Evidence map›Paper›PMID 25610627›Full record

ReviewIUCrJ2015

Data to knowledge: how to get meaning from your result.

Helen M Berman, Margaret J Gabanyi, Colin R Groom, John E Johnson, Garib N Murshudov, Robert A Nicholls, Vijay Reddy, Torsten Schwede, Matthew D Zimmerman, John Westbrook and 1 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in IUCrJ, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing 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

8 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Optimal structure determination from sub-optimal diffraction data.Protein science : a publication of the Protein Society · 2022
    Article
  5. Article
  6. Article
  7. The Cambridge Structural Database.Acta crystallographica Section B, Structural science, crystal engineering and materials · 2016
    Article
  8. 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

11 authors.

Helen M BermanCenter for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
Margaret J GabanyiCenter for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
Colin R GroomCambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, England.
John E JohnsonDepartment of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
Garib N MurshudovMRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England.
Robert A NichollsMRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England.
Vijay ReddyDepartment of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA.
Torsten SchwedeBiozentrum, University of Basel, Klingelbergstrasse 50-70, 4056 Basel, Switzerland ; SIB-Swiss Institute of Bioinformatics, Basel, Switzerland.
Matthew D ZimmermanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.
John WestbrookCenter for Integrative Proteomics Research, Department of Chemistry and Chemical Biology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
Wladek MinorDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Funding

Core H: MicrobiologyU54GM093342 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI CRONAN, JOHN E. · 2010 to 2015
$34.6M
Midwest Center for Structural GenomicsU54GM094585 · NIGMS · UNIVERSITY OF CHICAGO · PI MINOR, WLADEK · 2010 to 2014
$33.7M
The NYSGRC: A Large Scale Center for PSI:BiologyU54GM094662 · NIGMS · ALBERT EINSTEIN COLLEGE OF MEDICINE, INC · PI SEIDEL, RONALD D · 2010 to 2014
$32.6M
The Protein Structure Inittiative KnowledgebaseU01GM093324 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI BERMAN, HELEN M · 2010 to 2015
$12.9M
X-RAY CRYSTALLOGRAPHY OF MACROMOLECULESR01GM053163 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI MINOR, WLADEK, OTWINOWSKI, ZBYSZEK · 1996 to 2014
$6.3M
Medical Research Council MC_UP_A025_1012NIAID NIH HHS HHSN272201200026CNIGMS NIH HHS R01 GM053163NIGMS NIH HHS U01 GM093324NIGMS NIH HHS U54 GM093342NIGMS NIH HHS U54 GM094585NIGMS NIH HHS U54 GM094662
6 · The paper itself

Abstract

Structural and functional studies require the development of sophisticated 'Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB 'super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

Indexed as

big datadatabasesdata depositionknowledge basesmeaning from data

Identifiers

PMID25610627
PMCPMC4285880

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.