PO-Physco Webex Meeting July 18th 2011- Annotations

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Adding Physcomitrella annotations to PO terms: PO-Physco Webex Meeting July 18th, 2011

Webex Conference Call; Date: Tuesday Monday July 18th, 2011, 11am PDT/2 pm EDT/8pm Germany


In attendance: POC: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU)

Collaborators: Stefan Rensing and Daniel Lang (absent) of the Physcomitrella group, University of Freiburg, Germany Cosmoss Moss Ontology


Summary:

- PJ reviewed the important details about how the annotation files are prepared and uploaded to our SVN

Discussion points:

-microarray data cut-off points, based on established protocols. Reference page or published reference

-primary identifier should probably be gene locus id, transcript- something that is stable and can be used across multiple resources

-Separate file are required for the PO and GO annotations

-Separate PO file for anatomy terms and stages

-PO can host the GO annotation files as well (combined MF, BP, CC) in the new directory being developed

-Once the data is in the ontology, we can start to look at gene expression comparison between homologous anatomical structures for inclusion in the paper

-Gene orthology and paraology data sets are available for about 30 species

For future analysis;

-SR: dehydration, rehydration and ABA libraries are available for analysis

-could be compared with libraries in maize, rice, Arabidosis

-see paper: UV response, sporophytic and gametophytic phase specific genes, comparison with Craterostigma and Arabidopsis

-PJ will help them get set up to submit to GO, DL may have already started doing this, paper on new version of genome in preparation

Others?


Link to annotation file format info: Assoc files and for the GAF 2.0 format.

Action items

  • SR will send us a logo for Cosmoss
  • LC will send SR and DL a link to the GAF 2.0 Format
  • PO and Cosmoss will try to coordinate a time for a live webex demo for the Moss 2011 meeting Sept 12-14th (Monday through Weds). Must be between 9am-noon and 1pm-3pm European Summer time. LC will look into possible times.

Others?

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