Manager Call 2016-03-2: Difference between revisions

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Update:  
Update:  


Following recommendations from a previous call, Paola sent to ELIXIR a revised version of the tools registry that does NOT include MOD-specific tools (i.e. MGI GO Browser, SGD Gene Ontology Slim Mapper, YeastMine) nor OBO-Edit. Anyone wishing for their MOD-specific tool to be listed in ELIXIR, please contact them separately. FYI, list is visible at https://docs.google.com/spreadsheets/d/1-Gu6EhBXTDr35vOU2MwUVOzGAWXTAkIdARdad9UShRw/edit#gid=1268003428
Following recommendations from a previous call, Paola sent to ELIXIR a revised version of the tools registry that does NOT include MOD-specific tools (i.e. MGI GO Browser, SGD Gene Ontology Slim Mapper, YeastMine) nor OBO-Edit. Anyone wishing for their MOD-specific tool to be listed in ELIXIR, please contact them separately. FYI, list sent to ELIXIR is visible at https://docs.google.com/spreadsheets/d/1-Gu6EhBXTDr35vOU2MwUVOzGAWXTAkIdARdad9UShRw/edit#gid=1268003428
 
Jon Ison alerts that "It may take some time for the entries to appear in bio.tools because it depends on a XSL->XML transformer which is under development".
 
Paola asked Jon how will these tools be labeled to show that they are GO-approved. Answer: "As for "GO approved", there's no support for that currently, however it will be considered in biotoolXSD 2.0, as an
annotation on general "collections" such as this: https://github.com/bio-tools/biotoolsxsd/issues/16"
 
Once that is in place, we may evaluate linking out from ELIXIR to GO.


Paola also added GOrilla among recommended third-party enrichment tools on the GO website, here http://geneontology.org/page/go-enrichment-analysis
Paola also added GOrilla among recommended third-party enrichment tools on the GO website, here http://geneontology.org/page/go-enrichment-analysis


Paola asked Jon Ison how will these tools be labeled to show that they are GO-approved. Will report back. Based on that, we may evaluate linking out from there (ELIXIR) to GO.
===GOC meeting agenda===
* Please add items to [[2016_Geneva_GOC_Meeting_Agenda]]
 
===GPAD changes for annotation provenance===
At the next GOA release (this month) we will announce changes to the GPAD format to accommodate tracking of annotation provenance. We will create new GPAD files with the extended columns, i.e., including source annotations for inference. External imports into GOA have been modified to capture details of the original MOD annotations. We will updated the GPAD specification to 1.2 (with the 11 extra columns). Difference with what was proposed at the Washington meeting is that all columns from the original annotation are being stored not just subset.
 
 
===Project Update===
We (Paola, David, Karen, Peter, Melanie) have begun working with Peter to align GO cilia-related processes with those in Reactome.




[[Category:GO Managers Meetings]]
[[Category:GO Managers Meetings]]

Latest revision as of 12:10, 2 March 2016

Follow-up on GO tools registry

For background, see

http://wiki.geneontology.org/index.php/Manager_Call_2016-02-03#GO_tools_registry

http://wiki.geneontology.org/index.php/Manager_Call_2016-02-03#GO_Tools_Registry_2

Update:

Following recommendations from a previous call, Paola sent to ELIXIR a revised version of the tools registry that does NOT include MOD-specific tools (i.e. MGI GO Browser, SGD Gene Ontology Slim Mapper, YeastMine) nor OBO-Edit. Anyone wishing for their MOD-specific tool to be listed in ELIXIR, please contact them separately. FYI, list sent to ELIXIR is visible at https://docs.google.com/spreadsheets/d/1-Gu6EhBXTDr35vOU2MwUVOzGAWXTAkIdARdad9UShRw/edit#gid=1268003428

Jon Ison alerts that "It may take some time for the entries to appear in bio.tools because it depends on a XSL->XML transformer which is under development".

Paola asked Jon how will these tools be labeled to show that they are GO-approved. Answer: "As for "GO approved", there's no support for that currently, however it will be considered in biotoolXSD 2.0, as an annotation on general "collections" such as this: https://github.com/bio-tools/biotoolsxsd/issues/16"

Once that is in place, we may evaluate linking out from ELIXIR to GO.

Paola also added GOrilla among recommended third-party enrichment tools on the GO website, here http://geneontology.org/page/go-enrichment-analysis

GOC meeting agenda

GPAD changes for annotation provenance

At the next GOA release (this month) we will announce changes to the GPAD format to accommodate tracking of annotation provenance. We will create new GPAD files with the extended columns, i.e., including source annotations for inference. External imports into GOA have been modified to capture details of the original MOD annotations. We will updated the GPAD specification to 1.2 (with the 11 extra columns). Difference with what was proposed at the Washington meeting is that all columns from the original annotation are being stored not just subset.


Project Update

We (Paola, David, Karen, Peter, Melanie) have begun working with Peter to align GO cilia-related processes with those in Reactome.

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