standards.md

+# The PhyloAlps Project
+
+[Home](home) |
+[Data](data) |
+[Standards](standards |
+[Model](model) |
+[Technologies](techno) |
+[User Profiles](profiles) |
+[Meetings](meetings)
+
+## 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)
+
+[OBO Foundry]:http://obofoundry.org/
+[HCLSIG]:https://www.w3.org/wiki/HCLSIG
+[TDWG]:http://www.tdwg.org/
+[BGCI]:https://www.bgci.org/
+[NCEI]:https://www.ncei.noaa.gov/
+[ISB]:http://biocuration.org/
+[Species 2000]:http://www.sp2000.org/
+[BioSharing]:  https://biosharing.org/
+
+[LSID]:https://github.com/tdwg/guid-as
+[SPICE]:https://link.springer.com/chapter/10.1007/3-540-44469-6_92
+[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/
+[ISA]:http://www.isacommons.org/
+[BioDBcore]:http://biocuration.org/community/standards-biodbcore/
+[TCS]:http://tdwg.napier.ac.uk/
+
+[GO]:http://www.geneontology.org/
+[PO]:http://obofoundry.org/ontology/po.html
+[GONG]:http://gong.man.ac.uk/
+[MGED]:http://mged.sourceforge.net/ontologies/MGEDontology.php
+
+[mage-ml]:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC126871/
+[kgml]:http://www.genome.jp/kegg/xml/
+[KEGG]:http://www.genome.jp/kegg/
+
+[Biocatalogue]:https://www.biocatalogue.org/
+[TSE]:http://taxonomicsearch.sourceforge.net/
+[BioCASE]:http://www.biocase.org/
+[iPhylo]:https://iphylo.blogspot.fr/2012/02/using-google-refine-and-taxonomic.html
+[MNHN TaxRef Match]:https://taxref.mnhn.fr/taxref-web/accueil
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