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Exploring biomedical ontology mappings with graph theory methods

Overview of attention for article published in PeerJ, March 2017
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Title
Exploring biomedical ontology mappings with graph theory methods
Published in
PeerJ, March 2017
DOI 10.7717/peerj.2990
Pubmed ID
Authors

Simon Kocbek, Jin-Dong Kim

Abstract

In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 21 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Japan 1 5%
Unknown 20 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 4 19%
Student > Master 3 14%
Professor 2 10%
Student > Ph. D. Student 2 10%
Student > Doctoral Student 1 5%
Other 0 0%
Unknown 9 43%
Readers by discipline Count As %
Computer Science 7 33%
Medicine and Dentistry 2 10%
Nursing and Health Professions 1 5%
Physics and Astronomy 1 5%
Agricultural and Biological Sciences 1 5%
Other 2 10%
Unknown 7 33%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 09 March 2017.
All research outputs
#13,307,934
of 22,957,478 outputs
Outputs from PeerJ
#6,994
of 13,370 outputs
Outputs of similar age
#157,625
of 310,726 outputs
Outputs of similar age from PeerJ
#184
of 302 outputs
Altmetric has tracked 22,957,478 research outputs across all sources so far. This one is in the 41st percentile – i.e., 41% of other outputs scored the same or lower than it.
So far Altmetric has tracked 13,370 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 17.3. This one is in the 45th percentile – i.e., 45% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 310,726 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 302 others from the same source and published within six weeks on either side of this one. This one is in the 38th percentile – i.e., 38% of its contemporaries scored the same or lower than it.