The PhyloAlps Project

Home | Data | User Profiles | Technologies

Data types

• Binomial name genus + species
• Herbarium pictures (photo server ? existing herbarium numeric model ?)
• DNA séquences
• Population distribution within an area
• Plotlist
• Phenotypic traits
• Genome skimming
• Silicathèque
• GPS coordinates
• Taxon coverage
• Noteworthy criteria

Data providers

• SAJF PhyloAlps Herbarium (work in progress), QR code (species and DNA sequence identification)
• CBNA Herbarium: Conservatoire Botanique National Alpin à Briançon
• GBIF: Global Biodiversity Information Facility (occurrences, observations, /!\ coverage)
• LECA Androsace: reference phenotypic traits for Alpine plants
• IFB: Institut Français pour la Bioinformatique
• FRB: Fondation pour la Recherche en Biodiversité
• BOLD: pas le génome complet (marqueurs taxonomiques, 2 gènes matK et rbcL)
• INSD: International Nucleotide Sequence Database Collaboration :
  • NCBI GenBank: National Center for Biotechnology Information
  • EMBL: European Molecular Biology Laboratory
  • DDBJ: DNA DB of Japan European Molecular Biology Lab (down for the moment)
• UniProtKB (Swiss-Prot) utilise EMBL
• Phylota: plants browser
• FloraAlpina (paper version only)
• Tela Botanica: association de botanique de référence pour la botanique numérique
• Plant list (cf. Kew project: exons sequencing)
• Biocatalogue: The Life Science Web Services Registry

Data models

• Gene ontologies
  • HCLSIG: W3C Health Care and Life Sciences Interest Group
  • GO: Gene Ontology
  • GONG: Gene Ontology Next Generation
  • MGED: Micro Array Gene Expression Data
• Standards
  • MAGE-ML: MicroArray Gene Expression Markup Language
  • KGML: KEGG Markup Language

Data quality

• Multiple stages data validation process
  • syntactic & semantic check (automatic)
  • outlier check (semi-automatic)
• Multi-criteria data trust model
• Issue tracking system
• Bridge the gap between multiple taxonomic referentials taxonomiques:
  • NCBI
  • Plant List
  • Plant ref
• Version control