The PhyloAlps Project

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Data types

• Linnaean taxonomy
  • Identifier
  • Basionym i.e. binomial name (genus + species)
  • Synonyms
    • Nomenclature synonym
    • Replaced synonym
• Herbarium (alcoothèque/silicathèque)
  • Photos (photo server ? existing herbarium numeric model ?)
  • Location (area/GPS coordinates)
  • Collection datetime
• Occurrences
  • Photos (photo server ? existing herbarium numeric model ?)
  • Location (area/GPS coordinates)
  • Observation datetime
  • Phenotypic traits
  • Noteworthy criteria
• DNA sequences
  • Genome skimming
  • RAD sequencing
  • Exons capture
• Population distribution within an area
• Taxon coverage

Data providers

• SAJF PhyloAlps Herbarium (work in progress), QR code (species and DNA sequence identification)
• CBNA Herbarium: Conservatoire Botanique National Alpin à Briançon
• LECA Androsace: Phenotypic traits for Alpine plants
• GBIF: Global Biodiversity Information Facility (occurrences, observations, /!\ coverage)
• IFB: Institut Français pour la Bioinformatique
• FRB: Fondation pour la Recherche en Biodiversité
• BOLD: metabarcoding (not complete genome, taxonomic markers, 2 genes: 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)
• 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 sources

Name	Data type	Availability	Access	Comment
PhyloAlps Herbarium	Nomenclature, Location, photos	SAJF data	QR codes	Work in progress
CBNA Herbarium	Nomenclature, location, photos		via GBIF
GBIF	Occurrences (Nomenclature, location, photos)	->	REST API	Crowdsourcing quality
Androsace	Phenotypic traits	LECA data	HMI
FloraAlpina	Phenotypic traits	©	Book	Paper version only
BOLD	DNA barcoding	© ->	REST API
NCBI GenBank E-utilities	Taxonomy, DNA data bank	ODbL	REST API
EMBL-EBI Ensembl	Taxonomy, DNA data bank	Third Party	REST API, SPARQL endpoint	Clients available for Perl/Python/Java
DDBJ WABI	Taxonomy, DNA data bank	©	REST API	Some docs in Japanese
Plant list	Binomial name, synonyms		HMI	> 10 data sources, 3-levels trust model
Tela Botanica eFlore	Binomial name, synonyms		REST API	Beta version
PlantMiner	Binomial name, synonyms	Available	REST API
iPlant TNRS	Binomial name, synonyms	Available	REST API	Fuzzy name matching
FCBN SIFlore	Distribution map	Unavailable	HMI

Data sharing

• Institutions
  • OBO Foundry: Open Biomedical Ontology Foundry
  • HCLSIG: W3C Health Care and Life Sciences Interest Group
  • TDWG: Biodiversity Information Standards group
  • BioSharing
• Interoperability frameworks
  • LSID: Life Science ID
  • SPICE: Species 2000 Interoperability Co-ordination Environment
  • BioCASE: Biological Collection Access SErvice
  • TSE: Taxonomic Search Engine
  • SDD: Structure of Descriptive Data
  • ABCD: Access to Biological Collections Data schema
  • DwC: Darwin Core
  • ISA: Investigation, Study and Assay framework
• Taxonomy modelisation
  • TCS: Taxonomic Concept (Transfer) Schema
• Ontologies
  • GO: Gene Ontology
  • GONG: Gene Ontology Next Generation
  • MGED: Micro Array Gene Expression Data
  • PO: Plant Ontology
• Gene-oriented Markup languages
  • MAGE-ML: MicroArray Gene Expression Markup Language
  • KGML: KEGG Kyoto Encyclopedia of Genes and Genomes 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
  • Tax Ref
• Version control