Difference between revisions of "WormBase-Caltech Weekly Calls"
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* 21 papers flagged as not having phenotypes | * 21 papers flagged as not having phenotypes | ||
* Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week | * Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week | ||
| + | |||
| + | |||
| + | == June 13, 2019 == | ||
| + | |||
| + | === IWM === | ||
| + | * Coordinating transportation of swag boxes to Pauley Pavilion | ||
| + | * Workshop on Saturday June 22, from 1pm to 2:30pm | ||
| + | * Saturday morning micropublication breakfast 7:30 - 8:30am | ||
| + | * Workshop | ||
| + | ** Presenters: it may be best to present as use cases rather than a research project | ||
| + | ** Chris will cover SimpleMine for Wen | ||
| + | ** Chris: won't do live demo; only screenshots, maybe some video | ||
| + | * Paul's lab will do marathon bibs to show lab affiliation and graphical abstract | ||
| + | * Paul's talk | ||
| + | ** Cover Alliance | ||
| + | ** New features | ||
| + | *** SObA (for new data) | ||
| + | *** Complete for protein-protein interactions | ||
| + | *** RNASeq tools | ||
| + | *** Updated automated gene concise descriptions? | ||
| + | ** Phenotype community curation | ||
| + | *** Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators) | ||
| + | ** Author First Pass | ||
| + | ** Micropublication | ||
| + | |||
| + | === SGD SAB === | ||
| + | * Paul attended | ||
| + | * Alliance publicity was discussed | ||
| + | * SAB likes the Alliance orthology features | ||
| + | * Working on topics: displaying papers and data | ||
| + | * Pathways: discussion about best approach | ||
| + | * Metabolic engineering | ||
| + | * Meta data about RNASeq data | ||
| + | ** SPELL tool, basically only tool of its kind available; need new tools | ||
| + | * Species-specific proteins: how best to find them? HMMs (Jackhammer)? | ||
| + | |||
| + | === Concise descriptions === | ||
| + | * Progress being made within the Alliance to update the automated concise gene descriptions | ||
| + | * We will still accept manually written descriptions and display them in parallel with automated descriptions | ||
| + | |||
| + | === Micropublications === | ||
| + | * If people are requesting manually written gene descriptions, they could submit a microreview | ||
| + | * Concern was expressed about how to handle a really high throughput of submissions: | ||
| + | ** Daniela: Working towards automating as much of the processing pipeline as possible | ||
| + | ** Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help | ||
| + | ** Not getting lots of submissions yet, probably won't be inundated in the near future | ||
| + | ** Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions | ||
| + | * Karen: Micropublications team will reach out to curators to help build submission forms for respective data types | ||
| + | |||
| + | === Undiagnosed Disease Network data === | ||
| + | * Andy Golden will meet with Ranjana and Chris at IWM to discuss | ||
| + | * Andy asked about protocol pages at WormBase? | ||
| + | * Paul: Bioprotocols and Protocols IO | ||
| + | * Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook) | ||
Revision as of 18:55, 13 June 2019
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
June 6, 2019
New SObA graphs
- May put graphs within existing widgets, but don't need to rush to get that ready for IWM
Phenotype association file format
- May be best to leave the format as is
- There are problems; paper IDs keep switching columns
- Would need to revisit the reasoning for why we do it that way
- When will the Alliance produce a similar/replacement file? Not sure
Phenotype requests
- Sent out 1140 emails on May 30
- Since have received 374 annotations from 54 papers (42 requested, 12 additional)
- 21 papers flagged as not having phenotypes
- Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
June 13, 2019
IWM
- Coordinating transportation of swag boxes to Pauley Pavilion
- Workshop on Saturday June 22, from 1pm to 2:30pm
- Saturday morning micropublication breakfast 7:30 - 8:30am
- Workshop
- Presenters: it may be best to present as use cases rather than a research project
- Chris will cover SimpleMine for Wen
- Chris: won't do live demo; only screenshots, maybe some video
- Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
- Paul's talk
- Cover Alliance
- New features
- SObA (for new data)
- Complete for protein-protein interactions
- RNASeq tools
- Updated automated gene concise descriptions?
- Phenotype community curation
- Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
- Author First Pass
- Micropublication
SGD SAB
- Paul attended
- Alliance publicity was discussed
- SAB likes the Alliance orthology features
- Working on topics: displaying papers and data
- Pathways: discussion about best approach
- Metabolic engineering
- Meta data about RNASeq data
- SPELL tool, basically only tool of its kind available; need new tools
- Species-specific proteins: how best to find them? HMMs (Jackhammer)?
Concise descriptions
- Progress being made within the Alliance to update the automated concise gene descriptions
- We will still accept manually written descriptions and display them in parallel with automated descriptions
Micropublications
- If people are requesting manually written gene descriptions, they could submit a microreview
- Concern was expressed about how to handle a really high throughput of submissions:
- Daniela: Working towards automating as much of the processing pipeline as possible
- Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
- Not getting lots of submissions yet, probably won't be inundated in the near future
- Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
- Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
Undiagnosed Disease Network data
- Andy Golden will meet with Ranjana and Chris at IWM to discuss
- Andy asked about protocol pages at WormBase?
- Paul: Bioprotocols and Protocols IO
- Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
