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multiple endproducts of genes Protein Ontology RnaO development GO SO PATO MAO RNA and protein sequences and structures NCBI Taxonomy genetic code Data formats, database schemas NCBI data model NEXUS format widely NeXML trees, models, meta-info pPOD workflows CHADO phenotypes, phylogenies TreeBase

Ontologies
PRO/PROEVO	http://www.bioontology.org/wiki/index.php/PRO	protein evolutionary families,
in development
http://proteinontology.info/	protein structure, function	implementation
http://roc.bgsu.edu/	RNA sequence, structure, motifs, alignments	in
		implementation
		implementation
http://www.bioontology.org/wiki/index.php/PATO	phenotypic and trait ontology
implementation
http://bips.u-strasbg.fr/LBGI/MAO/mao.html	multiple alignments of DNA,
implementation
http://www.ncbi.nlm.nih.gov/Taxonomy/	Organismal classification,
used widely
http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/DATAMODL.HTML
sequences, alignments, annotations	used at NCBI
Maddison, et al., 1997	character data, trees, assumptions, sets, notes	used
https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard	character data,
in development
	processing of data related to phylogenetic analysis
in development
http://www.gmod.org/wiki/index.php/Schema	sequence, genotypes,
used in GMOD
http://www.treebase.org	character data, trees, meta-info on analyses	in use