Evidence map›Paper›PMID 25110584›Full record

ArticleF1000Research2014

BridgeDb app: unifying identifier mapping services for Cytoscape.

Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R Pico

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in F1000Research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
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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

7 authors.

Jianjiong GaoKravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Chao ZhangInstitute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA.
Martijn van IerselGeneral Bioinformatics, Reading, Birkshire, RG4 7RT, UK.
Li ZhangSchool of Computer Science and Engineering, Changchun University of Technology, Changchun, 130012, China.
Dong XuDepartment of Computer Science,C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
Nikolaus SchultzKravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA ; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
Alexander R PicoGladstone Institutes, San Francisco, CA 94158, USA.

Funding

TR&D 3 - Network Guided Machine LearningP41GM103504 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2012 to 2024
$17.3M
WikiPathways Project: At the Intersection of Big Data and Researcher KnowledgeR01GM100039 · NIGMS · J. DAVID GLADSTONE INSTITUTES · PI PICO, ALEXANDER R · 2012 to 2020
$3.4M
NIGMS NIH HHS P41 GM103504NIGMS NIH HHS R01 GM100039
6 · The paper itself

Abstract

The BridgeDb app for Cytoscape allows users to map and annotate identifiers of genes, proteins and metabolites in the context of biological networks. The app greatly simplifies the identifier mapping process in Cytoscape by providing a unified interface to different mapping resources and services. The app also provides a programming interface via Cytoscape Commands that can be utilized for identifier mapping by other Cytoscape apps. In this article we provide a technical guide to the BridgeDb app for mapping identifiers in Cytoscape.

Identifiers

PMID25110584
PMCPMC4111116

What OpenQuestion holds

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LicenceCC BY
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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.