Difference between revisions of "Questions and Issues Dec, 2011"
| Line 20: | Line 20: | ||
2 Database_Object_ID: Pp1s47_77V2 | 2 Database_Object_ID: Pp1s47_77V2 | ||
| − | 3 Database_Object_symbol: if you have assigned a gene symbol the give that if not repeat | + | 3 Database_Object_symbol: if you have assigned a gene symbol the give that if not repeat the value from column-2 Pp1s47_77V2 |
| − | |||
4 Qualifier: Optional | 4 Qualifier: Optional | ||
| Line 27: | Line 26: | ||
5 PO:ID should go here | 5 PO:ID should go here | ||
| − | 6 Database:reference | + | 6 Database:reference (provide a publication id with this expression data. If not available type in a PMID of the genome paper as of now. Current value e.g. GB:PHYPADRAFT_181133 is not acceptable. Looks like GB:PHYPADRAFT_181133 is an alias(synonym). |
| − | provide a publication id with this expression data. | + | Note: may have more than 1 but only the 1st one is displayed. |
| − | |||
| − | |||
| − | |||
| − | |||
| + | current: GB:PHYPADRAFT_181133|PMID:18762443|PMID:18079367 | ||
| − | + | PMID:18762443 Lang,et al. (2008). Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends in Plant Science, 13, 542-549. | |
| − | + | PMID:18079367 Rensing et al. (2008). The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319, 64-69. | |
| − | |||
| − | |||
| − | + | 7 Evidence code: IEP | |
| − | + | 8 with or from: leave it blank for now | |
| − | |||
| − | + | 9 Aspect 'A' if the PO id in column-5 is for anatomy-ok | |
| − | + | 10 Database_Object_name: gene name if you have any. If not leave it blank.optional | |
| − | + | 11 Synonym: list all the aliases (synonyms) and deprecated IDs separated by the pipe (|) character. e.g. Phypa_181133|PHYPADRAFT_181133 | |
| − | + | ||
| − | + | 12 Database_Object_type: 'mRNA' ok | |
| − | |||
| − | |||
| + | 13 taxon: this is fine as it stands | ||
| − | + | 14 date: this is fine as it stands | |
| + | |||
| + | 15 Assigned_by: plantco.de|cosmoss.org ok | ||
| − | 16 | + | 16 Annotation_extension: TBA |
| − | 17 | + | 17 Gene product form ID: provide the gene model id if you know one that's specific for expression (remember one model ID /lane). By default it is for the longest canonical/consensus gene model id. |
| − | |||
| − | |||
=GO Annotations= | =GO Annotations= | ||
Revision as of 02:49, 15 November 2011
Go back to: Cosmoss-_Physcomitrella page
Also see Cosmoss, the Physcomitrella patens resource site.
Go to:Background info on Physco biology and culture
Excepted from email exchanges:
Reference page for the microarray data
It would be helpful to have a reference page or published reference to the microarray data cut-off points, based on established protocols.
SR: We are already working on converting all expression data that will go public via Genevestigator after the conference.
GAF 2.0 File format
Columns 1 Database: cosmoss_PpV1.2
2 Database_Object_ID: Pp1s47_77V2
3 Database_Object_symbol: if you have assigned a gene symbol the give that if not repeat the value from column-2 Pp1s47_77V2
4 Qualifier: Optional
5 PO:ID should go here
6 Database:reference (provide a publication id with this expression data. If not available type in a PMID of the genome paper as of now. Current value e.g. GB:PHYPADRAFT_181133 is not acceptable. Looks like GB:PHYPADRAFT_181133 is an alias(synonym). Note: may have more than 1 but only the 1st one is displayed.
current: GB:PHYPADRAFT_181133|PMID:18762443|PMID:18079367
PMID:18762443 Lang,et al. (2008). Exploring plant biodiversity: the Physcomitrella genome and beyond. Trends in Plant Science, 13, 542-549.
PMID:18079367 Rensing et al. (2008). The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science, 319, 64-69.
7 Evidence code: IEP
8 with or from: leave it blank for now
9 Aspect 'A' if the PO id in column-5 is for anatomy-ok
10 Database_Object_name: gene name if you have any. If not leave it blank.optional
11 Synonym: list all the aliases (synonyms) and deprecated IDs separated by the pipe (|) character. e.g. Phypa_181133|PHYPADRAFT_181133
12 Database_Object_type: 'mRNA' ok
13 taxon: this is fine as it stands
14 date: this is fine as it stands
15 Assigned_by: plantco.de|cosmoss.org ok
16 Annotation_extension: TBA
17 Gene product form ID: provide the gene model id if you know one that's specific for expression (remember one model ID /lane). By default it is for the longest canonical/consensus gene model id.
GO Annotations
DL sent a GOA file and it looks like the same format that we would need for the structure terms. I am not sure how to go about getting them submitted to the GO- Pankaj,
