Difference between revisions of "Ensembl Database"
From LMU BioDB 2013
Kevinmcgee (Talk | contribs) (Added Answers to Ensembl Database project) |
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| − | # The database accessed is called Ensembl http://uswest.ensembl.org/index.html | + | #The database accessed is called Ensembl http://uswest.ensembl.org/index.html |
| − | # The purpose of this database is to collect, organize and distribute data resources to help support research regarding the genetics and genomics of chordates. [http://nar.oxfordjournals.org/content/41/D1/D48.full.pdf+html] | + | #The purpose of this database is to collect, organize and distribute data resources to help support research regarding the genetics and genomics of chordates. [http://nar.oxfordjournals.org/content/41/D1/D48.full.pdf+html] |
| − | # Ensembl contains genome information for 70 species. There is a focus on humans and major vertebrate model organisms, for example, the mouse, zebrafish and rat. [http://nar.oxfordjournals.org/content/41/D1/D48.full.pdf+html] | + | #Ensembl contains genome information for 70 species. There is a focus on humans and major vertebrate model organisms, for example, the mouse, zebrafish and rat. [http://nar.oxfordjournals.org/content/41/D1/D48.full.pdf+html] |
| − | # | + | #Ensembl contains 70 species on their site. Of these 70, 61 are fully supported and 58 of the 61 have full gene annotations. For a list of all the species contained on Ensembl, follow this link : http://uswest.ensembl.org/info/about/species.html |
| − | # | + | #Ensembl automatically annotates updated genomes, integrates it with other biological data and makes it available on the web. |
| − | # What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])? | + | #What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])? |
| − | # | + | #Ensembl is maintained jointly between the European Bioinfermatics Institute (EBI), which is a subsection of the European Molecular Biology Lab (EMBL) and the Wellcome Trust Sanger Institute (WTSI). Both the EBI and the WTSI are located on the same campus in Hinxton, United Kingdom. |
| − | + | #A majority of the funding for Ensembl comes from the Wellcome Trust, although they also receive funding from the National Human Genome Research Institute, the EMBL, and the Biotechnology and Biological Science Research Council. | |
| − | # | + | #All information can be publicly accessed on Ensembl. Ensembl has a license agreement stating that data can be redistributed, but it must be properly copyrighted back to them. |
| − | # | + | #Ensembl is updated on a monthly basis, and was last updated at the beginning of September. |
| − | # | + | #When Ensembl imports data from other sources, it links back to the original resource of information. |
| − | # | + | # Information can be downloaded in a variety of ways, and can run up to many gigabytes of information. Data can be downloaded in the following file formats: FASTA, annotated sequence, MySQL, GTF, EMF flatfile dumps, GVF, BED format files, Tarball |
| − | + | # The website is very user friendly and very organized. At the top, the first button on the navigation bar is called “Using This Website” clicking on it brings you to a help page with a navigation bar on the side leading to brief tutorials of the site’s features. | |
| − | # | + | |
| − | + | ||
| − | + | ||
#* Run a sample query. Do the results make sense? | #* Run a sample query. Do the results make sense? | ||
| − | [[User:Vkuehn| Viktoria Kuehn]] | + | [[User:Vkuehn| Viktoria Kuehn]] [[User:Kevinmcgee | Kevin McGee]] |
[[Week 5]] | [[Week 5]] | ||
Revision as of 22:27, 29 September 2013
- The database accessed is called Ensembl http://uswest.ensembl.org/index.html
- The purpose of this database is to collect, organize and distribute data resources to help support research regarding the genetics and genomics of chordates. [1]
- Ensembl contains genome information for 70 species. There is a focus on humans and major vertebrate model organisms, for example, the mouse, zebrafish and rat. [2]
- Ensembl contains 70 species on their site. Of these 70, 61 are fully supported and 58 of the 61 have full gene annotations. For a list of all the species contained on Ensembl, follow this link : http://uswest.ensembl.org/info/about/species.html
- Ensembl automatically annotates updated genomes, integrates it with other biological data and makes it available on the web.
- What type (or types) of database is it (sequence, structure model organism, or specialty [what?]; primary or “meta”; curated electronically, manually [in-house], manually [community])?
- Ensembl is maintained jointly between the European Bioinfermatics Institute (EBI), which is a subsection of the European Molecular Biology Lab (EMBL) and the Wellcome Trust Sanger Institute (WTSI). Both the EBI and the WTSI are located on the same campus in Hinxton, United Kingdom.
- A majority of the funding for Ensembl comes from the Wellcome Trust, although they also receive funding from the National Human Genome Research Institute, the EMBL, and the Biotechnology and Biological Science Research Council.
- All information can be publicly accessed on Ensembl. Ensembl has a license agreement stating that data can be redistributed, but it must be properly copyrighted back to them.
- Ensembl is updated on a monthly basis, and was last updated at the beginning of September.
- When Ensembl imports data from other sources, it links back to the original resource of information.
- Information can be downloaded in a variety of ways, and can run up to many gigabytes of information. Data can be downloaded in the following file formats: FASTA, annotated sequence, MySQL, GTF, EMF flatfile dumps, GVF, BED format files, Tarball
- The website is very user friendly and very organized. At the top, the first button on the navigation bar is called “Using This Website” clicking on it brings you to a help page with a navigation bar on the side leading to brief tutorials of the site’s features.
- Run a sample query. Do the results make sense?
