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Abstract Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos.
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Trait-Based Research on Rotifera: The Holy Grail or Just Messy?
In recent years, trait-based research on plankton has gained interest because of its potential to uncover general roles in ecology. While trait categories for phytoplankton and crustaceans have been posited, rotifer trait assessment has lagged behind. Here, we reviewed the literature to assess traits key to their life histories and provided a data matrix for the 138 valid genera of phylum Rotifera. We considered seven traits: habitat type, trophi type, presence of lorica and foot, predation defense attributes, corona type, and feeding traits. While most traits were morphological attributes and supposedly easy to assess, we were faced with several challenges regarding trait assignment. Feeding traits were especially difficult to assess for many genera because relevant information was missing. Our assembled trait matrix provides a foundation that will initiate additional research on rotifer functional diversity, diminish the misclassification of rotifer genera into trait categories, and facilitate studies across trophic levels.
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- Award ID(s):
- 2051710
- PAR ID:
- 10492500
- Editor(s):
- Manca, M.M. Granata
- Publisher / Repository:
- Water
- Date Published:
- Journal Name:
- Water
- Volume:
- 15
- Issue:
- 8
- ISSN:
- 2073-4441
- Page Range / eLocation ID:
- 1459
- Subject(s) / Keyword(s):
- aquatic ecology functional ecology corona community dynamics food guild ratio functional groups rotifer trophi
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/w15081459
