full record

ArticleDatabase : the journal of biological databases and curation2014

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.

Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Celen, Cecilia N Arighi, Hongzhan Huang, K Vijay-Shanker, Cathy H Wu

Open access · goldAbstract 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 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing papers in PubMed
2.3field-weighted citation impact, top 11% of its field
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

15 citing papers in PubMed, 23 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Mining clinical attributes of genomic variants through assisted literature curation in Egas.Database : the journal of biological databases and curation · 2016
    Article
  8. Article
  9. Predicting CK2 beta-dependent substrates using linear patterns.Biochemistry and biophysics reports · 2015
    Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Scaling drug indication curation through crowdsourcing.Database : the journal of biological databases and curation · 2015
    Article
  15. 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

10 authors at 5 institutions in 2 countries.

Manabu ToriiCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Gang LiCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Zhiwen LiCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Rose OughtredCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Francesca DiellaCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Irem CelenCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Cecilia N ArighiCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA arighi@dbi.udel.edu.
Hongzhan HuangCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
K Vijay-ShankerCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Cathy H WuCenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USACenter for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA, Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA, Structural and Computational Biology Unit, EMBL (European Molecular Biology Laboratory), 69117 Heidelberg, Germany, Department of Biochemistry, Molecular and Cellular Biology, Protein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA.
Princeton University · USGeorgetown University Medical Center · USUniversity Hospital Heidelberg · DEEuropean Molecular Biology Laboratory · DEGeorgetown University · US

Funding

BioGRID: an open resource for biological interactions and network analysisR01RR024031 · NCRR · SINAI HEALTH SYSTEM · PI TYERS, MIKE · 2007 to 2011
$3.2M
Linking Text Mining and Data Mining for Biomedical Knowledge DiscoveryG08LM010720 · NLM · UNIVERSITY OF DELAWARE · PI WU, CATHY H. · 2010 to 2012
$438k
NCRR NIH HHS R01RR024031NLM NIH HHS G08LM010720
6 · The paper itself

Abstract

Protein phosphorylation is central to the regulation of most aspects of cell function. Given its importance, it has been the subject of active research as well as the focus of curation in several biological databases. We have developed Rule-based Literature Mining System for protein Phosphorylation (RLIMS-P), an online text-mining tool to help curators identify biomedical research articles relevant to protein phosphorylation. The tool presents information on protein kinases, substrates and phosphorylation sites automatically extracted from the biomedical literature. The utility of the RLIMS-P Web site has been evaluated by curators from Phospho.ELM, PhosphoGRID/BioGrid and Protein Ontology as part of the BioCreative IV user interactive task (IAT). The system achieved F-scores of 0.76, 0.88 and 0.92 for the extraction of kinase, substrate and phosphorylation sites, respectively, and a precision of 0.88 in the retrieval of relevant phosphorylation literature. The system also received highly favorable feedback from the curators in a user survey. Based on the curators' suggestions, the Web site has been enhanced to improve its usability. In the RLIMS-P Web site, phosphorylation information can be retrieved by PubMed IDs or keywords, with an option for selecting targeted species. The result page displays a sortable table with phosphorylation information. The text evidence page displays the abstract with color-coded entity mentions and includes links to UniProtKB entries via normalization, i.e., the linking of entity mentions to database identifiers, facilitated by the GenNorm tool and by the links to the bibliography in UniProt. Log in and editing capabilities are offered to any user interested in contributing to the validation of RLIMS-P results. Retrieved phosphorylation information can also be downloaded in CSV format and the text evidence in the BioC format. RLIMS-P is freely available. DATABASE URL: http://www.proteininformationresource.org/rlimsp/

Indexed as

Databases, ProteinInternetPhosphoproteinsAnimalsComputational BiologyData MiningHumansUser-Computer InterfacePhosphoproteins

Identifiers

PMID25122463
PMCPMC4131691
OpenAlexW2105217514

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.