Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS.

GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.

Mining Plant Genomic and Genetic Data Using the GnpIS Information System.

GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

A hominid tooth from Bulgaria: the last pre-human hominid of continental Europe.

A hominid upper premolar was discovered in the Azmaka quarry, near Chirpan (Bulgaria). The associated fauna, especially the co-occurrence of Choerolophodon and Anancus among the proboscideans, and Cremohipparion matthewi and Hippotherium brachypus among the hipparions, constrains the age of the locality to the second half of the middle Turolian (ca. 7 Ma), making it the latest pre-human hominid of continental Europe and Asia Minor. The available morphological and metric data are more similar to those of Ouranopithecus from the Vallesian of Greece than to those of the early to middle Turolian hominids of Turkey and Georgia, but the time gap speaks against a direct phyletic link, and Turolian migration from the east cannot be rejected.