Difference between revisions of "Annotation"
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* [[Textpresso]] is a text mining package for biological literature. | * [[Textpresso]] is a text mining package for biological literature. | ||
* [[PubSearch]] is a web-based literature curation tool to allow curators to search and annotate genes to keywords from articles. | * [[PubSearch]] is a web-based literature curation tool to allow curators to search and annotate genes to keywords from articles. | ||
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+ | == 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. | ||
[[Category:Annotation]] | [[Category:Annotation]] | ||
[[Category:GMOD Components]] | [[Category:GMOD Components]] |
Revision as of 12:27, 3 June 2009
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 (soon to be added) 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.
- PubSearch is a web-based literature curation tool to allow curators to search and annotate genes to keywords from articles.
Community Annotation
Community annotation is an area of growing interest to the GMOD community.