Skip to content

GitLab

P
phylodoc
Last edited by Anthony Hombiat
Page history
This is an old version of this page. You can view the most recent version or browse the history.

data

The PhyloAlps Project

Home | Data | Standards | Model | Technologies | User Profiles | Meetings | Biblio

Data

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: Station Alpine Joseph Fourier
  • CBNA: Conservatoire Botanique National Alpin à Briançon
  • LECA: Laboratoire d'ECologie Alpine
  • GBIF: Global Biodiversity Information Facility (occurrences, observations, /!\ coverage)
  • IFB: Institut Français pour la Bioinformatique
  • FRB: Fondation pour la Recherche en Biodiversité
  • INSD: International Nucleotide Sequence Database collaboration :
    • NCBI: National Center for Biotechnology Information
    • EMBL: European Molecular Biology Laboratory
    • DDBJ: DNA DB of Japan European Molecular Biology Lab (down for the moment)
  • Tela Botanica: association de botanique de référence pour la botanique numérique
  • USDA: United States Department of Agriculture
  • MoBot: Missouri Botanical garden
  • MNHN: Musée National d'Histoire Naturelle

Data sources

Name Data type Availability Access Comment
SAJF PhyloAlps Herbarium Nomenclature, location, photos SAJF data QR codes Work in progress
CBNA Herbarium Nomenclature, location, photos CC BY via GBIF
USDA Plants Nomenclature, location, photos © -> public domain REST API
GBIF Occurrences (nomenclature, location, photos) CC0 -> CC BY-NC REST API Crowdsourcing quality
LECA Androsace Phenotypic traits LECA data HMI
FloraAlpina Phenotypic traits © Book Paper version only
BOLD DNA barcoding © -> CC BY-NC-ND REST API not complete genome, taxonomic markers, 2 genes: matK et rbcL
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
MNHN TaxRef Taxonomy Available Download
Mobot APG Taxonomy HTML Web pages
Phylota DNA data bank HMI
The Plant list  Nomenclature, synonyms CC BY-NC-ND HMI > 10 data sources, 3-levels trust model
Tela Botanica eFlore Nomenclature, synonyms CC BY-NC-SA REST API Beta version
FCBN SIFlore Distribution map Unavailable HMI

Taxonomic Name Resolution Services

Name Sources NCBI MoBoT TPL TaxRef Example Comment
PlantMiner 2 X X link
iPlant 6 X link
OpenTreeOfLife Taxonomy 2 X X X POST only requests Taxonomy AND Phylogeny
GlobalNameResolver 182 X X X link
GBIF Species API 54 X X X link
EOL 50 link
ITIS 5 X link
TSE 5 X no available server

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:
  • Version control