Evidence map›Paper›PMID 28365730›Full record

ArticleDatabase : the journal of biological databases and curation2017

Biocuration in the structure-function linkage database: the anatomy of a superfamily.

Gemma L Holliday, Shoshana D Brown, Eyal Akiva, David Mischel, Michael A Hicks, John H Morris, Conrad C Huang, Elaine C Meng, Scott C-H Pegg, Thomas E Ferrin and 1 more

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Database : the journal of biological databases and curation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Gemma L HollidayDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
Shoshana D BrownDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
Eyal AkivaDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
David MischelDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
Michael A HicksDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.
John H MorrisDepartment of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
Conrad C HuangDepartment of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
Elaine C MengDepartment of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
Scott C-H PeggGladstone Institutes, San Francisco, CA 94158, USA.
Thomas E FerrinDepartment of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.
Patricia C BabbittDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.

Funding

Core H: MicrobiologyU54GM093342 · NIGMS · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI CRONAN, JOHN E. · 2010 to 2015
$34.6M
Theoretical and Computational ApproachesP01GM071790 · NIGMS · UNIVERSITY OF ILLINOIS URBANA-CHAMPAIGN · PI RAUSHEL, FRANK M. · 2004 to 2013
$15.5M
GENETICS TRAINING PROGRAM FOR PHD CANDIDATEST32GM007790 · NIGMS · STANFORD UNIVERSITY · PI BRUNET, ANNE, KINGSLEY, DAVID M · 1985 to 2020
$12.8M
Resource for Biocomputing Visualization and InformaticsP41GM103311 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2012 to 2017
$8.2M
Laying the Foundation of Genomic EnzymologyR01GM060595 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BABBITT, PATRICIA CLEMENT · 2000 to 2018
$5.4M
NIGMS NIH HHS P01 GM071790NIGMS NIH HHS P41 GM103311NIGMS NIH HHS R01 GM060595NIGMS NIH HHS T32 GM007790NIGMS NIH HHS U54 GM093342
6 · The paper itself

Abstract

With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD. Database URL: http://sfld.rbvi.ucsf.edu/.

Indexed as

Databases, ProteinGene OntologyMolecular Sequence AnnotationEnzymesStructural Homology, ProteinStructure-Activity RelationshipEnzymes

Identifiers

PMID28365730
PMCPMC5467563

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.