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Add the Standards menu item to all the wiki pages authored by Anthony Hombiat's avatar Anthony Hombiat
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data.md
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[Home](home) |
[Data](data) |
[Standards](standards |
[Model](model) |
[Technologies](techno) |
[User Profiles](profiles) |
......@@ -61,9 +62,9 @@ FloraAlpina | Phenotypic traits | © | Book | Paper version only
**[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 |
**[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 |
......@@ -74,45 +75,11 @@ Name | Sources | NCBI | The Plant List | MNHN TaxRef | Example |Comment
--- | --- | --- | --- | --- | --- | ---
[PlantMiner] | [2](http://www.plantminer.com/) | | X | | [link](http://www.plantminer.com/tpl?taxon=Leontopodium%20alpinum) |
[iPlant] | [6](http://tnrs.iplantc.org/sources.html) | X | | | [link](http://tnrs.iplantc.org/tnrsm-svc/matchNames?names=Leontopodium%20alpinum) |
**[OpenTreeOfLife Taxonomy]** | [2](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.0) | X | X | | POST only requests |
**[OpenTreeOfLife Taxonomy]** | [2](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.0) | X | X | | POST only requests |
**[GlobalNameResolver]** | [182](http://resolver.globalnames.org/data_sources) | X | X | | [link](http://resolver.globalnames.org/name_resolvers.json?names=Leontopodium%20alpinum) |
**[GBIF Species API]** | [54](http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c) | X | X | | [link](http://api.gbif.org/v1/species/match?name=Leontopodium%20alpinum) |
[EOL] | [50](http://eol.org/collections/97700?sort_by=3&view_as=3) | | | | [link](http://eol.org/api/search/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)
......@@ -128,17 +95,17 @@ Name | Sources | NCBI | The Plant List | MNHN TaxRef | Example |Comment
[SAJF]:https://www.jardinalpindulautaret.fr/accueil
[LECA]:http://www-leca.ujf-grenoble.fr/
[biocatalogue]:https://www.biocatalogue.org/
[MoBot]:http://www.mobot.org/
[MNHN]:https://www.mnhn.fr/
[CBNA]:http://www.cbn-alpin-biblio.fr/
[GBIF]:http://www.gbif.org/
[LECA Androsace]:http://androsace.ujf-grenoble.fr/
[IFB]:https://www.france-bioinformatique.fr/
[FRB]:http://www.fondationbiodiversite.fr/fr/
[BOLD]:http://www.boldsystems.org/
[INSD]:https://www.ncbi.nlm.nih.gov/genbank/collab/
[NCBI]:https://www.ncbi.nlm.nih.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/
......@@ -150,10 +117,14 @@ Name | Sources | NCBI | The Plant List | MNHN TaxRef | Example |Comment
[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/
[PlantMiner]:http://www.plantminer.com
[iPlant]:http://tnrs.iplantcollaborative.org/about.html
[MNHN TaxRef]:https://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref
[GBIF Species API]:http://www.gbif.org/developer/species
[OpenTreeOfLife Taxonomy]:https://github.com/OpenTreeOfLife/germinator/wiki/Taxonomy-API-v3
[GlobalNameResolver]:http://resolver.globalnames.org/api
[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/
......@@ -170,34 +141,3 @@ Name | Sources | NCBI | The Plant List | MNHN TaxRef | Example |Comment
[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
[OBO Foundry]:http://obofoundry.org/
[hclsig]:https://www.w3.org/wiki/HCLSIG
[TDWG]:http://www.tdwg.org/
[BGCI]:https://www.bgci.org/
[BioSharing]: https://biosharing.org/
[Species 2000]:http://www.sp2000.org/
[ISB]:http://biocuration.org/
[NCEI]:https://www.ncei.noaa.gov/
[TCS]:http://tdwg.napier.ac.uk/
[BioCASE]:http://www.biocase.org/
[GlobalNameResolver]:http://resolver.globalnames.org/api
[SPICE]:https://link.springer.com/chapter/10.1007/3-540-44469-6_92
[TSE]:http://taxonomicsearch.sourceforge.net/
[SDD]:https://github.com/tdwg/wiki-archive/blob/master/twiki/data/SDD/WebHome.txt
[ABCD]:https://github.com/tdwg/wiki-archive/blob/master/twiki/data/ABCD/WebHome.txt
[DwC]:http://rs.tdwg.org/dwc/
[BioDBcore]:http://biocuration.org/community/standards-biodbcore/
[ISA]:http://www.isacommons.org/
[iPhylo]:https://iphylo.blogspot.fr/2012/02/using-google-refine-and-taxonomic.html
[GO]:http://www.geneontology.org/
[GONG]:http://gong.man.ac.uk/
[MGED]:http://mged.sourceforge.net/ontologies/MGEDontology.php
[PO]:http://obofoundry.org/ontology/po.html
[mage-ml]:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC126871/
[kgml]:http://www.genome.jp/kegg/xml/
[KEGG]:http://www.genome.jp/kegg/
[LSID]:https://github.com/tdwg/guid-as
[Mobot APG]:www.mobot.org/MOBOT/research/APweb/
[GBIF Species API]:http://www.gbif.org/developer/species
[MNHN TaxRef Match]:https://taxref.mnhn.fr/taxref-web/accueil
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