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{|
{|
 +
Ontologies
|-
|-
-
!Ontologies
+
PRO/PROEVO
-
!PRO/PROEVO
+
|http://www.bioontology.org/wiki/index.php/PRO
-
!http://www.bioontology.org/wiki/index.php/PRO
+
|protein evolutionary families,
-
!protein evolutionary families,
+
|-
|-
-
|multiple endproducts of genes
+
multiple endproducts of genes
|in development
|in development
|-
|-
-
Protein Ontology
+
Protein Ontology
-
|http://proteinontology.info/ |protein structure, function
+
|http://proteinontology.info/
 +
|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 development
+
|in
|-
|-
-
|GO
+
development
-
| implementation
+
|-
|-
-
|SO
+
GO
-
| implementation
+
|
 +
|
 +
|implementation
 +
|-
 +
SO
 +
|
 +
|
 +
|implementation
|-
|-
-
|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
 +
|-
 +
|implementation
|implementation
|-
|-
-
|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
|-
|-
-
|NCBI Taxonomy
+
NCBI Taxonomy
-
|http://www.ncbi.nlm.nih.gov/Taxonomy/
+
|http://www.ncbi.nlm.nih.gov/Taxonomy/
-
|Organismal classification, genetic code
+
|Organismal classification,
 +
|-
 +
genetic code
|used widely
|used widely
|-
|-
-
|Data formats,
+
Data formats, database schemas
-
| 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
 +
|-
 +
 
 +
|-
 +
 
 +
|-
 +
 
 +
|-
 +
 
|-
|-
-
|NCBI data model http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/DATAMODL.HTML
 
-
|sequences, alignments, annotations used at NCBI
 
|}
|}

Revision as of 14:58, 9 April 2008

Ontologies PRO/PROEVO 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
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
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