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Etherpad for meeting notes: http://firuta.huh.harvard.edu:9000/FP-2011Mar29

User: David Lowery | User: Zhimin Wang | User: BertramLudaescher | User: Paul J. Morris | User: James Macklin | User: Lei Dou | User: Tim McPhillips | User:
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  1. Brief Reports from Tucson meeting with Hong Cui's semantic markup project
  2. Brief Report from Chicago SI2I meeting.
  3. REU
  4. Goals for SPNHC workflow demonstration
  5. Consider FP service for Symbiota portal for duplicates use case and beyond (http://symbiota.org/tiki/tiki-index.php)


  • Bob
  1. Spent week in Tucson on Hong Cui's Biosemantics literature mining project
  2. More playing with SMW, trying to import skos properties
  3. Telecon with Paolo Ciccarese, Paul, Zhimin about data extensions to AO. See AnnotationMotivationAndExpectation
  • Paul
    • Also spent week in Tuscon, FNA and Hong Cui's semantic markup project.
    • Substantive progress on data extension for AO Annotation Ontology, expanded on and refined examples.
  • James
  1. Also, spent week in Tucson on Hong Cui's Biosemantics literature mining project and considering a new web presence for the Flora of North America (part of an FP demonstration outcome)
  • Lei, Tim and Bertram
  1. Attended S2I2 meeting in Chicago (Bertram)
  2. Evaluating services which might be useful for curation, e.g. IPNI, GNI and geomancer etc., and trying to figure out how to integrate them in SPNHC demo.
  3. Working on refinement of provenance browser
  • Zhimin
  1. Deploying demo to Firuta
  2. Reading paper about semantic of update in database with regard to the push part of our annotation
  3. Continue interface design

Meeting Notes

Filtered Push Team Meeting 2011 Mar 29

Present: Zhimin, Paul, David, Bertram, Lei, James, Tim (coming in later).


1. Brief Reports from Tucson meeting with Hong Cui's semantic markup project

James: Annual meeting of project parsing literature, connection is Flora of North America. Other involved parties include the Treatase, and HAO. Several CS folks. (Thursday, Friday). Also, Monday, Tuesday, Wednesday, FNA parsing and web presence meeting. FNA trying to migrate from old web presence with limited support to a new supportable place for the floras (including both legacy and yet to be published floras). One portion of discussion: moving FNA into Semantic Media Wiki.

SMW home: http://semantic-mediawiki.org/wiki/Semantic_MediaWiki Another important installation http://data-gov.tw.rpi.edu/wiki at RPI Tetherless World project

Bob: Hong also getting involved in mining grey literature, which is way harder.

Paul: Clear than human intervention, particularly ontology building important for further refinement.

2. Brief Report from Chicago SI2I meeting.

Bertram: Biosynth center at field museum. Chris Norris and Jim Beach hosting. Group included both engineers, buisness, workflow, biodiveristy collections people. Topic of workshop: digitization of biological collections. Included tour of field musem collections. Associated automation conference/trade show, group went to visit that trade show. Specify 6 demonstration with embedded duplicate detection. Might be good client components for a FP network. Had good discussion with Amanda about Kepler workflow client to FP. Human in the loop workflow went over well with the audience. Has presentation ready for internal circulation. Several other interesting presentations. (e.g. http://www.apiaryproject.org, more in the meeting notes that I'll forward)

Review Lei's video of Workflow.

Sidenote: A more closed presence somewhere for internal collaboration of material not ready for public distribution would be helpfull.

Bertram: Where are we with structured descriptions of annotations:

Bob: See: http://bioportal.bioontology.org/ broader issue of curation of ontologies. Answered question you didn't ask. Tell darwin core maintainers that they need a better darwin core.

Paul: See http://etaxonomy.org/ontologies/ao/ for current examples.

Bob: Be skeptical when you read these examples, we haven't fully brough them up this weeks' discussions with Paolo, and Paolo is refactoring AO itself. W3C effort will involve refactoring that is still in his head.

James: need Protege to look at these? Bob, Paul, can make some of it from text editor.

Discussion of Specify duplicate finding functionality.

3. REU

Bob, James, Paul to put together brief paragraphs this week.

4. Goals for SPNHC workflow demonstration

Lei: Set of use cases for quality control, has brief list of potential services, IPNI, GNI, Biogeomancer, Geolocate. One issue, using GNI, finding lexical groups, documented API doesn't match presentation found on website. Specify 6 integrates Geolocate, (Biogeomancer not there? or integrated with google earth), OneMind. Looking at these to see if there is specific biological information available.

Paul: FNA phenology service.

James, to explore fesability of this with Hong.

Discussion of data for demonstration, could be culled from GBIF cache, could be synthetic. Consider discussion with Andrew Richardson - New England Camera phenology network.

Lei: More technical questions for Friday.

James: Want to show a couple of examples. Want to focus on showing data qualtiy issues.

Bertram: Keep the feasable over the fanciful.

James: Whole purpose of democamp is to demonstrate the feasable.

5. Consider FP service for Symbiota portal for duplicates use case and beyond (http://symbiota.org/tiki/tiki-index.php)

James: Symbiota, portal with services for data quality and data massaging, aggregation of data from various collections along with maps and images. Developer is a botanist. Interest in duplicate detection, something like 50 different collections. Where can we go to show people what can be done with connected data. Northeastern herbarium collections network likely to use Symbiota as portal.

Exsiccatae - published sets of duplicates, particularly in cryptogams. Exsiccatae

James to work on list of potential clients/collaborators, and benefits for each.

Zhimin: Tim mentioned lastweek, probably good for us to have a place to show the progress of the project.

Bertram: Reorganization of web presence.

Tim: Started on this on the wiki. Began organizing content.

Bob: Low hanging fruit is categories for pages. Categorize current pages into some good functional groupings.

James: Good by SPNHC to have a more organized presence.

Bob: Finalize when to meet at SPNHC.