Questions and Issues Dec, 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:

DbxRefs for Annotations

Need to create stanza

maizeGDB example:

abbreviation: MaizeGDB

database: Maize Genetics and Genomics Database

object: Anything with a MaizeGDB Object ID Number or Gene Model Name

example_id: MaizeGDB:881225

generic_url: http://www.maizegdb.org/

url_syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]

url_example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225

Physcomitrella Proposed, based on the assoc file:

abbreviation: cosmoss_PpV1.2

database: plantco.de|cosmoss.org

object: Anything with a Cosmoss accession number

example_id: cosmoss_PpV1.2:Pp1s47_77V2.1

generic_url: https://www.cosmoss.org/annotation/genonaut

url_syntax: https://www.cosmoss.org/annotation/genonaut/annotation/search?accession=[example_id]

url_example: https://www.cosmoss.org/annotation/genonaut/annotation/search?accession=Pp1s47_79V6.1

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 Cosmoss gene ID wiki

GAF 2.0 File format

Example from *.gaf2 file

Columns

1. Database: cosmoss_PpV1.2

2. Database_Object_ID: Pp1s47_77V2 This is fine

For more info on the 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. Note: may have more than 1 but only the last one is displayed.

current: GB:PHYPADRAFT_181133|PMID:18762443|PMID:18079367 (this is fine)

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.

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.

What is the status of this?

GO Annotations

DL sent a GOA file and it looks like the same format that we would need for the structure terms. Need to find out how to go about getting them submitted to the GO