Annotation Conf. Call 2019-05-14
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, Petra, Rob, Sabrina, Shur-Jen, Stacia, Suzi A, Tanya