JP Mar 17 16 - Revision history

Jupreziosi at 18:54, 17 March 2016

2016-03-17T18:54:45Z

2016-03-17T18:53:57Z

2016-03-17T18:53:52Z

2016-03-17T18:51:52Z

2016-03-17T18:32:41Z

2016-03-17T18:05:04Z

2016-03-17T18:02:27Z

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2016-03-17T17:48:43Z

← Older revision		Revision as of 18:54, 17 March 2016
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	Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.		Want to map the whole transcriptome (relative expressions?) GO Slim terms and compare to gene of interest (relative expression?) GO Slim terms.
		+
		+	Wrote a code to extract gene id from a list of given gene names. Needed to manually search the gene id for the translated POUFs.

← Older revision		Revision as of 18:53, 17 March 2016
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	*this looks promising		*this looks promising
		+

	Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.		Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

@@ Line 16: / Line 16: @@
 using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo
 *nothing
 Using generic human given by website
 Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

← Older revision		Revision as of 18:51, 17 March 2016
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	using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo		using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo
		+	*nothing
		+	Using generic human given by website

← Older revision		Revision as of 18:32, 17 March 2016
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	Resources:		Resources:
		+
		+	Generic GO term Mapper:
		+
		+	http://go.princeton.edu/cgi-bin/GOTermMapper
		+
		+	using the goslim_generic.obo from the OWLTools page: http://www.geneontology.org/ontology/subsets/goslim_generic.obo
		+

	Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.		Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.

← Older revision		Revision as of 18:05, 17 March 2016
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	http://www.animalgenome.org/bioinfo/tools/catego/		http://www.animalgenome.org/bioinfo/tools/catego/
		+
		+
		+	g:
		+
		+	http://biit.cs.ut.ee/gprofiler/gconvert.cgi

@@ Line 9: / Line 9: @@
-Resource:
+Resources:
 Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.
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 http://geneontology.org/page/go-slim-and-subset-guide

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 Wrote our first status report after our oral presentation on the 15th.
 GO Slim:
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 Resource:
-Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. This script is an option of OWLTools, and it can be used to either create a new gene association file, which contains the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term."
+Map2Slim option in OWLTools: "Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim.
 http://geneontology.org/page/go-slim-and-subset-guide