Difference between revisions of "Questions and Issues Dec, 2011"
| Line 13: | Line 13: | ||
| − | =File format= | + | =GAF 2.0 File format= |
Columns | Columns | ||
| − | 1 | + | 1 Database: cosmoss_PpV1.2 |
| − | 2 | + | 2 Database_Object_ID: Pp1s47_77V2 |
| − | |||
| − | |||
| − | 3 | + | 3 Database_Object_symbol: if you have assigned a gene symbol the give that if not repeat |
| − | the value from column-2 | + | the value from column-2 Pp1s47_77V2 |
| − | 4 | + | 4 Qualifier: Optional |
| − | 5 | + | 5 PO:ID should go here |
| − | 6 | + | 6 Database:reference |
| + | provide a publication id with this expression data. | ||
If not available type in a PMID of the genome | If not available type in a PMID of the genome | ||
paper as of now. Current value e.g. GB:PHYPADRAFT_181133 is not | paper as of now. Current value e.g. GB:PHYPADRAFT_181133 is not | ||
acceptable. Looks like GB:PHYPADRAFT_181133 is an | acceptable. Looks like GB:PHYPADRAFT_181133 is an | ||
alias(synonym). | alias(synonym). | ||
| + | |||
7 this is fine as it stands | 7 this is fine as it stands | ||
| Line 64: | Line 64: | ||
17 provide the gene model id if you know one that's specific for | 17 provide the gene model id if you know one that's specific for | ||
expression (remember one model ID /lane). By default it is for | expression (remember one model ID /lane). By default it is for | ||
| − | the longest canonical/consensus gene model id. | + | the longest canonical/consensus gene model id. |
| − | |||
| − | |||
=GO Annotations= | =GO Annotations= | ||
Revision as of 02:24, 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).
7 this is fine as it stands
8 leave it blank for now
9 replace 'X' with 'S' if the PO id in column-5 is for anatomy.
'G' if the PO id in column 5 is for growth stage.
10 gene name if you have any. If not leave it blank.
11 list all the aliases (synonyms) and deprecated IDs separated by
the pipe (|) character. e.g. Phypa_181133|PHYPADRAFT_181133
12 replace 'transcript' by 'mRNA'
13 this is fine as it stands
14 this is fine as it stands
15 Is this expression data done by 'plantco.de' or 'COSMOSS'. If
they are the same I suggest putting 'COSMOSS' otherwise it's fine.
We are working on getting the following two columns to be added to all the annotation files. Therefore, please take this opportunity to do so for Physcomitrella.
16 Leave it bank for now
17 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,
