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You are here: Home Community Minutes Mini Group meetings OMERO/HIC Meetings 2012.01.20

2012.01.20

Attending: Jason, Emma, Simon, Alison, Keith, Duncan, Scott

Agenda

  1. Action Items

    • JASON: steering committee slides - done
    • SIMON: Refactoring prep for code rebase - ongoing
    • SIMON: datatables - ongoing
    • SIMON: Institute fortnightly deploy/feedback cycle in new year - ongoing
    • HIC FOLK (ALISON?): Arrange next meeting as f2f @ HIC (with Josh video/tele-conferenced in) - done - here we are!
  2. Review

    • Import & Store Project Extracts
    • View project data
    • Log access to project data
  3. Planning

    • Determine objectives for next few weeks
      • Rebase against develop & possibly pull some elements into the main OMERO distribution
      • [#6213] Refactor code siloAPI & websilo
      • Update websilo to django 1.3.1 - brings OMERO/HIC development into line with main OMERO development
      • HIC Workflow Mapping - from master anon. dataset through project extraction (Metformin) - Scott & Alison to collaborate and determine workflow / UI
      • [#7382] Audit Log UX & Data Visualisation
    • Longer term plan
      • import master anon. datasets into OMERO.tables
      • input metadata about project, e.g. some subset of data input to PM system
      • run queries against OMERO.tables to extract project dataset from master & store in OMERO.silo
      • Display the result in OMERO.websilo
      • Project Metadata display
  4. Any other business

Attending

Notes

Attending: Alison, Scott (notes) , Duncan, Keith, Emma, Simon, Josh (notes)

Action Items

  • JASON: steering committee slides - done

  • SIMON: Refactoring prep for code rebase - ongoing

  • SIMON: datatables - ongoing

  • SIMON: Institute fortnightly deploy/feedback cycle in new year - ongoing

  • HIC FOLK (ALISON?): Arrange next meeting as f2f @ HIC (with Josh video/tele-conferenced in) - done - here we are!

  • Simon: Work in progress related to rebasing.

  • Alison: 2 weekly meeting every Friday

  • Duncan: Rooms booked here or can come to UoD

  • Duncan: Meet in person every couple of weeks.

  • Simon: review of where we are, after a year, planning for next few weeks and for longer term. Working * with Alison what we aim to achieve. Review

  • Import & Store Project Extracts

  • Simon: data you give to researchers, what you’d give in safe haven shared folder

  • View project data

  • Simon: Being able to view the data

  • Log access to project data

  • Simon: An audit trail for the data.

  • Simon: Takes output from SQL and allows you to view it.

  • Duncan: strategy meeting, deemed that researcher workflow was to be later on Planning

  • Determine objectives for next few weeks

  • Rebase against develop & possibly pull some elements into the main OMERO distribution [#6213] Refactor code siloAPI & websilo

  • Update websilo to django 1.3.1 - brings OMERO/HIC development into line with main OMERO development

  • HIC Workflow Mapping - from master anon. dataset through project extraction (Metformin) - * Scott & Alison to collaborate and determine workflow / UI [#7382] Audit Log UX & Data Visualisation Longer term plan

  • import master anon. datasets into OMERO.tables

  • input metadata about project, e.g. some subset of data input to PM system

  • run queries against OMERO.tables to extract project dataset from master & store in * * OMERO.silo

  • Display the result in OMERO.websilo

  • Project Metadata display

  • Other Business

Meeting start: 14:00

  • Duncan: Hic steering committee was good.

    • refelected on slides we saw
    • Agreeing on what we would be doing
    • Data cleaning needed to be done as you pull data through to the researchers.
  • Scott: data cleaning happens as data transitions from source to project data sets

  • Duncan: Talk to users to find what the standard things are

    • Cuts down cleaning done by researchers.
    • Directions in GoDarts, Describing dosage.
    • Bio-chem test codes that mean the same thing.
    • Work with researchers to agree a few common ones
    • Paper with suggestions exists
  • Duncan: reinforced what had been done and the general plan

  • Simon: On Monday we met with Alison, provide Alison with a tool with auditing and authorisation. Data logging from point it comes to HIC, full trail from moment NHS data comes in.

  • Alison: No audit trail as of yet.

  • Duncan: What we want to see, what are we looking for in the logs.

  • Simon: Auditor to double check these things.

    • real usage data from Alison, we need to give you a good incentive to use the tool
    • (next point on agenda) Longer-term plan for next 8-10 months is to take master anon. metformin study to take
  • GoDarts chosen as it contains a lot of data sets, Alison: not a great project, some irregularities

  • Simon: load the data sets in to OMERO, describe the project we are going to do the extract from. Write the queries for OMERO to extract the data sets, to show that the mirror data is the same, with the addition of the auditing information. Better than 2-3 tools and manual process. We can spend the next few weeks on what data we need for each point, and mock up interfaces and build and refine the system.

  • Taking advantages from OMERO microscopy and giving you the benefits of that

  • Duncan: how data comes across from SQL to OMERO.

  • Alison: Data is anonymised in prescribing.

  • Simon: loading in larger data sets, show that OMERO can support that.

  • Alison: PROCHI dos based app. Important and difficult/involved process to test

  • Simon: Just the data sets involved in a project, small number

  • Alison: key work elements related to getting the data extracted and imported in OMERO

  • Simon: Push to get data in to OMERO.

  • Duncan: no one appointed yet to new position.

  • Alison: a day a week may be difficult.

  • Scott: space for 1 day a week to visit and get a view on stuff.

  • Simon: Things that will fill next 6 weeks.

  • Keith: not hard to work out what data

  • Alison: Half a day to get details on the plan

  • Simon: and josh skyped in to assist

  • Simon: can use HIC server to use the real data.

  • Alison: SOP, anonymised data has to be encrypted.

  • Keith: Decrypt on our side.

  • Duncan: part of ship.

  • Simon: we have mappings of AnoCHIs to ProCHIs

    • Verify with Andy where the server is w.r.t SOPs.
  • Keith: dev3 / devci

  • Alison: gigs of data, takes a while to extract.

  • Keith: transferring the data will take time.

  • Duncan: Project metadata displayed, could be done

  • Simon: extracting key info from the PM system.

  • Duncan: 4 stages of HIC data release to Safe Haven.

    • Accessing data in HIC is changing, Caldicott only required for identification.
    • Caldicott only really used for recruitment
  • Simon: determine obj for next 3 weeks

    • HIC workflow mapping, metformin
    • Map out what is happening and what data is avaialble in the workflow, so we can compare our output to something
  • Duncan: Help to determine our process

  • Simon & Alison: Visibility on data extraction tools and DRUM meeting was good conversation

  • Simon: write same queries aginast omero tables instead of SQL.

    • selection of data
  • Duncan: on the approval side, sorting data requirements is handled by Alison.

  • Alison: PM system?

  • Simon: HIC project data management system, possibility in the future, overlap in existing tools. comparison against existing tools. Gives confidence in OMERO and having the auditing.

  • Alison: Data compliance tab

  • Duncan: New PM system coming online.

  • Scott & Keith: Auditing of the approval process.

  • Duncan: Peer reviewed process?

  • Simon: Create project extract workflow and auditing trail thenlook to extend that.

  • Duncan: Auditing of safe haven at some point

  • Simon: Yeah, phase 3 of project. Allowing for future developments.

  • Duncan: Fear factor from BIG brother watching every keystroke.

  • Alison: linking cross project (via use of PROCHIs)

  • Duncan: multiple projects, supervisor for multiple projects.

    • Not quite sure what they could do if it was just one project.
  • Simon: Unique indv. in a geo loc area. on a drug for HIV, could narrow it down to an indv.

  • Duncan: Triangulation of individuals.

    • Disclosure control, 1 person in an area or presribe a drug by area. When we release data we don’t do that.
    • If they try to hone in on an individual.
    • Could see evidence of that.
  • Keith & Alison & Duncan: no real evidence, more on back of other ‘news’ items of lost CDs.

  • Simon: Lookup of anochi has been done.

  • Keith: Frank Sulivan, share register. People that are pro-research studies. Your data has been used in these studdies.

  • Simon: Calco Jack finding people for projects

  • Duncan: (Shaun)

  • Keith: Might encourage them to share data, if they can see what it has been used for, build confidence.

  • Simon: Adding remaining stories; @@Keith setup on trac

  • Simon: Check email list for hic mail addresses.

  • Alison: Some anon. data sets soon.

    • Some example projects that these data sets have been used in.
  • Simon: 6-8 months time, from pull of NHS we can drop it in to OMERO and test it. Alongside current system. (Check SOPs. As part of SHIP?)

  • Duncan: McKensie lecture: omero lecture/workshop to talk about it. SHIP. In Dundee

  • Josh: Workflows, web team. Interesting in being involved. Maybe with Alison. So that it feeds in to later project

Done: 15:00

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