Evidence map›Paper›PMID 30406744›Full record

ReviewEcoSal Plus2018

The EcoCyc Database.

Peter D Karp, Wai Kit Ong, Suzanne Paley, Richard Billington, Ron Caspi, Carol Fulcher, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Peter E Midford and 9 more

Abstract readReview
In one paragraph

Review in EcoSal Plus, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.

0numbers the graph read from it
0cells of the map it votes in
65citing 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

65 citing papers in PubMed.

  1. Article
  2. Article
  3. SeaB is a conservedInfection and immunity · 2026
    Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Article

5 more citing papers are in PubMed but not listed here.

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

19 authors.

Peter D KarpBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Wai Kit OngBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Suzanne PaleyBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Richard BillingtonBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Ron CaspiBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Carol FulcherBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Anamika KothariBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Markus KrummenackerBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Mario LatendresseBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Peter E MidfordBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Pallavi SubhravetiBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Socorro Gama-CastroPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
Luis Muñiz-RascadoPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
César Bonavides-MartinezPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
Alberto Santos-ZavaletaPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
Amanda MackieDepartment of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
Julio Collado-VidesPrograma de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, México.
Ingrid M KeselerBioinformatics Research Group, SRI International, Menlo Park, CA 94025.
Ian PaulsenDepartment of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.

Funding

The EcoCyc Model Organism Database for Escherichia coli [SRI Proposal ECU 14-631]U24GM077678 · NIGMS · SRI INTERNATIONAL · PI KARP, PETER D · 2006 to 2018
$12.3M
The EcoCyc Model Organism Database for Escherichia coliR01GM077678 · NIGMS · SRI INTERNATIONAL · PI KARP, PETER D · 2019 to 2022
$4.6M
Gene Regulation: E.coli Database Integrated ModelingR01GM071962 · NIGMS · CENTER FOR GENOMIC SCIENCES · PI COLLADO-VIDES, JULIO · 2004 to 2011
$2.4M
NIGMS NIH HHS R01 GM071962NIGMS NIH HHS R01 GM077678NIGMS NIH HHS U24 GM077678
6 · The paper itself

Abstract

EcoCyc is a bioinformatics database available at EcoCyc.org that describes the genome and the biochemical machinery of

Indexed as

Databases, GeneticGenome, BacterialSoftwareComputational BiologyEscherichia coli K12Escherichia coli ProteinsGene Expression Regulation, BacterialInternetMetabolic Flux AnalysisMetabolic Networks and PathwaysUser-Computer InterfaceEscherichia coli Proteins

Identifiers

PMID30406744
PMCPMC6504970

What Socratic holds

Textmetadata
LicenceTDM
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 Socratic graph.