Date
Attendees
Karen Ketchum, Rajesh, Anand, Henry, John, Paul Rudnick, Michael Holck, Mike MacCoss, Gilberto Fragoso
Agenda
- Data release
- Release of LUAD Acetylome data to coincide with the publication of the two major LUAD studies from CPTAC and Academia Sinica in Cell (July 9)
- Publication details added to Lung cancer studies from CPTAC3 and Academia Sinica (July 13)
- Updates on Scientific committee, next steps
- CPTAC data portal migration discussion
- Next dataset release priorities
- CPTAC3 UCEC Acetylome - ongoing
- CPTAC3 Lung Squamous Cell Carcinoma (LSCC) - proteome, phosphoproteome, acetylome - waiting for data from DCC
- Ongoing work (previous and ongoing sprints) -
- Release acetylome datasets, bug fixes
- Released a data submission template as a spreadsheet workbook
- search bar improvements - text annotation, ordering of results, etc
- release of a data submission template as a spreadsheet workbook
- worked on ability to reuse the previously released biospecimens for new studies
- reorganizing heatmap files, API updates to use the new PDC study identifier (e.g. PDC000nnn)
- Workspace feature enhancements include -
- ability to load annotations during file upload that will help in streamline study creation,
- ability to accept data_source (submiiter or PDC) and embargo_date
- file-set validation based on instrument specific file formats , e.g. Sciex models,
- adding support for Acetylome, etc
- Other minor improvements
- External interactions
- MSFragger webinar - mention of PDC - SBG integration
- SBG talk at next bi weekly call
- Other items
Discussion items
| Time | Item | Who | Notes |
|---|---|---|---|
| LUAD Acetylome data released last week and supports two publications, one of which uses the new IDs for PDC. | |||
| Scientific Committee: haven't heard from 2 people, but Mike MacCoss has reached out and internal discussions were held on how to organize the call. Proposing 1.5-2 hr. call. Topics: Data hosting, development efforts, findability, APIs. Short 15 presentations with ~10 min of time for feedback. Looking for feedback on agenda. Paul Rudnick volunteers to do section on CDAP output/APIs. Doodle poll to be sent out for times - targeting early to mid August. | |||
| CPTAC data portal migration: discuss where we stand and what steps are needed to make the migration happen. Same presentation as on Monday. CPTAC Download slide was added per category. 2019 and 2020 (up to July 13). Phase 2 and external data is most downloaded in 2019. Phase 3 data is up in downloads in 2020 compared to 2019. Methods studies in Phase 3 not included in PDC at this time. Question: what is priority for bringing these forward? Mike MacCoss thinks method data is valuable as benchmark by bioinformaticians. Previous priority was cancer cohorts (clinical), maybe need to increase priority on method data. Cost of downloads: $3K/month for 16TB of data/month. | |||
| went over next data sets and ongoing work. Submission template released. SBG coming to next call. |
