2010-05-18 Tuesday Meeting
Agenda
Remember: Agenda must be complete (with estimated times) on the day before the meeting. Any additions after that must go at the bottom (AOCB)
Accepting minutes from last meeting
Matters Arising (<10 mins)
- Tagging Group: Meeting on Friday morning (10:15ish)
- Andrew: Contact list about when we release the next major schema (and Paris)
- Ola: respond to web start question
- Brian: 2 QA tickets need loking at
Status Update (20 mins)
- Summary of last week visit (Will)
- Namespaces for tags (Andrew)
Testing Script (20 mins)
AOCB (<5 mins)
- ROI Mask additions?
Notes
Minutes accepted
- Chris: annotation change seems fine
matters arising
-
Annotation
- Changing schema, one rename
- Chris: annotating annotations will be hard to code-generated
- Code-gen went through previously
- in schema and 4.2 releases
- forum/email items were or will be handled
-
Annotation
EM summary
- reduction of submissions; not offering many features
- looking into features which people want to bring them back
- a certain number of papers require it (enforced?)
- feature 1: more than the final structure but also the raw data
- feature 2: maps/masks of chains (segmentation of volume)
-
OMERO: need image-image links
- Use annotation as a proof-of-principle
- Ingvar gave a presentation
- writing MRC format?
-
next steps:
-
demonstrate interaction via OMERO
- linking eman2 and spider and open astec viewer
- they use all different languages / formats
- will be a while before don't need external tools
- focus on using processing as demo
- deadline? * first year report in autumn
-
how to represent an EMAN2 project in OMERO (processing workflows)
- currently uses a local berk. DB
-
demonstrate interaction via OMERO
-
Didn't discuss
- communication channels
- trac / tickets / etc.
-
Misc
- Goal of using applet / viewer
-
Need for having a real user on board
- Jason has already contacted some
- Usual problem of selling the benefits
Namespace for tags
- Andrew: bad form to not be filling the ns in our own annotations
- Purpose of ns: gives us is to know where annotations came from
- Chris/Josh: would rather have "ome.org/" rather than ".../"
- Chris: we care about things that were imported & things exported
- Also need to consider the relationship to Namespace
- Jean-Marie: cF. mavkeMovie.py. Need to setup a standard
- Josh: can use a ".../legacy" namespace for the upgrade
- Jean-Marie: Currently use namespaces in a functional/interpretative way
- Will: are we going to get collisions on the namespaces?
- Chris: namespaces weren't designed for origins
- Josh: namespaces were initially designed for defining the intpretation of the SA
-
Andrew: why did we just add "tag", it's another string?
- "We think term/xml is good on their own"
- Potentially use references to namespaces (top-level)
- Agreed: have to clean up our own namespaces
- Rest to be discussed later
-
Jason: @Tabling and asking in Paris?
- Yes/no: do ask in Paris, but we need to get something ready for release
Testing scenario
- Brian was supposed to prepare one (not present)
- David had something on the UI website (couldn't be found)
-
@Will & Jean-Marie prepare something for Thursday
- Writing up all the movies
- Add that to a wiki page: http://trac.openmicroscopy.org.uk/omero/wiki/TestScripts
- @Jason will provide a list in the next day and a half
- http://wiki.secondlife.com/wiki/Category:Test_Scripts
Importer status
- Jean-Marie tested Friday->Monday all test_images_good
- 5-10% passed (imported at all)
- Brian's changes as of Friday, ~15%
- As of Monday with Chris and Brian, ~40%
-
As of now, ~75%
- Goal by end of today is to have everything going in
- Some are silly things (enum not matching, -60 for pos. integer)
- Then will have to verify the metadata
- Start on Thursday to do validation
- Filters / filter sets going in (no light paths currently)
- NB: Export image won't provide much information
- 4.2 will export in entirety
-
Name accounts datasets with name of folder?
- Using testengine to setup, and then need visual validation
- Melissa? Y Carlos? N
- Only test_images_good
- See "New Metadata store" ticket (#2361)
Misc
-
Josh:
- configuration / deployment code to be committed on return
- database upgrade not done. may need to share plpgsql effort in June
-
Andrew:
- RoiMask? @fix it!
-
Josh:
Post-mtg mtg: annotations / namespaces
- Donald: is ns "source" or "intent"?
- Jean-Marie: for TermAnnotation we decided against version
- Helpful to compare to XML?
- Josh: NS/schema are extra layer of validation
- Jean-Marie: But we don't have multiple namespaces like XML
- Will: if you support multiple namespaces, then it's fine
-
Andrew: ns & origin discussion is not quite right
- URL in XML NS about where it comes from
- that part doesn't define what created the XML
- "ome.org/tag" doesn't say "this tag from omero"
- but "this interpretation of tag by omero"
- Josh: can "" or null not implicitly mean "openmicroscopy.org"
- Jean-Marie: making the model more usable
- Andrew: fine with a default
- Donald: trying to prevent empties
-
Using for 2 purposes
- Rating namespace
- Friday talked about using namespace term-annotation for external entity
- Will: in some cases it's how to display in GUI (displayed, etc.)
- Josh: is a single namespace just not useful enough?
-
Suggestion: drop the REQUIRED and suggest multiple namespaces in Dundee?
- Andrew: still worried that we'll never get namespaces
- Josh: could we not make empty ns's well-defined? (but some people will want to use them)
- Donald: thought that the Namespace was the beginning of this
- Josh: agreed, just need to test well, which is why it's available now
-
Donald: just merging the code today, starting to work with arrays of strings
- good testing. should know. have good scripts for testing.
- @Discuss in Paris
- Jean-Marie: still think we mismatch source v. intent
- Andrew: Caitlin had a notion of a creator (Photoshop)
- Also discuss in Paris?
-
Josh: relationship to RDF
- Donald: alternative storage?
- Josh: still have to consider
- Donald: should we in general ask about how people have extended OMERO