2013Jun19

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Etherpad for meeting notes: http://firuta.huh.harvard.edu:9000/FP-2013Jun19

Reminder: Change of meeting time effective Sept 4: (12-1 Eastern 9-10 Pacific).

Agenda

  • Project/Package Refactoring: Developer Documentation
  • Annual NSF project report: update GoogleDocs doc by June 24th.
  • NEVP TCN Support
    • Overview of state of project
    • Timelines for deployment
  • SPNHC Demonstration
    • Walkthrough of current state.
    • Example data and workflow.
  • MCZbase Driver

Non-Tech

  • Third Project Programmer, Burndown.
  • Recent Contacts
  • Collaborations
    • Specify/Symbiota
    • SCAN TCN
    • NEVP TCN

For Future meetings

Reports

  • Paul
    • With lots of help from David, Maureen, and Tianhong, have demo running with Specify6+AnnotationProcessor on laptop, FP Node infrastructure including Kepler with QC workflows, and Symbiota running on FP2 and FP3 VMs. Found and resolved lots of issues, both bugs and configuration. We can credibly show all the elements that we want to show. There are some service or data issues that need to be resolved with the workflows to enhance some of the data QC cases that we want to show.

Notes

FilteredPush Team Meeting 2013 June 19 Present: Bertram, Maureen, Bob, David, Patrick, Tianhong, James, Paul Agenda

  • Project/Package Refactoring: Developer Documentation
 Bob recommends a tag be made that says something about where the old code is before doing the refactoring
  • Annual NSF project report: update GoogleDocs doc by June 24th.

Bertram: I submitted an NSF report recently (final report for Kepler/CORE), with Research.gov and found many inconveniences: e.g. re-enter personnel, publications, etc. The system will NOT allow you to submit the report until you've entered all required fields. There are many required fields for pubs.. And the system will not tell you why you cannot submit and what fields are missing. I learned this by calling the NSF Help Desk.. James: Have added citations. Bertram: good! :) I had hoped previously entered ones would be copied. Also previous personnel etc. needed to be readded.

  • Support for NEVP TCN
    • Overview of state of project

FilteredPush What things are functional, what are we still working on. What's working:

  • the annotation side of the system; being able to describe particular business operations ike new determinations & georeferences, notifying interested parties, and ingesting them into a local Specify database.
  • integration with Symbiota
  • functioning Kepler analytical engine

What's not done:

  • duplicate detection

Infrastructure: 3 vms in Florida at iDigBio. One of those will be turned into a prod system for SCAN Patrick: Two major activities in last year: Collection (storage unit) level metadata - into QR Codes assocated with folders (species units). Second: production of hardware/software system "digitization apparatus" - capture information from specimens, from the QR Codes and from the labels (by keystroking and voice recognition). Data from primary digitization apparatus extracted into RDF/XML New Determination Annotation documents, ingest of these into Symbiota - then go on to FP to collections. Deployment and testing of generation and ingest of these documens (as well as iPlant image storage integration) needs to be done.

    • Timelines for deployment

Harvard: Mid July, installation and testing of digitization apparatus by team from OK, plan to go on line about mid-August. Other installations starting up in same time frame. Data coming from primary digitization apparatii to NEVP Symbiota instance by about mid August. Institutions: Harvard, Mid August. Yale starting in about 2 years. UNH and UMass Amherst and possibly Brown will be starting as early as mid-august. Action: Deploy annotation processor with Specify Driver at UNH, UMass, Brown, Annotation Processor with Specify-HUH driver at Harvard. Action: FP Node for NEVP on iDigBio VM, turn on FP integration in NEVP Symbiota instance. Action: Finish development of New Occurrence Annotations into Specify code in AnnotationProcessor. Patrick: Don't need to have ingest of data into Specify for smaller institutions occurring immedately, could have some backlog. Paul: Target HUH and one of the Specify institutions for initial deployment in Mid August, follow with other one or two after initial bugs have been worked out. Patrick: then roll out to the final two institutions. Where things stand with Emu integration may affect Yale rollout. Maureen: No contact with Emu developers since our initial discussions of the API. Augmentation: In Symbiota record habitat (with a controlled vocabulary) and phenological state (with a controlled vocabulary - leafing out state and flowering state). Will need annotations (and vocabulary terms) Lat and Long and metadata from town centroids - can produce annotations in bulk (or update in bulk in situ). Need: Annotations for Habitat and Phenological state. Target Sept 1, hand crafted habitat/phenology example annotations. Augmentation happening in years 3 and 4. James QC analysis probably valuable during augmentation, duplicate finding less critical. Patrick: Key bit connecting data back from Symbiota to the Specify databases. Morphbank would be nice, but not critical. James: Botanical network a key bit of FP, expecting NEVP as core, expanding to other parties joining in the network - duplicate detection more important for them. Patrick: Interface - the workshop at the CNH meeting? James: Yes for annotation processing, not for duplcate management. James: CNH a good chance to meet and see progress. Patrick: Need Blurb for agenda about FP UI workshop, few sentences. James: We can do that. Paul: Add Patrick to this call for the next couple of months? Patrick: That makes sense. Bob: Old duplicate finding code looks like it won't need much work, main work probably on UI.

  • SPNHC Demonstration
    • Walkthrough of current state.
    • Example data and workflow.
  • MCZbase Driver
  no word yet from Brendan

Non-Tech

  • Third Project Programmer, Burndown.
  • Recent Contacts
  • Collaborations
    • Specify/Symbiota
    • SCAN TCN