2013 Bar Harbor GOC Meeting Agenda: Difference between revisions
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===Thurs 3 Oct (Pre-Meeting Working Groups)=== | ===Thurs 3 Oct (Pre-Meeting Working Groups)=== | ||
These pre-meeting working groups will meet at [http://www.jax.org/about/directions.html The Jackson Laboratory]. Please arrive 30 minutes before the session you wish to attend so you can get a badge and escort. | These pre-meeting working groups will meet at [http://www.jax.org/about/directions.html The Jackson Laboratory]. Please arrive 30 minutes before the session you wish to attend so you can get a badge and escort. | ||
* 9:30am - 10:30am '''Web documentation, Drupal transition''' (room ERB 1421) | * 9:30am - 10:30am '''Web documentation, Drupal transition''' (room ERB 1421) | ||
Line 13: | Line 11: | ||
** 4:00pm - 5:00pm '''PAINT''' group discussion: This is a working group meeting for those PAINT curators and developers in town on Thur. (room NRB 3035) | ** 4:00pm - 5:00pm '''PAINT''' group discussion: This is a working group meeting for those PAINT curators and developers in town on Thur. (room NRB 3035) | ||
===Friday 4 Oct | ==Agenda== | ||
The SAB report from April 2013 (Cambridge) was very specific and productive [https://docs.google.com/document/d/1njii8D0XLCS-c1hdjs8hH1IbPwj0Qcc-Z7JgfxTseFo/edit]. We will be meeting with them again in March 2014 and need to show progress on their useful recommendations. Therefore the focus of this meeting is to identify targeted projects that we can demonstrate to them in the (roughly) six intervening months. Establishing priorities, point people who will handle coordination, and monthly milestones. | |||
===Friday 4 Oct - Annotation Impact & Usability=== | |||
Breakfast on your own | Breakfast on your own | ||
8:30 start (lunch | 8:30 start (lunch 12:30-2:00, breaks at 10:30 and 3:30) | ||
# GO-pal transition (GO + Drupal = GO-pal) | |||
#Annotation | #* Term enrichment front & center | ||
## Quality control reports and how to manage them efficiently | #** Gold Standard Annotation Sets (Rama) | ||
# | #* Other key use cases | ||
# | #** Scicrunch registry (improvement on neuroLex?) | ||
# | #** GO analysis gotcha page (PLoS article?) | ||
# | #* GO stats | ||
# | # Engaging the user community (GO help responsibilities) | ||
#* A Gene Ontology MOOC (Coursera, EdX, Udacity, etc.) to train and answer "I want to ..." questions | |||
#* Obligatory blog during each rota on latest annotation paper that was discussed | |||
# Incorporation of external annotations. | |||
#* Discuss which evidence codes to use for annotation predictions. | |||
#* Discuss strategies for incorporation, including non-MOD IEAs | |||
#* Reactome annotations, their use of ev.codes etc | |||
#* Proposal to integrate protein binding annotations | |||
# Annotation workflow (Quality control reports and how to manage them efficiently) | |||
#* Review of [http://build.berkeleybop.org/view/GAF/ Jenkins GAF QC checks and inferences] | |||
#**Location of files and what they contain - Heiko | |||
#**Examples from the MGI file and discussion of most efficient ways to deal with reports - David H. | |||
#* With/From column IDs (what is mandatory, how to move this to Jenkins for checking) | |||
#* Tutorial on column 16 (Rachael) | |||
# PAINT annotation update (Paul T) | # PAINT annotation update (Paul T) | ||
# PAINT tool update (Suzi) | # PAINT tool update (Suzi) | ||
Line 36: | Line 45: | ||
##SGD's Migration to Protein2GO (Rama) | ##SGD's Migration to Protein2GO (Rama) | ||
##Integration of Text Mining Tools with Protein2GO (Kimberly) | ##Integration of Text Mining Tools with Protein2GO (Kimberly) | ||
====<i>Conference Dinner at 5:30 pm Cafe This Way</i>==== | ====<i>Conference Dinner at 5:30 pm Cafe This Way</i>==== | ||
===Saturday 5 Oct | ===Saturday 5 Oct: Ontology)=== | ||
Breakfast on your own | Breakfast on your own | ||
Line 46: | Line 54: | ||
8:30 start (lunch at 12:30, breaks at 10:30 and 3:30) | 8:30 start (lunch at 12:30, breaks at 10:30 and 3:30) | ||
#Ontology Development | #Ontology Development (Judy) | ||
## Biological content | ## Biological content | ||
### Neuronal cell components and integration with NIF (Paola) | ### Neuronal cell components and integration with NIF (Paola) |
Revision as of 19:50, 27 September 2013
Thurs 3 Oct (Pre-Meeting Working Groups)
These pre-meeting working groups will meet at The Jackson Laboratory. Please arrive 30 minutes before the session you wish to attend so you can get a badge and escort.
- 9:30am - 10:30am Web documentation, Drupal transition (room ERB 1421)
- 11:00am - 12:00pm Ontology group discussion: OWL/OBO editing workflow (room NRB 3035)
- 12:00pm - 1:00pm Lunch at Roscoe's
- 12:50pm - 1:30pm Lab tour (optional; Mark Wanner leading)
- 1:30pm - 2:30pm Annotation extensions: for those already making c16 annotations and ontology developers; This group will be finalizing what they want to present to the whole GOC during this meeting (room ERB 2519)
- Annotation tools (the following discussions are interrelated. Attendance only if contributing to all 3
- 2:30pm - 3:00pm CAT working group: next steps moving from Protein2GO to free-standing CAT (independent of UniProt)(room ERB 2519)
- 3:00pm - 4:00pm: LEGO group discussion (room NRB 3035)
- 4:00pm - 5:00pm PAINT group discussion: This is a working group meeting for those PAINT curators and developers in town on Thur. (room NRB 3035)
Agenda
The SAB report from April 2013 (Cambridge) was very specific and productive [1]. We will be meeting with them again in March 2014 and need to show progress on their useful recommendations. Therefore the focus of this meeting is to identify targeted projects that we can demonstrate to them in the (roughly) six intervening months. Establishing priorities, point people who will handle coordination, and monthly milestones.
Friday 4 Oct - Annotation Impact & Usability
Breakfast on your own
8:30 start (lunch 12:30-2:00, breaks at 10:30 and 3:30)
- GO-pal transition (GO + Drupal = GO-pal)
- Term enrichment front & center
- Gold Standard Annotation Sets (Rama)
- Other key use cases
- Scicrunch registry (improvement on neuroLex?)
- GO analysis gotcha page (PLoS article?)
- GO stats
- Term enrichment front & center
- Engaging the user community (GO help responsibilities)
- A Gene Ontology MOOC (Coursera, EdX, Udacity, etc.) to train and answer "I want to ..." questions
- Obligatory blog during each rota on latest annotation paper that was discussed
- Incorporation of external annotations.
- Discuss which evidence codes to use for annotation predictions.
- Discuss strategies for incorporation, including non-MOD IEAs
- Reactome annotations, their use of ev.codes etc
- Proposal to integrate protein binding annotations
- Annotation workflow (Quality control reports and how to manage them efficiently)
- Review of Jenkins GAF QC checks and inferences
- Location of files and what they contain - Heiko
- Examples from the MGI file and discussion of most efficient ways to deal with reports - David H.
- With/From column IDs (what is mandatory, how to move this to Jenkins for checking)
- Tutorial on column 16 (Rachael)
- Review of Jenkins GAF QC checks and inferences
- PAINT annotation update (Paul T)
- PAINT tool update (Suzi)
- Common Annotation Tool update
- SGD's Migration to Protein2GO (Rama)
- Integration of Text Mining Tools with Protein2GO (Kimberly)
Conference Dinner at 5:30 pm Cafe This Way
Saturday 5 Oct: Ontology)
Breakfast on your own
8:30 start (lunch at 12:30, breaks at 10:30 and 3:30)
- Ontology Development (Judy)
- Biological content
- Neuronal cell components and integration with NIF (Paola)
- Apoptosis annotation update (Paola)
- Proposed Giardia/unicellular eukaryote cc expansion (Paola)
- cell cycle (Jane)
- virus project update (Becky)
- Uberon/CL/GO developments (David OS)
- Update on Cross products- internal and external ontologies (David H)
- TermGenie Template Updates
- CHEBI - http://www.biomedcentral.com/1471-2164/14/513
- Display of external ontologies in AmiGO 2
- Transition to OWL update (Chris)
- Inference of LEGO diagrams from GO annotations and external sources (Chris)
- Reactome Discussion
- Automated translation of Reactome & BioPAX to LEGO/OWL (Chris)
- Glycolysis example for comparison (David H)
- Pathways in GOC
- Relationship between GOC and various pathway representations including wikipathways
- Reactome Discussion
- Proposed json file format for GO annotations (up to LEGO-expressivity) (Chris)
- Molecular Function alignment with Rhea (Chris)
- Biological data interpretation (aka enrichment) (Chris)
- AmiGO 2 + Drupal site - your friends in the GO (Seth + Moni)
- GO-FAQ and GO-help
- Biological content
- Group Picture
- Biological Usability
- LEGO and pathways (Paul T)
Field Trips: Enjoy Acadia National Park. 4:00pm
Sunday 6 Oct (Usability) (NOTE: MIGHT BE ALL MOVED TO SATURDAY)
- Future Meetings
- GOC meeting next Spring (Jim Hu, Paul Thomas) (College Station, Texas) will include SAB meeting
- Possibility of an Annotation Camp in the near future (discuss dates/venue)
- Papers published and in progress
- Wrap Up