Annotation Conf. Call 2019-05-14: Difference between revisions
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Only 2 terms found in SO so far: | Only 2 terms found in SO so far: | ||
|| EXP annotations | {| | ||
| 114 | GO:0070888 E-box binding | SO:0001158 E_box_motif | |- | ||
| 12 | GO:0035497 cAMP response element binding | SO:0001843 CRE | ! EXP annotations | ||
| 10 | GO:0034056 estrogen response element binding | | ! GO term | ||
| 3 | GO:0035538 carbohydrate response element binding | | ! SO term | ||
| 2 | GO:0070594 juvenile hormone response element binding | | |- | ||
| 3 | GO:0071820 N-box binding | | | 114 | ||
| 8 | GO:0044323 retinoic acid-responsive element binding | | | GO:0070888 E-box binding | ||
| 5 | GO:0010736 serum response element binding | | | SO:0001158 E_box_motif | ||
| 4 | GO:0032810 sterol response element binding | | |- | ||
| 5 | GO:0070644 vitamin D response element binding| | | 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 30: | Line 65: | ||
=== 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 = | = Minutes = | ||
*Present: | *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
- 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