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data

The PhyloAlps Project

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

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
EOL Nomenclature Third party REST API

Taxonomic Name Resolution Services

Name Sources Example Comment
PlantMiner The Plant List, Brazilian Flora 2020 [http://www.plantminer.com/tpl?taxon=Leontopodium%20alpinum]
iPlant TNRS MoBoT Tropicos, NCBI, KEW, ILDIS, USDA Plants DB, The Global Compositae Checklist http://tnrs.iplantc.org/tnrsm-svc/matchNames?names=Leontopodium%20alpinum
OpenTreeOfLife Taxonomy NCBI taxonomy, GBIF Backbone taxonomy curl -X POST https://api.opentreeoflife.org/v3/tnrs/match_names -H "content-type:application/json" -d '{"names":["Aster","Symphyotrichum","Barnadesia"]}' POST only requests
GlobalNameResolver 182 sources http://resolver.globalnames.org/name_resolvers.json?names=Leontopodium%20alpinum
GBIF Species API 54 sources http://api.gbif.org/v1/species/match?name=Leontopodium%20alpinum

Data sharing

  • Institutions
    • OBO Foundry: Open Biomedical Ontology Foundry
    • HCLSIG: W3C Health Care and Life Sciences Interest Group
    • TDWG: Biodiversity Information Standards group
    • BGCI: Botanic Gardens Conservation International
    • NCEI: National Center for Environmental Information
    • ISB: International Society for Biocuration
    • Species 2000
    • BioSharing
  • Standards & frameworks
    • LSID: Life Science ID
    • SPICE: Species 2000 Interoperability Co-ordination Environment
    • SDD: Structure of Descriptive Data
    • ABCD: Access to Biological Collections Data schema
    • DwC: Darwin Core
    • ISA: Investigation, Study and Assay framework
    • BioDBcore: generic description of the core attributes of biological databases
    • TCS: Taxonomic Concept (Transfer) Schema
  • Ontologies
    • GO: Gene Ontology
    • PO: Plant Ontology
    • GONG: Gene Ontology Next Generation
    • MGED: Micro Array Gene Expression Data
  • Gene-oriented Markup languages
    • MAGE-ML: MicroArray Gene Expression Markup Language
    • KGML: KEGG Kyoto Encyclopedia of Genes and Genomes Markup Language
  • Tools
    • Biocatalogue: The Life Science Web Services Registry
    • TSE: Taxonomic Search Engine
    • BioCASE: Biological Collection Access SErvice
    • iPhylo: Taxonomic id reconciliation with Google Refine
    • MNHN TaxRef Match: Taxonomic id reconciliation (work in progress)

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