Questions and Issues Dec, 2011 - Revision history

Cooperl: moved Questions and Issues Nov,2011 to Questions and Issues Dec, 2011

2011-12-20T22:03:55Z

2011-12-20T22:03:28Z

2011-12-20T22:02:19Z

2011-12-15T19:01:08Z

Notes from email (12-15-11) about Accession names and numbers:

2011-12-15T19:00:55Z

Notes from email (12-15-11) about Accession names and numbers:

2011-12-15T18:57:33Z

Notes from email (12-15-11) about the database versions:

2011-12-15T18:56:52Z

DbxRefs for Annotations

2011-12-15T18:56:31Z

DbxRefs for Annotations

2011-12-15T17:53:41Z

DbxRefs for Annotations

2011-12-15T17:53:27Z

DbxRefs for Annotations

@@ Line 7: / Line 7: @@
-Info about Physco on Genevestigator
+Info about Physco on [https://www.genevestigator.com Genevestigator]:
 "In its figures, Genevestigator displays expression values from probesets, because these are the real physical entities that were measured on the microarrays. However, you can enter gene identifiers in a variety of formats, and Genevestigator will search for probe sets that represent these genes on the microarrays. CLASSIC and ADVANCED user can use asterisks (*) for wildcard searches.
 For the selected Organism / Array type, the following gene identifier formats are available:
-• NCBI Gene (e.g. phypadraft_128494) • Phytozome (e.g. Phypa_64616) • Cosmoss (e.g. Phypa_161460) • PLAZA (e.g. 152715)
+• NCBI Gene (e.g. phypadraft_128494)

← Older revision		Revision as of 22:02, 20 December 2011
Line 4:		Line 4:

	Go to: [[Background info on Physco biology and culture]]		Go to: [[Background info on Physco biology and culture]]
		+
		+
		+
		+	Info about Physco on Genevestigator
		+	"In its figures, Genevestigator displays expression values from probesets, because these are the real physical entities that were measured on the microarrays. However, you can enter gene identifiers in a variety of formats, and Genevestigator will search for probe sets that represent these genes on the microarrays. CLASSIC and ADVANCED user can use asterisks (*) for wildcard searches.
		+	For the selected Organism / Array type, the following gene identifier formats are available:
		+	• NCBI Gene (e.g. phypadraft_128494) • Phytozome (e.g. Phypa_64616) • Cosmoss (e.g. Phypa_161460) • PLAZA (e.g. 152715)
		+
		+
		+

	Excepted from email exchanges:		Excepted from email exchanges:

@@ Line 55: / Line 55: @@
 The number after the decimal point is the '''version of the annotation''' (V6): i.e V1.6 is assembly 1 annotation 6.
 *Issue to be aware of:
@@ Line 62: / Line 61: @@
 This has the glitch that V1.2 entries are listed as belonging to the "playground" database.

@@ Line 55: / Line 55: @@
 The number after the decimal point is the '''version of the annotation''' (V6): i.e V1.6 is assembly 1 annotation 6.
 '''Numbering the Cosmoss Gene ID (CGI):'''
@@ Line 60: / Line 70: @@
 The trailing  \.\d+ i.e. .1 in Pp1s2_12V6.1 refers to splice variant 1.
-*V1.6 was the first annotation release to contain splice variants
+In V1.2 all transcripts/proteins have .1 (in theory). The exception to this rule is split genes: if a locus was split in two models in V1.2 the two genes have .1 and .2.  V1.6 was the first annotation release to contain splice variants

← Older revision		Revision as of 18:57, 15 December 2011
Line 48:		Line 48:


−	==Notes from email (12-15-11) about ~~the database versions~~:==	+	==Notes from email (12-15-11) about Accession names and numbers:==

	'''Numbering the Cosmoss Assembly versions:'''		'''Numbering the Cosmoss Assembly versions:'''

← Older revision	Revision as of 22:03, 20 December 2011
(No difference)

← Older revision		Revision as of 18:56, 15 December 2011
Line 48:		Line 48:


−	*Notes from email (12-15-11) about the database versions:	+	==Notes from email (12-15-11) about the database versions:==

	'''Numbering the Cosmoss Assembly versions:'''		'''Numbering the Cosmoss Assembly versions:'''

@@ Line 27: / Line 27: @@
 url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225
@@ Line 43: / Line 42: @@
 generic_url: https://www.cosmoss.org/annotation/genonaut
-url_syntax: https://www.cosmoss.org/annotation/genonaut/annotation/search?accession=[example_id]
+url_syntax: https://www.cosmoss.org/annotation/genonaut?accession=ACCESSION&version=V1.2
-url_example: https://www.cosmoss.org/annotation/genonaut/annotation/search?accession=Pp1s47_79V6.1
+*V1.6 was the first annotation release to contain splice variants
 See helpful link to [https://www.cosmoss.org/physcome_project/wiki/CGI Cosmoss gene ID wiki]

@@ Line 50: / Line 50: @@
 Problem exists that the web page https://www.cosmoss.org/annotation/genonaut does not have pages for many of the genes in the file
-Helpful link to [https://www.cosmoss.org/physcome_project/wiki/CGI Cosmoss gene ID wiki]
+See helpful link to [https://www.cosmoss.org/physcome_project/wiki/CGI Cosmoss gene ID wiki]
 =GAF 2.0 File format=

← Older revision		Revision as of 17:53, 15 December 2011
Line 49:		Line 49:

	Problem exists that the web page https://www.cosmoss.org/annotation/genonaut does not have pages for many of the genes in the file		Problem exists that the web page https://www.cosmoss.org/annotation/genonaut does not have pages for many of the genes in the file
		+
		+	Helpful link to [https://www.cosmoss.org/physcome_project/wiki/CGI Cosmoss gene ID wiki]

	=GAF 2.0 File format=		=GAF 2.0 File format=