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You are here: Home Community Minutes Mini Group meetings OMERO/HIC Meetings 2011.05.14

2011.05.14

Attending: Andy, Josh, Simon

Notes

  • Andy: status update for Andrew

  • Are there any blockers?

  • Anything that HIC can help with.

  • Simon: still working on script

  • Should be in the expected position from last time next week?

  • Data In / Out finished

  • Have been side-tracked by the Getting Started documentation

  • Josh: should also env up as a researcher-developer overview page

  • Simon: even better. Have been working with Will for trails

    • Through the wiki for how to write scripts
  • Andy: important for down the road when OMERO team moves on

    • Others will need to maintain
    • Andy may need to start writing scripts even before the researchers.
  • Job adverts

  • Andy: have we heard anything?

  • @@josh: Access to Alfresco and/or a Zip of the files

  • GoDARTS/Data

  • Andy: Have a meeting to work out the exact workflow

  • Jason holding off for the input/output script (?)

  • Earliest will be June

  • Simon: would be godo to have some idea of the workflow

  • Andy: making sure data in/out for start of June

  • Andy: gone second half of June, may be a dead month

  • Josh: don't want anyone's expectations too high

  • Simon: was aiming for today, but hopefully caught up by the middle/end of next week

    • Then set a soft deadline.
  • News/HW

  • Andrew has authorized a new physical host server

  • Current also hosts Citrix; resources will get shared between two boxes

  • Maybe move OMERO over and expand drive; a bit more flexility.

  • Looking at a data

  • scidc is diabetes

  • most important is CHI_master_index (one record per person)

  • then biochemistry

  • then HbA1c, bmi, prescribing

  • then smr01 (linkage to external data set)

  • can ignore descriptor at the moment

  • hardcode 100 rows for the moment

  • CHImaster_ALL is longitundinal, demographic data

    • Table structure is different
    • ALL has more than one record per person
  • gro (general register / death)

    • death should match to CHI_master_index
  • scidc

    • @@Andy will come back with prescribing joins
    • Josh: might be interesting to have the join information in the schema as well
    • Andy: had thought about a command-line tool to slurp in the files
    • Josh: same here.
  • Andy: This is typical of any experiment. Every joins on prochi, with other tables

  • Josh: do we need to reify these other concepts?

  • Andy: not for the moment.

  • Keep in mind

    • Variable names in the column names are not
    • GoDARTs team likes their names in a certain style
    • @@Josh: aliasing support in storage.
    • @@Andy will be check what columns have been changed from underlying table
    • Josh: May be a place where want to use LSID
    • Andy: new extract of GoDARTS data is in process
      • Hopefully we can work with that clean data
      • At that time we could add "original_name"
    • Josh: need to handle multiple aliases?
      • Andy: too complicated for a pilot.
  • Simon: currently working on uploading

    • Josh: any column types missing?
    • Simon: not yet.
    • Andy: data types - integers, reals, floats,
    • Andy: one issue is an integer column with null handling.
      • Josh: how many columns don't have a NULL-valid value
      • @@Andy: perhaps add PositiveInt,etc. values to the schema
        • Not a short-term doable; that doesn't exist.
    • Andy: hic extracts are DAY/MON/YEAR, but specified in header
      • also erroneous dates!
      • Josh: do we store them as strings?
      • No. Store as date. Though the researcher may tell us otherwise.
      • but all in the same timezone
    • Josh: string lengths?
      • Andy: Need to work out what the longest value was.
      • 255 tends to work
      • but it's trial and error
      • often come out with a lot of space around it.
      • prochi however is 10.
      • @@Andy will ask around
  • Josh: Looks we're approaching a common description language.

    • Andy: already used extensively internally
    • ... to generate Word DOCs, etc.
    • All in C#
    • May be able to make things nicer on the Windows side.
  • Misc

  • Next talk May 27

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