Difference between revisions of "2014 Barcelona GOC Meeting Agenda"

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<p>
 
We realize the midday break is long. This was done for two reasons. First because all three days are quite full we wanted to give people some opportunity to walk about the city, and second because dinner in Barcelona is usually quite late and this puts us on the local schedule. We can discuss further on Monday morning if anyone feels strongly there is a need to change this approach. Bear in mind that whatever is decided we still require three full working days.
 
We realize the midday break is long. This was done for two reasons. First because all three days are quite full we wanted to give people some opportunity to walk about the city, and second because dinner in Barcelona is usually quite late and this puts us on the local schedule. We can discuss further on Monday morning if anyone feels strongly there is a need to change this approach. Bear in mind that whatever is decided we still require three full working days.
 +
== Minutes ==
 +
https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit?usp=sharing
  
 
==Monday 13 October==
 
==Monday 13 October==
Line 20: Line 22:
 
# Site content (Moni)
 
# Site content (Moni)
 
#* GO site/docs development. (Moni, Seth) [https://trello.com/c/F7MnDGig/60-website-usability trello]
 
#* GO site/docs development. (Moni, Seth) [https://trello.com/c/F7MnDGig/60-website-usability trello]
#** Review list of missing website content, ACTION: get volunteers to complete each missing item
+
#** Review list of non-functional URLs as seen on [https://github.com/kltm/go-site/issues/10 GitHub issue #10], and review other missing content. ACTION: recruit volunteers to complete each missing item
#** Video tutorials, ACTION: discuss suggestions for other tutorials
+
#** Video tutorials. ACTION: collect suggestions for additional tutorials
 +
#** Improving documentation (Chris)
 +
#*** [http://geneontology.org/page/download-ontology ontology downloads]
 +
#*** documentation on annotations needs to be more user-friendly - [http://geneontology.org/page/annotation /page/annotation]
 
#* Google analytics ([https://trello.com/c/OfHYkQCl/99-review-google-analytics-data trello]) (Seth/Rama)
 
#* Google analytics ([https://trello.com/c/OfHYkQCl/99-review-google-analytics-data trello]) (Seth/Rama)
# AmiGO feedback and development (Seth)
+
# AmiGO feedback and development (Seth) [http://berkeleybop.org/document/amigo-2-update-college-station-goc]
#* Shared QuickGO graphics
+
# Infrastructure improvements (Seth)
 +
#* Shared QuickGO graphics - nothing to report
 +
#* Migration of all cron jobs to Jenkins [https://trello.com/c/KymgLaN1/49-migrate-all-cron-jobs-to-jenkins trello] - status
 +
#* RHEA pipeline ([https://trello.com/c/w4kSpzEo/61-rhea-pipeline trello]) - no change
 +
#* mySQL retirement (Chris) [https://trello.com/c/Vnb65OHn/64-mysql-retirement trello]
 
#* Cloud deployment ([https://trello.com/c/lPap8TUe/66-amigo-cloud-deployment trello])
 
#* Cloud deployment ([https://trello.com/c/lPap8TUe/66-amigo-cloud-deployment trello])
 
#* Golr refactoring ([https://trello.com/c/JJhrfKlE/55-refactoring-golr-loading trello])
 
#* Golr refactoring ([https://trello.com/c/JJhrfKlE/55-refactoring-golr-loading trello])
Line 32: Line 41:
 
#** What types of files can/should we provide?
 
#** What types of files can/should we provide?
 
#** How should we distribute annotations to protein complexes and/or other entities, e.g. ncRNAs?
 
#** How should we distribute annotations to protein complexes and/or other entities, e.g. ncRNAs?
#* Improving documentation
 
#** ontology downloads
 
#** documentation on annotations needs to be more user-friendly
 
 
# GO Help Desk ([https://trello.com/c/ab3jdptM/21-user-support-go-help trello])
 
# GO Help Desk ([https://trello.com/c/ab3jdptM/21-user-support-go-help trello])
 
#* Adding people to the rota
 
#* Adding people to the rota
 
#* Assigning the help desk  
 
#* Assigning the help desk  
 
#* adding to FAQ
 
#* adding to FAQ
 +
# Meta
 +
#* Switch from wiki to google docs for GOC internal material? I have a folder here: [https://drive.google.com/?authuser=0#folders/0B8kRPmmvPJU3dFhhcWhTSmlUcDA drive] (Chris)
 +
# Workshops for groups/organizations who develop and maintain tools which are widely used for GO analysis. With the aim being to help users get the best out of GO data analysis.
 +
#* to give talks on their tools.
 +
#* hold these at conferences like ISMB/ECCB etc. Or a dedicated one off workshop with members of the GOC and groups who develop tools
 
# Public submission of annotations ([https://trello.com/c/8FLd0QRD/104-review-documentation-for-public-submission-of-annotations-make-sure-it-is-user-friendly trello])
 
# Public submission of annotations ([https://trello.com/c/8FLd0QRD/104-review-documentation-for-public-submission-of-annotations-make-sure-it-is-user-friendly trello])
 
#* Documentation reviewed (Moni)
 
#* Documentation reviewed (Moni)
Line 45: Line 56:
 
#* Preparation for synapse meeting at Stanley Institute
 
#* Preparation for synapse meeting at Stanley Institute
 
#** Who will go, use of Noctua, ease of submission, etc.
 
#** Who will go, use of Noctua, ease of submission, etc.
 
+
# GO Enrichment Analysis (Judy, Paul, Chris, Suzi) [https://trello.com/c/t4nft5uU/72-gene-enrichment-tool trello]
# GO Enrichment Analysis (Judy, Paul, Chris, Suzi)
 
 
#* Summary of discussion on mail list - [http://geneontology.org/meeting/consortium/Barcelona2014/go-interpretation-analysis-2014.pptx ppt] (Chris)
 
#* Summary of discussion on mail list - [http://geneontology.org/meeting/consortium/Barcelona2014/go-interpretation-analysis-2014.pptx ppt] (Chris)
 
#*report on needs/ improvements in AmiGO tool (Seth, Paul)
 
#*report on needs/ improvements in AmiGO tool (Seth, Paul)
Line 54: Line 64:
 
#* Benchmarking data sets
 
#* Benchmarking data sets
 
#* ISMB Workshop
 
#* ISMB Workshop
#**Judy working on white paper 'Gene Enrichment Analysis using the GO: the good, the bad, the ugly.' I will have early draft at meeting.
+
#**Dec deadline for workshop proposal for ISCB/ECCB in Dublin, July 2015
 
+
#***mixture of tool design reports and updates on GO structures for developers
===Common Curation Environment and LEGO annotations===
+
#**Judy/Moni/ others interested in working on white paper 'Gene Enrichment Analysis using the GO: the good, the bad, the ugly.'
The objective is to have environment into which all curators can enter data and from which each group can extract data files.
 
# Noctua development (Chris, Seth, Heiko, Suzi)
 
#* Progress Report and Timeline for releases and annotation usage - [http://geneontology.org/meeting/consortium/Barcelona2014/noctua-timeline-2015.pptx] (Chris/Suzi)
 
#* LEGO Specification - an updated version. (TENTATIVE - pending discussions Huaiyu, 20')
 
#* LEGO models of annotation extensions (David OS)
 
#* BioPax imports
 
#** Reactome import progress ([https://trello.com/c/r4UHukGV/71-lego-import-from-reactome trello])
 
#* Export to legacy formats ([https://trello.com/c/PlnGYO8e/54-owl-gaf-roundtripping trello]) http://build.berkeleybop.org/job/export-lego-to-legacy/
 
#** Translation scripts (GAF<-->GPAD, LEGO/OWL<-->GAF/GPAD)
 
# Textpresso Central/Capella (Michael Mueller)
 
# Update on Protein2GO, including annotation to IntACT IDs (Tony 15-20mins)
 
  
 
==Tuesday 14 October==
 
==Tuesday 14 October==
 
===Phylogenetic Annotation===
 
===Phylogenetic Annotation===
 
# PAINT curation updates, analysis and Jamboree debrief (Huaiyu, Pascale, 30')
 
# PAINT curation updates, analysis and Jamboree debrief (Huaiyu, Pascale, 30')
# Autophagy in PAINT: lessons learned (Marc F, Pascale)
+
# Autophagy in PAINT: lessons learned (Marc F, Pascale) [[File:Autophagy_Marc.pptx]]
# Annotations, including NOTs, to isoforms; different functions for isoforms (Karen remotely? [could this be done 2 pm or later if both Karen and Darren Natale are to call in]  Judy/David can present)
+
# Annotations, including NOTs, to isoforms; different functions for isoforms (Karen remotely? [could this be done 2 pm or later if both Karen and Darren Natale are to call in]  Judy can present)
 
#*can we identify these from annotation files?  do we exclude these genes from PAINT curation?
 
#*can we identify these from annotation files?  do we exclude these genes from PAINT curation?
 
# Family tree quality assessment/improvement with curated orthologs from PomBase & ZFIN (Paul)
 
# Family tree quality assessment/improvement with curated orthologs from PomBase & ZFIN (Paul)
 
# Jenkins running of PAINT GAF file updates (Suzi)
 
# Jenkins running of PAINT GAF file updates (Suzi)
 +
# jsPaint status -- no update (Chris)
  
 
===Literature Annotation===
 
===Literature Annotation===
# With/From field cardinality proposal (Rachael 30-45min) (Decisions: what is the cardinality of the with field for each evidence code? Can we use pipes/commas consistently as we do for extensions? If an 'AND' is converted to an 'OR' is this really a weaker statement or a different statement-do we need a 3rd delimiter?)
+
# With/From field cardinality proposal (Rachael 30-45min) (Decisions: what is the cardinality of the with field for each evidence code? Can we use pipes/commas consistently as we do for extensions? If an 'AND' is converted to an 'OR' is this really a weaker statement or a different statement-do we need a 3rd delimiter?) [[File:Multiple_values_in_with_field_2.pptx]]
# Annotation extension relationships: how to use them (Ruth 30-45 min)
+
# Annotation extension relationships: how to use them (Ruth 30-45 min) [[File:AnnotationExtensionV2.pptx]]
 
# Cross-species entries in Annotation Extensions - is there any value in this information for GO?  (Re-visiting an earlier discussion we had about this in Cambridge, 2013.) (Kimberly 15-20 min)
 
# Cross-species entries in Annotation Extensions - is there any value in this information for GO?  (Re-visiting an earlier discussion we had about this in Cambridge, 2013.) (Kimberly 15-20 min)
# Discussion of catabolism and biosynthesis (Pascale)
+
# Use of expanded evidence codes and interactions with ECO (Kimberley, with input from others - 15-20 minutes)
# Discussion on 'protein dimerization activity' vs. e.g. 'protein homotetramerization' (MF vs BP).  
+
#* Are any groups currently using expanded ECO codes for GO annotation?
#* See summary here: http://sourceforge.net/p/geneontology/ontology-requests/11087/ (Paola 45 min incl. discussion) and https://sourceforge.net/p/geneontology/ontology-requests/10909/  
+
#* Can existing tools (Protein2GO, GO web site, AmiGO) accommodate the codes?
# Refresher/overview of available TG templates (Jane)
+
#*Any reasons not to start using expanded ECO codes? Is turn around time for new ECO term requests sufficient?
 +
# Discussion of catabolism and biosynthesis (Pascale) [[http://wiki.geneontology.org/index.php/File:PG-metabolism-barcelona.pptx]]
 +
# Discussion on 'protein dimerization activity' vs. e.g. 'protein homotetramerization' (MF vs BP). [[File:Oligomerization_etc.pptx]]
 +
#* See summary here: http://sourceforge.net/p/geneontology/ontology-requests/11087/ (Paola 30-45 min incl. discussion) and https://sourceforge.net/p/geneontology/ontology-requests/10909/
 +
 
 +
==Wednesday 15 October==
 +
===Literature Annotation (cont.)===
 +
# Refresher/overview of available TG templates (Jane - 15 min)
 
# GO annotations for IntAct complexes
 
# GO annotations for IntAct complexes
# Capturing assays in a controlled fashion - example, rubidium assays - [https://sourceforge.net/p/geneontology/ontology-requests/11241/ SF11241] and [http://wiki.geneontology.org/index.php/Ontology_meeting_2014-10-09#Rubidium-related_terms ontology meeting agenda 2014-10-09]
+
#* GO annotation (Rama) [[File:IntActGO.pptx]]
 +
#* Update on Protein2GO, including annotation to IntACT IDs (Tony 15-20mins)
 
# Annotation QA
 
# Annotation QA
#* Val's annotation matrix
+
#* Jenkins GAF QC checks and inferences (Heiko, Rama)
 +
#* Monique Zahn: Quality control process in neXtProt (about 15 minutes)
 +
#* Val's - Problems for annotation specificity i) has_part ii) loss of annotation specificity through term relocation
  
===Annotation Workflow===
+
* Update on FAQ (Seth, Moni) [[Media:Go-faq-update-2014-10.pdf|quick slides]]
# Jenkins GAF QC checks and inferences (Heiko, Rama)
+
 
# GPAD pipeline
+
===Common Curation Environment and LEGO annotations===
# Monique Zahn: Quality control process in neXtProt (about 15 minutes)
+
The objective is to have environment into which all curators can enter data and from which each group can extract data files.
 +
# Clarity vs Expressiveness in GO & LEGO - striking a balance (David OS working on a white paper on this).
 +
# Noctua development (Chris, Seth, Heiko, Suzi) [https://trello.com/c/m4QJKjhu/102-noctua-development trello]
 +
#* Progress Report and Timeline for releases and annotation usage - [http://geneontology.org/meeting/consortium/Barcelona2014/noctua-timeline-2015.pptx] (Chris/Suzi)
 +
#* LEGO Specification - an updated version. (Huaiyu 20')  [http://wiki.geneontology.org/images/b/bb/LEGO_specfication.pdf Slides]
 +
#* LEGO models of annotation extensions (David OS)
 +
#* BioPax imports
 +
#** Reactome import progress ([https://trello.com/c/r4UHukGV/71-lego-import-from-reactome trello])
 +
#* Export to legacy formats ([https://trello.com/c/PlnGYO8e/54-owl-gaf-roundtripping trello]) http://build.berkeleybop.org/job/export-lego-to-legacy/
 +
#** Translation scripts (GAF<-->GPAD, LEGO/OWL<-->GAF/GPAD)
 +
# Textpresso Central/Capella (Kimberly, Michael Mueller, Paul S.)
  
==Wednesday 15 October==
 
 
===Ontology Production and R&D===
 
===Ontology Production and R&D===
 
# Sourceforge back-log; how to address?
 
# Sourceforge back-log; how to address?
 
#* Sourceforge jamboree worked, but now we are near 300 again
 
#* Sourceforge jamboree worked, but now we are near 300 again
# Pilot project to replace NCI thesaurus 'biological process' branch with GO biological process [https://docs.google.com/document/d/1ozliyTh-QPyyUdYjk8P1mhygWCWtCnZKX9FNGvU-XlM/edit# doc] (Chris)
+
# Pilot project to replace NCI thesaurus 'biological process' branch with GO biological process [https://trello.com/c/6l0qo0vd/114-integration-with-ncit trello] (Chris)
# GO and human disease (Chris) <-- this now incorporated into GO-analysis section
+
# Proposed changes to Molecular Function (Jane)
 +
# Progress in moving GO editing to OWL. (David OS)
 +
# Roche/GO project (David OS)
 
# High-level protein family classification and application to annotation deepening ([https://trello.com/c/yOniQ2Uv/92-automated-deepening-using-logical-definitions trello]) (Jane)
 
# High-level protein family classification and application to annotation deepening ([https://trello.com/c/yOniQ2Uv/92-automated-deepening-using-logical-definitions trello]) (Jane)
 
#* Can we use PRO classes for protein families?
 
#* Can we use PRO classes for protein families?
 
#* [http://geneontology.org/meeting/consortium/Barcelona2014/auto-deepening-of-protein-binding.pptx deepening protein binding] (Chris, Jane)
 
#* [http://geneontology.org/meeting/consortium/Barcelona2014/auto-deepening-of-protein-binding.pptx deepening protein binding] (Chris, Jane)
# Proposed changes to Molecular Function (Jane)
+
# inference of 'part_of' relationships (Chris) [https://trello.com/c/2KZ3lH6D/107-strategy-for-inference-of-part-of-relationships trello]. Not sure if we need to go into this here?
# Progress in moving GO editing and annotation extension relations to OWL. (David OS)
 
# Clarity vs Expressiveness in GO - striking a balance (David OS working on a white paper on this).
 
# Roche/GO project (David OS)
 
# inference of 'part_of' relationships (Chris)
 
 
 
===Software infrastructure - part 2 ===
 
# Migration of all cron jobs to Jenkins - status
 
# GOlr loading refactoring (Seth)
 
# jsPaint status
 
  
# RHEA pipeline - no change
+
==Group Photo==
# mySQL retirement (Chris)
+
[[File:2014_GOC_Barcelona.JPG|800px|thumb|left|2014 GOC Group Photo at Barcelona]]

Latest revision as of 06:53, 31 August 2015

back to 2014_Barcelona_Meeting_Logistics

Daily schedule

  • Start: 9 AM
  • Morning coffee break: 10:30 to 11:00
  • Lunch: 13:00 + break until 16:00
  • Afternoon session: 16:00 to 20:00


Coffee and snacks will be served at 16:00

We will be updating the trello board as we go.

  • Please ensure that all outstanding items from the trello board are covered here in the agenda under the appropriate heading.

We realize the midday break is long. This was done for two reasons. First because all three days are quite full we wanted to give people some opportunity to walk about the city, and second because dinner in Barcelona is usually quite late and this puts us on the local schedule. We can discuss further on Monday morning if anyone feels strongly there is a need to change this approach. Bear in mind that whatever is decided we still require three full working days.

Minutes

https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit?usp=sharing

Monday 13 October

User support and interaction

  1. Site content (Moni)
    • GO site/docs development. (Moni, Seth) trello
      • Review list of non-functional URLs as seen on GitHub issue #10, and review other missing content. ACTION: recruit volunteers to complete each missing item
      • Video tutorials. ACTION: collect suggestions for additional tutorials
      • Improving documentation (Chris)
    • Google analytics (trello) (Seth/Rama)
  2. AmiGO feedback and development (Seth) [1]
  3. Infrastructure improvements (Seth)
    • Shared QuickGO graphics - nothing to report
    • Migration of all cron jobs to Jenkins trello - status
    • RHEA pipeline (trello) - no change
    • mySQL retirement (Chris) trello
    • Cloud deployment (trello)
    • Golr refactoring (trello)
  4. Public consumption of GO content
    • Linked data version of GO. trello (Chris)
    • Other
      • What types of files can/should we provide?
      • How should we distribute annotations to protein complexes and/or other entities, e.g. ncRNAs?
  5. GO Help Desk (trello)
    • Adding people to the rota
    • Assigning the help desk
    • adding to FAQ
  6. Meta
    • Switch from wiki to google docs for GOC internal material? I have a folder here: drive (Chris)
  7. Workshops for groups/organizations who develop and maintain tools which are widely used for GO analysis. With the aim being to help users get the best out of GO data analysis.
    • to give talks on their tools.
    • hold these at conferences like ISMB/ECCB etc. Or a dedicated one off workshop with members of the GOC and groups who develop tools
  8. Public submission of annotations (trello)
    • Documentation reviewed (Moni)
    • Users able to syntactically validate submissions online (Heiko)
    • CANTO deployment
    • Preparation for synapse meeting at Stanley Institute
      • Who will go, use of Noctua, ease of submission, etc.
  9. GO Enrichment Analysis (Judy, Paul, Chris, Suzi) trello
    • Summary of discussion on mail list - ppt (Chris)
    • report on needs/ improvements in AmiGO tool (Seth, Paul)
      • intersection with Panther db often down
    • What are the right tools/algorithms to use for different types of input data?
      • E.g. microarray vs RNA-seq; dealing with bias
    • Benchmarking data sets
    • ISMB Workshop
      • Dec deadline for workshop proposal for ISCB/ECCB in Dublin, July 2015
        • mixture of tool design reports and updates on GO structures for developers
      • Judy/Moni/ others interested in working on white paper 'Gene Enrichment Analysis using the GO: the good, the bad, the ugly.'

Tuesday 14 October

Phylogenetic Annotation

  1. PAINT curation updates, analysis and Jamboree debrief (Huaiyu, Pascale, 30')
  2. Autophagy in PAINT: lessons learned (Marc F, Pascale) File:Autophagy Marc.pptx
  3. Annotations, including NOTs, to isoforms; different functions for isoforms (Karen remotely? [could this be done 2 pm or later if both Karen and Darren Natale are to call in] Judy can present)
    • can we identify these from annotation files? do we exclude these genes from PAINT curation?
  4. Family tree quality assessment/improvement with curated orthologs from PomBase & ZFIN (Paul)
  5. Jenkins running of PAINT GAF file updates (Suzi)
  6. jsPaint status -- no update (Chris)

Literature Annotation

  1. With/From field cardinality proposal (Rachael 30-45min) (Decisions: what is the cardinality of the with field for each evidence code? Can we use pipes/commas consistently as we do for extensions? If an 'AND' is converted to an 'OR' is this really a weaker statement or a different statement-do we need a 3rd delimiter?) File:Multiple values in with field 2.pptx
  2. Annotation extension relationships: how to use them (Ruth 30-45 min) File:AnnotationExtensionV2.pptx
  3. Cross-species entries in Annotation Extensions - is there any value in this information for GO? (Re-visiting an earlier discussion we had about this in Cambridge, 2013.) (Kimberly 15-20 min)
  4. Use of expanded evidence codes and interactions with ECO (Kimberley, with input from others - 15-20 minutes)
    • Are any groups currently using expanded ECO codes for GO annotation?
    • Can existing tools (Protein2GO, GO web site, AmiGO) accommodate the codes?
    • Any reasons not to start using expanded ECO codes? Is turn around time for new ECO term requests sufficient?
  5. Discussion of catabolism and biosynthesis (Pascale) [[2]]
  6. Discussion on 'protein dimerization activity' vs. e.g. 'protein homotetramerization' (MF vs BP). File:Oligomerization etc.pptx

Wednesday 15 October

Literature Annotation (cont.)

  1. Refresher/overview of available TG templates (Jane - 15 min)
  2. GO annotations for IntAct complexes
    • GO annotation (Rama) File:IntActGO.pptx
    • Update on Protein2GO, including annotation to IntACT IDs (Tony 15-20mins)
  3. Annotation QA
    • Jenkins GAF QC checks and inferences (Heiko, Rama)
    • Monique Zahn: Quality control process in neXtProt (about 15 minutes)
    • Val's - Problems for annotation specificity i) has_part ii) loss of annotation specificity through term relocation

Common Curation Environment and LEGO annotations

The objective is to have environment into which all curators can enter data and from which each group can extract data files.

  1. Clarity vs Expressiveness in GO & LEGO - striking a balance (David OS working on a white paper on this).
  2. Noctua development (Chris, Seth, Heiko, Suzi) trello
    • Progress Report and Timeline for releases and annotation usage - [3] (Chris/Suzi)
    • LEGO Specification - an updated version. (Huaiyu 20') Slides
    • LEGO models of annotation extensions (David OS)
    • BioPax imports
      • Reactome import progress (trello)
    • Export to legacy formats (trello) http://build.berkeleybop.org/job/export-lego-to-legacy/
      • Translation scripts (GAF<-->GPAD, LEGO/OWL<-->GAF/GPAD)
  3. Textpresso Central/Capella (Kimberly, Michael Mueller, Paul S.)

Ontology Production and R&D

  1. Sourceforge back-log; how to address?
    • Sourceforge jamboree worked, but now we are near 300 again
  2. Pilot project to replace NCI thesaurus 'biological process' branch with GO biological process trello (Chris)
  3. Proposed changes to Molecular Function (Jane)
  4. Progress in moving GO editing to OWL. (David OS)
  5. Roche/GO project (David OS)
  6. High-level protein family classification and application to annotation deepening (trello) (Jane)
  7. inference of 'part_of' relationships (Chris) trello. Not sure if we need to go into this here?

Group Photo

2014 GOC Group Photo at Barcelona