Evidence map›Paper›PMID 28583809›Full record

ArticleJournal of biomedical informatics2017

An empirical analysis of ontology reuse in BioPortal.

Christopher Ochs, Yehoshua Perl, James Geller, Sivaram Arabandi, Tania Tudorache, Mark A Musen

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of biomedical informatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Article
  2. The Immunopeptidomics Ontology (ImPO).Database : the journal of biological databases and curation · 2024
    Article
  3. Article
  4. Article
  5. An Extendible Realism-Based Ontology for Kinship.CEUR workshop proceedings. · 2023
    Article
  6. Semantic standards of external exposome data.Environmental research · 2021
    Review
  7. Enhancing the Representational Power of i2b2 through Referent Tracking.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2018
    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

6 authors.

Christopher OchsComputer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA. Electronic address: cro3@njit.edu.
Yehoshua PerlComputer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA.
James GellerComputer Science Department, New Jersey Institute of Technology, Newark, NJ 07102, USA.
Sivaram ArabandiONTOPRO, Houston, TX, USA.
Tania TudoracheStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.
Mark A MusenStanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305, USA.

Funding

STANFORD COMPOSITE(RMI)U54HG004028 · NHGRI · STANFORD UNIVERSITY · PI MUSEN, MARK A · 2005 to 2014
$36.2M
Collaborative Development of Biomedical Ontologies and TerminologiesR01GM086587 · NIGMS · STANFORD UNIVERSITY · PI MUSEN, MARK A · 2009 to 2016
$4.1M
Protege: A Knowledge-Engineering Environment for Advancing Biomedical SciencesR01GM121724 · NIGMS · STANFORD UNIVERSITY · PI MUSEN, MARK A · 2017 to 2020
$2.3M
A family-based framework of quality assurance for biomedical ontologiesR01CA190779 · NCI · NEW JERSEY INSTITUTE OF TECHNOLOGY · PI PERL, YEHOSHUA · 2015 to 2017
$1.8M
NCI NIH HHS R01 CA190779NHGRI NIH HHS U54 HG004028NIGMS NIH HHS R01 GM086587NIGMS NIH HHS R01 GM121724
6 · The paper itself

Abstract

Biomedical ontologies often reuse content (i.e., classes and properties) from other ontologies. Content reuse enables a consistent representation of a domain and reusing content can save an ontology author significant time and effort. Prior studies have investigated the existence of reused terms among the ontologies in the NCBO BioPortal, but as of yet there has not been a study investigating how the ontologies in BioPortal utilize reused content in the modeling of their own content. In this study we investigate how 355 ontologies hosted in the NCBO BioPortal reuse content from other ontologies for the purposes of creating new ontology content. We identified 197 ontologies that reuse content. Among these ontologies, 108 utilize reused classes in the modeling of their own classes and 116 utilize reused properties in class restrictions. Current utilization of reuse and quality issues related to reuse are discussed.

Indexed as

Biological OntologiesSoftwareVocabulary, ControlledQuality ControlBioPortalContent reuseOntology modelingOntology reuseOntology structural analysis

Identifiers

PMID28583809
PMCPMC5557647

What OpenQuestion 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 OpenQuestion graph.