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{|
{|
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!Ontologies
+
|Ontologies
|-
|-
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!PRO/PROEVO
+
|PRO/PROEVO
|http://www.bioontology.org/wiki/index.php/PRO
|http://www.bioontology.org/wiki/index.php/PRO
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|protein evolutionary families,
+
|protein evolutionary families, multiple endproducts of genes
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|-
+
-
multiple endproducts of genes
+
|in development
|in development
|-
|-
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Protein Ontology
+
|Protein Ontology
|http://proteinontology.info/
|http://proteinontology.info/
|protein structure, function
|protein structure, function
|implementation
|implementation
|-
|-
-
RnaO
+
|RnaO
|http://roc.bgsu.edu/
|http://roc.bgsu.edu/
|RNA sequence, structure, motifs, alignments
|RNA sequence, structure, motifs, alignments
-
|in
+
|in development
-
|-
+
-
development
+
|-
|-
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GO
+
|GO
|
|
|
|
|implementation
|implementation
|-
|-
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SO
+
|SO
|
|
|
|
|implementation
|implementation
|-
|-
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PATO
+
|PATO
|http://www.bioontology.org/wiki/index.php/PATO
|http://www.bioontology.org/wiki/index.php/PATO
|phenotypic and trait ontology
|phenotypic and trait ontology
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|-
 
-
 
|implementation
|implementation
|-
|-
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MAO
+
|MAO
|http://bips.u-strasbg.fr/LBGI/MAO/mao.html
|http://bips.u-strasbg.fr/LBGI/MAO/mao.html
|multiple alignments of DNA,
|multiple alignments of DNA,
|-
|-
-
RNA and protein sequences and structures
+
|RNA and protein sequences and structures
|implementation
|implementation
|-
|-
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NCBI Taxonomy
+
|NCBI Taxonomy
|http://www.ncbi.nlm.nih.gov/Taxonomy/
|http://www.ncbi.nlm.nih.gov/Taxonomy/
|Organismal classification,
|Organismal classification,
|-
|-
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genetic code
+
|genetic code
|used widely
|used widely
|-
|-
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Data formats, database schemas
+
|Data formats, database schemas
|-
|-
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NCBI data model
+
|NCBI data model
|http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/DATAMODL.HTML
|http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/DATAMODL.HTML
|-
|-
-
 
+
|
|sequences, alignments, annotations
|sequences, alignments, annotations
|used at NCBI
|used at NCBI
|-
|-
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NEXUS format
+
|NEXUS format
|Maddison, et al., 1997
|Maddison, et al., 1997
|character data, trees, assumptions, sets, notes
|character data, trees, assumptions, sets, notes
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|used
+
|used widely
|-
|-
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widely
+
|NeXML
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|-
+
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NeXML
+
|https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard
|https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard
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|character data,
+
|character data, trees, models, meta-info
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|-
+
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trees, models, meta-info
+
|in development
|in development
|-
|-
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pPOD
+
|pPOD
|
|
-
|processing of data related to phylogenetic analysis
+
|processing of data related to phylogenetic analysis workflows
-
|-
+
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workflows
+
|in development
|in development
|-
|-
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CHADO
+
|CHADO
|http://www.gmod.org/wiki/index.php/Schema
|http://www.gmod.org/wiki/index.php/Schema
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|sequence, genotypes,
+
|sequence, genotypes, phenotypes, phylogenies
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|-
+
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phenotypes, phylogenies
+
|used in GMOD
|used in GMOD
|-
|-
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TreeBase
+
|TreeBase
|http://www.treebase.org
|http://www.treebase.org
|character data, trees, meta-info on analyses
|character data, trees, meta-info on analyses
|in use
|in use
|-
|-
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+
|
|-
|-
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+
|
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|-
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+
|
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|-
-
 
+
|
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|}
|}

Revision as of 15:02, 9 April 2008

Ontologies
PRO/PROEVO http://www.bioontology.org/wiki/index.php/PRO protein evolutionary families, multiple endproducts of genes in development
Protein Ontology http://proteinontology.info/ protein structure, function implementation
RnaO http://roc.bgsu.edu/ RNA sequence, structure, motifs, alignments in development
GO implementation
SO implementation
PATO http://www.bioontology.org/wiki/index.php/PATO phenotypic and trait ontology implementation
MAO http://bips.u-strasbg.fr/LBGI/MAO/mao.html multiple alignments of DNA,
RNA and protein sequences and structures implementation
NCBI Taxonomy http://www.ncbi.nlm.nih.gov/Taxonomy/ Organismal classification,
genetic code used widely
Data formats, database schemas
NCBI data model http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/DATAMODL.HTML
sequences, alignments, annotations used at NCBI
NEXUS format Maddison, et al., 1997 character data, trees, assumptions, sets, notes used widely
NeXML https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard character data, trees, models, meta-info in development
pPOD processing of data related to phylogenetic analysis workflows in development
CHADO http://www.gmod.org/wiki/index.php/Schema sequence, genotypes, phenotypes, phylogenies used in GMOD
TreeBase http://www.treebase.org character data, trees, meta-info on analyses in use
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