Questions and Issues Dec, 2011

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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:

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.

should be PMID:18079367|GB:PHYPADRAFT_181133|PMID:18762443

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.

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.


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,

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