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phylodoc
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data

The PhyloAlps Project

Home | Data | User Profiles | Technologies

Data types

  • Binomial nomenclature genus + species (Carl Von Linné)
  • 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

  • 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)
  • 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 :
  • UniProtKB (Swiss-Prot) utilise EMBL
  • Phylota: plants browser
  • FloraAlpina (electronic version ?)
  • Tela Botanica: association de botanique de référence pour la botanique numérique
  • Plant list (cf. Kew project: exons sequencing)
  • Biocatalogue

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:
  • Version control