Towards FAIR Principles in Biodiversity Research: Enabling computable taxonomic descriptions and ecological data with Phenoscript

By

Tarasov, Sergei I.
Montanaro, Giulio
Losacco, Federica
Porto, Diego

Type

Article

Date of Publication

2023-8-30

Original Publication

Metabarcoding and metagenomics

Volume

7

Pages

1--2

Subjects

Ecology , FAIR Data , ontologies , phenomics , semantic description , taxonomy

Contributed by

Pensoft Publishers

Language

English

Published by

Bulgaria Pensoft Publishers 2017-

Identifiers

DOI: https://doi.org/10.3897/biss.7.111862

 

Abstract

Taxonomic descriptions hold immense phenotypic data, but their natural language (NL) format poses challenges for computer analysis. In this talk, we will present Phenoscript, a user-friendly computer language enabling computer-readable species descriptions and automated phenotype comparisons, in accordance with FAIR (Findable, Accessible, Interoperable, Reusable) principles.<br> Phenoscript facilitates the creation of semantic species descriptions that represent a knowledge graph composed of terms from predefined biological ontologies. A Phenoscript description resembles a NL description, but follows a specific language grammar. We have developed the Phenospy package: a Python-based Phenoscript toolkit. Phenospy converts Phenoscript descriptions into both NL format, facilitating scientific publication, and the Web Ontology Language (OWL) format, enabling downstream analysis and computable phenotypic comparisons. OWL is a standard for sharing semantic data on the Web. While initially designed for phenotypes, Phenoscript can be extended to create semantic ecological data, encompassing environmental traits, functional traits, and species interactions. We will discuss the integration of species and ecological traits encoded in Phenoscript into downstream analysis, highlighting its potential for phenomic-level research in biology.