IMIS | Flanders Marine Institute
 

Flanders Marine Institute

Platform for marine research

IMIS

Publications | Institutes | Persons | Datasets | Projects | Maps
[ report an error in this record ]basket (0): add | show Print this page

Transforming the study of organisms: phenomic data models and knowledge bases
Thessen, A.E.; Walls, R.L.; Vogt, L.; Singer, J.; Warren, R.; Buttigieg, P.L.; Balhoff, J.P.; Mungall, C.J.; McGuinness, D.L.; Stucky, B.J.; Yoder, M.J.; Haendel, M.A. (2020). Transforming the study of organisms: phenomic data models and knowledge bases. PLoS computational biology 16(11): e1008376. https://dx.doi.org/10.1371/journal.pcbi.1008376
In: PLoS computational biology. ISSN 1553-7358; e-ISSN 1553-734X, more
Peer reviewed article  

Available in  Authors 

Authors  Top 
  • Thessen, A.E.
  • Walls, R.L.
  • Vogt, L.
  • Singer, J.
  • Warren, R.
  • Buttigieg, P.L.
  • Balhoff, J.P.
  • Mungall, C.J.
  • McGuinness, D.L.
  • Stucky, B.J.
  • Yoder, M.J.
  • Haendel, M.A.

Abstract
    The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

All data in the Integrated Marine Information System (IMIS) is subject to the VLIZ privacy policy Top | Authors