Wiki Table Editor
From Wiki
(Difference between revisions)
| Line 1: | Line 1: | ||
{| | {| | ||
| - | + | |Ontologies | |
|- | |- | ||
| - | + | |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/ | |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 | + | |
|- | |- | ||
| - | GO | + | |GO |
| | | | ||
| | | | ||
|implementation | |implementation | ||
|- | |- | ||
| - | SO | + | |SO |
| | | | ||
| | | | ||
|implementation | |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, | |Organismal classification, | ||
|- | |- | ||
| - | genetic code | + | |genetic code |
|used widely | |used widely | ||
|- | |- | ||
| - | Data formats, database schemas | + | |Data formats, database schemas |
|- | |- | ||
| - | 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 | ||
|- | |- | ||
| - | NEXUS format | + | |NEXUS format |
|Maddison, et al., 1997 | |Maddison, et al., 1997 | ||
|character data, trees, assumptions, sets, notes | |character data, trees, assumptions, sets, notes | ||
| - | |used | + | |used widely |
|- | |- | ||
| - | + | |NeXML | |
| - | | | + | |
| - | NeXML | + | |
|https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard | |https://www.nescent.org/wg_evoinfo/Future_Data_Exchange_Standard | ||
| - | |character data, | + | |character data, trees, models, meta-info |
| - | + | ||
| - | trees, models, meta-info | + | |
|in development | |in development | ||
|- | |- | ||
| - | pPOD | + | |pPOD |
| | | | ||
| - | |processing of data related to phylogenetic analysis | + | |processing of data related to phylogenetic analysis workflows |
| - | + | ||
| - | workflows | + | |
|in development | |in development | ||
|- | |- | ||
| - | CHADO | + | |CHADO |
|http://www.gmod.org/wiki/index.php/Schema | |http://www.gmod.org/wiki/index.php/Schema | ||
| - | |sequence, genotypes, | + | |sequence, genotypes, phenotypes, phylogenies |
| - | + | ||
| - | phenotypes, phylogenies | + | |
|used in GMOD | |used in GMOD | ||
|- | |- | ||
| - | 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 | ||
|- | |- | ||
| - | + | | | |
|- | |- | ||
| - | + | | | |
|- | |- | ||
| - | + | | | |
|- | |- | ||
| - | + | | | |
|- | |- | ||
|} | |} | ||
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 |
