Annotation Conf. Call 2019-05-14: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
 
(12 intermediate revisions by 3 users not shown)
Line 6: Line 6:


=== Communication ===
=== Communication ===
** Remind people about [https://gitter.im/geneontology/go-annotation Gitter] as an option to communicate with other curators
* Remind people about [https://gitter.im/geneontology/go-annotation Gitter] as an option to communicate with other curators


=== Transcription Factor Annotations ===
=== Transcription Factor Annotations ===
* TF annotations: All: People will need to migrate transcription factor annotations to specific TF binding terms to use GO+SO extensions
* TF annotations: All: People will need to migrate transcription factor annotations to specific TF binding terms to use GO+SO extensions
Only 2 terms found in SO so far:
{|
|-
! EXP annotations
! GO term
! SO term
|-
| 114
| GO:0070888 E-box binding
| SO:0001158 E_box_motif
|-
| 12
| GO:0035497 cAMP response element binding
| SO:0001843 CRE
|-
| 10
| GO:0034056 estrogen response element binding
|
|-
| 3
| GO:0035538 carbohydrate response element binding
|
|-
| 2
| GO:0070594 juvenile hormone response element binding
|
|-
| 3
| GO:0071820 N-box binding
|
|-
| 8
| GO:0044323 retinoic acid-responsive element binding
|
|-
| 5
| GO:0010736 serum response element binding
|
|-
| 4
| GO:0032810 sterol response element binding
|
|-
| 5
| GO:0070644 vitamin D response element binding
|
|}


=== PAINT ===
=== PAINT ===
Line 15: Line 64:


=== Annotation Pipelines ===
=== Annotation Pipelines ===
* Annotation pipelines and guidelines: We'd like to have information about each group's annotation guidelines and how annotations are processes and presented/exporter to users.  
* Annotation pipelines and guidelines: We'd like to have information about each group's annotation guidelines and how annotations are processes and presented/exporter to users.
* This is somewhat more detailed information on annotation file management than what we were able to collect on the survey.
* Laying the groundwork for more consistency in annotation.
** What do groups import? What do groups filter?
* WB and Zfin have added their [https://drive.google.com/drive/folders/1Lq6agbunvqGZ3pZwOfQYhKVNOUPr5DQx documentation].


== MOD Import into Noctua ==
== MOD Import into Noctua ==
*MGI and WB are working on a pipeline to import all of their manual annotations into Noctua
* MGI and WB are working on a pipeline to import all of their manual annotations into Noctua
* https://github.com/geneontology/gocamgen/issues
* Updates:
**With/From now imported; protein binding -> has_input
**Basic annotation extensions
* Guidelines on the wiki:  http://wiki.geneontology.org/index.php/Noctua_MOD_Imports
* Spreadsheet for testing: https://docs.google.com/spreadsheets/d/1XFuD6LOyFKXNk94jIK8zv1TrESfwCJo-RnrXQ3tzmJg
 
== Matrisome Project ==
* Several in-silico analyses for different organisms have produced a protein set identified as the 'matrisome' - comprehensive list of ECM proteins
* Rachael Huntley annotated mammalian matrisome
* Other groups have been contacted - WB, FlyBase, Zfin (?)
* It would be good to make sure we are annotating this work consistently
* Future call to discuss?
 
= Minutes =
*Present: David, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Judy, Karen, Kevin M, Laurent-Philippe, Li, Marie-Claire, Midori, Pascale, Patrick M, Petra, Rob, Sabrina, Shur-Jen, Stacia, Suzi A, Tanya


[[Category:Annotation Working Group]]
[[Category:Annotation Working Group]]

Latest revision as of 11:32, 14 May 2019

Agenda

GOC meeting debrief/announcements

Communication

  • Remind people about Gitter as an option to communicate with other curators

Transcription Factor Annotations

  • TF annotations: All: People will need to migrate transcription factor annotations to specific TF binding terms to use GO+SO extensions

Only 2 terms found in SO so far:

 EXP annotations GO term SO term
114 GO:0070888 E-box binding SO:0001158 E_box_motif
12 GO:0035497 cAMP response element binding SO:0001843 CRE
10 GO:0034056 estrogen response element binding
3 GO:0035538 carbohydrate response element binding
2 GO:0070594 juvenile hormone response element binding
3 GO:0071820 N-box binding
8 GO:0044323 retinoic acid-responsive element binding
5 GO:0010736 serum response element binding
4 GO:0032810 sterol response element binding
5 GO:0070644 vitamin D response element binding

PAINT

  • Remind people they can provide guidance for PAINT annotation: PAINT Annotations: to prevent over-propagation to paralogs: submit GitHub tickets explaining that the list of gene products associated with this process is complete and that paralogs should not be associated with the term.

Annotation Pipelines

  • Annotation pipelines and guidelines: We'd like to have information about each group's annotation guidelines and how annotations are processes and presented/exporter to users.
  • This is somewhat more detailed information on annotation file management than what we were able to collect on the survey.
  • Laying the groundwork for more consistency in annotation.
    • What do groups import? What do groups filter?
  • WB and Zfin have added their documentation.

MOD Import into Noctua

Matrisome Project

  • Several in-silico analyses for different organisms have produced a protein set identified as the 'matrisome' - comprehensive list of ECM proteins
  • Rachael Huntley annotated mammalian matrisome
  • Other groups have been contacted - WB, FlyBase, Zfin (?)
  • It would be good to make sure we are annotating this work consistently
  • Future call to discuss?

Minutes

  • Present: David, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Judy, Karen, Kevin M, Laurent-Philippe, Li, Marie-Claire, Midori, Pascale, Patrick M, Petra, Rob, Sabrina, Shur-Jen, Stacia, Suzi A, Tanya