# The PhyloAlps Project

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[Data](data) |
[Standards](standards) |
[TNRS](tnrs) |
[Model](model) |
[Architecture](archi) |
[Technologies](techno) |
[User Profiles](profiles) |
[Meetings](meetings) |
[Biblio](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/toponym)
    * 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 |
**[EURO+MED]** | Taxonomy | Unavailable | HMI |
[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 |
[GeoNames] | Reverse Geocoding | ![CC BY] | REST API | 

### 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:
  * [NCBI]
  * [The Plant List]
  * [MNHN TaxRef]
  * [Mobot APG]
  * [EURO+MED]
* Version control

[SAJF]:https://www.jardinalpindulautaret.fr/accueil
[LECA]:http://www-leca.ujf-grenoble.fr/
[MoBot]:http://www.mobot.org/
[MNHN]:https://www.mnhn.fr/
[CBNA]:http://www.cbn-alpin-biblio.fr/
[GBIF]:http://www.gbif.org/
[IFB]:https://www.france-bioinformatique.fr/
[FRB]:http://www.fondationbiodiversite.fr/fr/
[INSD]:https://www.ncbi.nlm.nih.gov/genbank/collab/
[NCBI]:https://www.ncbi.nlm.nih.gov/
[USDA]:https://www.usda.gov/

[BOLD]:http://www.boldsystems.org/
[LECA Androsace]:http://androsace.ujf-grenoble.fr/
[GenBank]:https://www.ncbi.nlm.nih.gov/genbank/
[EMBL]:http://embl.org/
[DDBJ]:http://www.ddbj.nig.ac.jp/
[UniProtKB]:https://www.ebi.ac.uk/uniprot
[Phylota]:http://phylota.net/
[The Plant list]:http://www.theplantlist.org/
[Kew project]:http://www.kew.org/
[Tela Botanica]:http://www.tela-botanica.org/
[Tela Botanica eFlore]:http://www.tela-botanica.org/wikini/eflore/wakka.php?wiki=EfloreApi01
[DDBJ WABI]:http://www.ddbj.nig.ac.jp/search/help/wabi/wabi-e.html
[CBNA Herbarium]:http://www.gbif.org/dataset/e08f0546-0224-4b0d-886d-4ab05f0c87e6
[MNHN TaxRef]:https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref
[Mobot APG]:www.mobot.org/MOBOT/research/APweb/
[EURO+MED]:http://www.emplantbase.org/home.html
[FCBN SIFlore]:http://siflore.fcbn.fr/?cd_ref=&r=metro
[NCBI GenBank E-utilities]:https://www.ncbi.nlm.nih.gov/books/NBK25500/
[EMBL-EBI Ensembl]:http://rest.ensembl.org/
[USDA Plants]:https://plants.usda.gov/
[GeoNames]: http://api.geonames.org/

[ODbL]:https://opendatacommons.org/licenses/odbl/
[CC0]:https://i.creativecommons.org/p/mark/1.0/88x31.png
[CC BY]:https://i.creativecommons.org/l/by/3.0/88x31.png
[CC BY-NC]:https://i.creativecommons.org/l/by-nc/3.0/nl/88x31.png
[CC BY-NC-SA]:https://i.creativecommons.org/l/by-nc-sa/3.0/nl/88x31.png
[CC BY-NC-ND]:https://i.creativecommons.org/l/by-nc-nd/3.0/nl/88x31.png