2015Mar24

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Etherpad for meeting notes: http://firuta.huh.harvard.edu:9000/FP-2015Mar24

Agenda

Non-Tech

  • Results of Meeting With AnnoSys
  • Publications
    • Paul/James: Collection Objects
    • Paul/Bob/David: QC Reports
    • Bob: Refactoring Dup finding cluster analysis
      • Bob: Access to larger scale infrastructure
    • Bob: List of additional topics
  • Schedule: Next call next week?.

Tech

  • Annotation Processor
  • State of Deployments
    • FP2.acis
      • Status of InvertEBase setup
    • FP3.acis
      • State for harvest for NEVP
  • Morphbank integration
  • Habitat, Phenology Ontology work.

Reports

  • Paul
    • Updates to symbiota RDF presentation of occurrence records to support FilteredPush-AnnoSys integration (to allow easy incorporation of a context of an annotation into the annotation.
    • Work on a scientific name validation tool derived from existing FP and Kuration code.
    • Met with Patrick and Bob to discuss knowlege representation of Habitat and phenophase for NEVP.

Notes

FilteredPush Team Meeting 2015 Mar 24

Present: David, Tim, Paul, Jim, James, Bob, Tianhong

Non-Tech

  • Results of Meeting With AnnoSys

Bob: Met with Lutz and David from AnnoSys, defined an architecture for exchanging annotations, made progress towards implementation. Including clear definition of what is needed to interchange annotations.

FP-AnnoSys meeting whiteboard diagram.jpg

David: Wrote an API to allow them to query for annotations with a date range.

Paul: We made significant progress on the hardest point of interchange, context.

David: We can now embedd context in annotations generated from Symbiota, added that ability to client helper and our symbiota hoods.

James: Shall we follow up with Walter?

Bob: Yes. We'd like to demonstrate something at TDWG.

David: Remaining work on our side is minor. Lutz is working on converting our annotations, bits of infrastructure needed on our side are needed anyway.

James: Can we obtain an executive summary to circulate?

Bob: Can start on on Friday.

  • Publications
    • Paul/James: Collection Objects

James: Have a draft circulated out to rest of authors. Would like to set a date. Need to add references. Dina group is aiming for workshop to finalize data model in late April.

Paul: Let's aim to have something ready to submit by Apr 17th.

    • Paul/Bob/David: QC Reports

No progress.

Paul, Bob, David to sit down for an hour on thursday and work on making a firmer outline.

    • Bob: Refactoring Dup finding cluster analysis

Bob: No progress.

      • Bob: Access to larger scale infrastructure

Bob: No word yet, time to poke the Brazilians again.

    • Bob: List of additional topics
  • Schedule: Next call next week?.

Next FP call in two weeks, on April 7th.

Tianhong: Need general feedback on circulated paper. Thanks to Jim for good feeback. Deadline is a week from now. Everyone also please check your affiliation. we can do it here:

Tianhong Song1, Bertram Ludäscher2, Saumen Dey1, James Hanken3, David Lowery4,6, James A. Macklin5, Timothy McPhillips2, Paul J. Morris3,4, Robert A. Morris4,6 1 Dept. of Computer Science, UC Davis, CA, USA 2 Graduate Sch. of Library and Information Science, UIUC, IL, USA 3 Museum of Comparative Zoology, Harvard University, MA, USA 4 Harvard University Herbaria, Cambridge, MA, USA 5 Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada 6 Computer Science Dept., University of Massachusetts, Boston, MA, USA

Tianhong: OK, will modify according to the above

Tech

  • Annotation Processor

David: Started looking at getting web application deployed for testing. Started work on implementing API for annotation digests (helped by work with AnnoSys). About a week or two away from getting back up with Camel infrastucture. Have also started into driver using specify hibernate classes, separated from buisness logic, trying to reuse those with spring, need to add busness logic.

  • State of Deployments
    • FP2.acis
      • Status of InvertEBase setup

David: Switch not on for InvertEBase symbiota instance, just need that switched. Seeing some issues with fedora and mulgara on FP2, may have annotations in wrong store. Need to check configuration.

    • FP3.acis

David: Up to date.

      • State for harvest for NEVP

David: Ran a harvest of occurrences. Ran into issue mid harvest, ran into a date issue.

  • Morphbank integration

David: Greg R. got back to us. They've updated their PHP version and they are ready to move forward. Getting an environment set up to mirror that to test, then check into trunk.

James: Should remind Greg that we are winding down.

  • Habitat, Phenology Ontology work.

Paul: Met with Patrick Sweeney (Bob, Paul, James, Joel, Heather). Talked about representation of Habitat (verbatim plus a list of to be determined controled vocabulary values), and phenophase (leafing fruiting, flowering state). Habitat, clearly two phases, capture verbatim values then encode. Provided Patrick with a list of values from the wild. Can be in locality description or in a habitat field, need annotation for carrying transciption of both. Phenophase looks like coding based on list of (practically tested) states of flowering, fruiting, leaf state. Phenophase codings map poorly to Plant Ontology terms. List from Richard is tested by multiple coding attempts of same specimens by undergraduates, produces codings on images in the wild, can be used to fill the science goals of the project. Some relationship to the encodings in FNA, but weak, as that data is on the order of "Flowering: July-August", and doesn't map well.

James: Good incentive to move forward with apple core, this is good place for these vocabularies to go for development.

Paul: Relationship to Kurator: Flowering time validator.

James: Target new implemetation in FNA of service, late spring or summer.

Tim: Put issue into Jira.

Paul: https://opensource.ncsa.illinois.edu/jira/browse/KURATOR-101