Difference between revisions of "Annotation"
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| − | Supporting annotation of biological data is a central goal of GMOD. Annotation can be done computationally or manually using | + | Supporting annotation of biological data is a central goal of GMOD. Annotation can be done computationally or manually using [[:Category:Community Annotation|community annotation]] or by [http://biocurator.org/ dedicated curatorial staff]. |
This page is about ''creating'' annotations. GMOD also has a number of solutions for ''[[Visualization|visualizing]]'' annotations. | This page is about ''creating'' annotations. GMOD also has a number of solutions for ''[[Visualization|visualizing]]'' annotations. | ||
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=== Computational Genome Annotation === | === Computational Genome Annotation === | ||
| + | <div class="emphasisbox"><div style="font-size: 120%"><center>"Genome annotation, not genome sequencing, is becoming the bottleneck in genomics today."</center></div> | ||
| + | <div style="text-align: right; font-size: 90%"> | ||
| + | First line of the [[MAKER]] paper.</div></div> | ||
* [[MAKER]] is a pipeline for annotating eukayotic genomic data. | * [[MAKER]] is a pipeline for annotating eukayotic genomic data. | ||
| − | * DIYA is a | + | * [[DIYA]] is a pipeline for annotation prokaryotic genomic data. |
* [[Ergatis]] is a web-based utility for creating and running reusable computational analysis pipelines. | * [[Ergatis]] is a web-based utility for creating and running reusable computational analysis pipelines. | ||
* [[Galaxy]] allows users to search remote resources, combine data from independent queries, and visualize/save the results. | * [[Galaxy]] allows users to search remote resources, combine data from independent queries, and visualize/save the results. | ||
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* [[Textpresso]] is a text mining package for biological literature. | * [[Textpresso]] is a text mining package for biological literature. | ||
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| − | [[Category:Community Annotation|community annotation | + | == Community Annotation == |
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| + | [[:Category:Community Annotation|Community annotation]] is an area of growing interest to the GMOD community. | ||
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| + | * [[Apollo]] is used in several community annotation efforts to maintain and curate genomic data. | ||
| + | * [[TableEdit]] is a popular [http://mediawiki.org/ MediaWiki] extension for updating tabular and database data. Work is currently under way to build a wiki front end to [[Chado]] using TableEdit. | ||
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[[Category:Annotation]] | [[Category:Annotation]] | ||
| + | [[Category:GMOD Components]] | ||
Latest revision as of 22:08, 29 October 2010
Supporting annotation of biological data is a central goal of GMOD. Annotation can be done computationally or manually using community annotation or by dedicated curatorial staff.
This page is about creating annotations. GMOD also has a number of solutions for visualizing annotations.
Contents
Genome Annotation
Manual Genome Annotation
- Apollo is the manual genome annotation tool of choice for GMOD users.
Computational Genome Annotation
First line of the MAKER paper.
- MAKER is a pipeline for annotating eukayotic genomic data.
- DIYA is a pipeline for annotation prokaryotic genomic data.
- Ergatis is a web-based utility for creating and running reusable computational analysis pipelines.
- Galaxy allows users to search remote resources, combine data from independent queries, and visualize/save the results.
- Genome grid project is a package of genome data analysis with methods, protocols, and documentation.
Publication Annotation
- Textpresso is a text mining package for biological literature.
Community Annotation
Community annotation is an area of growing interest to the GMOD community.
