Home of the SEED - Revision history

TerryDisz at 20:52, 11 June 2010

2010-06-11T20:52:03Z

2009-11-23T20:03:02Z

added link to FIGfam page

2008-12-18T20:31:31Z

2008-12-18T20:29:44Z

2008-12-18T20:26:30Z

2008-12-18T20:25:29Z

2008-12-18T20:22:21Z

2008-12-18T20:21:59Z

2008-12-18T20:18:58Z

2008-12-18T20:09:18Z

← Older revision		Revision as of 20:52, 11 June 2010
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	[[Image:Data_lifecycle3.png\|frame\|thumbnail\|50px\|Flow of data in the SEED.]]		[[Image:Data_lifecycle3.png\|frame\|thumbnail\|50px\|Flow of data in the SEED.]]

−	Curation of genomic data ([[Glossary#Annotation\|annotation]]) is done via the curation of [[Glossary#Subsystem\|subsystems]] by an expert annotator across many genomes, not ~~one~~ a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes\|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([http://seed-viewer.theseed.org/seedviewer.cgi?page=FigFamViewer FIGfams]). These FIGfams form the core component of our RAST automated annotation technology.	+	Curation of genomic data ([[Glossary#Annotation\|annotation]]) is done via the curation of [[Glossary#Subsystem\|subsystems]] by an expert annotator across many genomes, not on a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes\|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([http://seed-viewer.theseed.org/seedviewer.cgi?page=FigFamViewer FIGfams]). These FIGfams form the core component of our RAST automated annotation technology.

← Older revision		Revision as of 20:03, 23 November 2009
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	[[Image:Data_lifecycle3.png\|frame\|thumbnail\|50px\|Flow of data in the SEED.]]		[[Image:Data_lifecycle3.png\|frame\|thumbnail\|50px\|Flow of data in the SEED.]]

−	Curation of genomic data ([[Glossary#Annotation\|annotation]]) is done via the curation of [[Glossary#Subsystem\|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes\|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([~~[Glossary#FIGfam\|~~FIGfams]]). These FIGfams form the core component of our RAST automated annotation technology.	+	Curation of genomic data ([[Glossary#Annotation\|annotation]]) is done via the curation of [[Glossary#Subsystem\|subsystems]] by an expert annotator across many genomes, not one a gene by gene basis. This is also detailed in our [[Annotating_1000_genomes\|manifesto]]. From the curated subsystems we extract a set of freely available protein families ([http://seed-viewer.theseed.org/seedviewer.cgi?page=FigFamViewer FIGfams]). These FIGfams form the core component of our RAST automated annotation technology.

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 * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
 * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures].
-* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using | Publications] page.
+* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using Publications] page.

@@ Line 13: / Line 13: @@
 * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
 * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures].
-* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using| Publications] page.
+* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using | Publications] page.

@@ Line 13: / Line 13: @@
 * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
 * Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures].
-* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using%20our%20tools| Publications] page.
+* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications#Using| Publications] page.

@@ Line 12: / Line 12: @@
 * We request that groups  using the SEED cite: Overbeek et al., [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16214803&query_hl=2&itool=pubmed_docsum|Nucleic Nucleic Acids Res 33(17)], 2005  ([http://www.theseed.org/SubsystemPaperSupplementalMaterial/index.html Supplementary material])
 * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
-* Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome|Standard Operating Procedures].
+* Our approaches to annotation, gene calling, etc. are outlined in a series of [http://www.nmpdr.org/FIG/wiki/view.cgi/SOP/WebHome| Standard Operating Procedures].
 * Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications] page.

@@ Line 13: / Line 13: @@
 * We request that groups using the RAST server cite: Aziz et al., [http://www.ncbi.nlm.nih.gov/pubmed/18261238?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum| BMC Genomics], 2008 ([http://www.theseed.org/RASTPaperSupplementalMaterial/index.html Supplementary material])
 * Our approaches to annotation, gene calling etc are outlined in a series of [[SOPs|Standard Operating Procedures]].
-* Read about how other groups have used our tools in their research on our [http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications|Publications] page.
+* Read about how other groups have used our tools in their research on our [[http://www.nmpdr.org/FIG/wiki/view.cgi/Main/Publications| Publications]] page.