VoCamp1/Meeting Notes

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Follow-up meetings

First follow-up teleconference

Friday, December 4 at 10 am EST (GMT -5)

Agenda and Goals

1) Follow-ups to VoCamp

2) Opportunities presented by ToLWeb



  • Arlin Stoltzfus
  • Karen Cranston
  • Brandon Chisham
  • Josh Reece
  • Anne Thessen
  • Chris Goddard
  • David Kidd
  • Peter Midford
  • Raven Travillian
  • Joel Sachs
  • Hilmar Lapp
  • Sheldon McKay
  • Nico Cellinese
  • Bill Piel

Active follow-ups:

  1. High level relations ontologically between trees and characters (Arlin)

Proposed follow-ups:

  1. Peter: last use case linking char data from Phenex NeXML file with Darwin core; would enable Phenoscape linking to all databases, not just those it already has a (social) relation with, e.g. ZFin. Q: How does making data available as NeXML help others reuse the data? Tangible outcomes?
  2. Hilmar: phyloreferencing reference implementations; SPARQL queries that interpret PhyloWS; RegNum would use for definitions and could also implement queries across resources; iPlant has two active use cases that involve labeling internal nodes (wrt TreeViz and APWeb); iPlant building database of phyloreferences, possible funding for hackathon type event?
  3. Karen: Symposium at SMBE? Examples of people actually linking data to do research (as opposed to use cases and making standards); Joel has a few examples but nothing has been published
  4. Arlin: Lack of adequate tutorials / demos; biological examples; how does link data help with integration; how do I expose my data? Joel says general tutorials exist but extending to biology is problematic due to difficulty of defining identifiers for key concepts (e.g. taxon names)

Tree of Life Web (ToLWeb)

  • David Maddison looking for someone to take over
  • Work with existing board and curators; find funding
  • Future ideas about ToLWeb need to focus on INTEGRATION (linked data, de-siloing); making it THE tree of life website
  • Stakeholder meeting to develop a vision - curators, users, other data providers, possibly at NESCent
  • Taxonomy (EOL) vs Phylogeny (ToLWeb); ToLWeb would provide the phylogenetic classification
  • EOL and ToLWeb also provide different different measures of biodiversity
  • Hilmar: ideas about ToLWeb circulating at NESCent for a while
  • Karen: EOL / BioSynC interested
  • Anne: EOL data all associated with names; how to map EOL names with phylogenetic names

Planning Meetings

Third Teleconference

Thursday, October 22 at 3:30 am EDT

Agenda and Goals

1) Training

2) Pitches



  • Arlin Stoltzfus
  • Karen Cranston
  • Enrico Pontelli
  • David Thau
  • David Kidd
  • Chris Goddard
  • Julie Thompson
  • Joel Sachs
  • Farshid Ahrestani
  • Raven Travillian
  • Peter Midford
  • Josh Reece
  • Hilmar Lapp
  • Nico Cellinese
  • Rutger Vos


  • RDF / RDFa / Sparkl / OWL / Linked Data (Farsheed will post OWL slides on wiki in advance of meeting; Joel to lead bootcamp with help from Phil, Enrico; focus on common misunderstandings)
  • Protege
  • Phylogenetics (Karen, Josh, Nico)
  • BioPortal / Gene Ontology (Hilmar, Phil)
  • Community resources for ontologies (BioPortal, OBO, TDWG, etc; Hilmar, Phil)
  • TDWG best practices for development & maintentance (Stan, John)


  • Encourage more pitches at this point; likely end up with 7-8 at the actual meeting
  • AllegroGraph might be available at meeting for testing; storing and querying triples; server and support provided; does license include any restrictions? Other option is Virtuoso
  • First morning of workshop (Saturday) will be Open Space activity to break out into subgroups
  • Status of TDWG ontology pitch. Arlin: What does this mean? Stan: see how can we enhance early TDWG ontology / merge with Darwin Core. Might be similarities with the pitch / bootcamp about TDWG processes?
  • Reasoning about related taxonomies. Nico: Do we need an introduction to the PhyloCode? perhaps as part of Phylogenetics bootcamp.
  • Use email list and wiki to discuss pitches in advance of the meeting!

Second Teleconference

Thursday, October 15 at 10:00 am EDT (8??am PDT, 16:00 CEST, 14:00 UTC). We will begin on time and end promptly at 11:00 EDT.

Agenda and Goals

Same as for Monday's telecon (go there for more detail).

  1. Introductions
  2. Questions about wiki and mailing list
  3. Review of VoCamp schedule and expectations
  4. Questions about expectations
  5. Further discussion until the hour is used up


present: Josh Reece, Sheldon MacKay, Arlin Stoltzfus, Rutger Vos, Hilmar Lapp, Bill Piel, Jeff Wilcke, Anne Thessen


  • RV: treebase, metadata, nexml, phyloWS
  • JR: phylogeography,
  • AS: evoinfo group, CDAO
  • HL: cyberinfrastructure, evoinfo, queries on trees
  • BP: treebase, iptol, taxonomic annotations
  • JW: SNoMed, vet sci, taxo model in SNoMed, term services lab; align bio-top, snomed and bfo
  • AT: eol, marine life, informatics for ecology
  • SM: phylogenetics, comparative genomics;

Use of shared resources (wiki, list)

  1. RV: OpenID new? separate accounts?
    • HL: yes, yes
  2. JR: Acronyms are confusing. How familiar should I get with resources before VoCamp?
    • SM: will expand acronyms. depends on interests
    • HL: focus on your interests

VoCamp schedule and expectations

  1. JR: how much focus on programming vs. abstractions?

Training and bootcamps

Participant ownership

Ideas for pitches

  1. Rutger: (please put this on the wiki pitch page)

First Teleconference

Monday, October 12 at 4:00 EDT (1pm PDT, 22:00 CEST, 20:00 UTC). We will begin on time and end promptly at 5:00 EDT.

Agenda and goals

  1. Introductions
    • Name
    • Disciplinary training ("field")
    • Primary research interest in 6 words or fewer
    • Names of ontology-related projects you have worked on
    • Primary VoCamp interest
  2. Questions about wiki and mailing list
  3. Review of VoCamp schedule and expectations
  4. Questions about expectations
  5. Further discussion until the hour is used up

Desired outcomes for today:

  • participants are aware of shared information resources, and know how to use them
  • participants (including organizers) know each other by name
  • participants know what is expected of them
    • they know what is going to happen at the VoCamp event
    • they know what are their roles before, during, & after VoCamp
    • they understand how to take ownership of the event


present: Sheldon MacKay, Mark Schildhauer, Stan Blum, Dave Thau, Arlin, Joel Sachs, Karen Cranston, Enrico Pontelli, John Wieczorek, Mark Wilkinson, Chris Goddard, Jim Case, Jonathan Rees, Rosemary Shrestha, Ravensara Travilian, Greg Whitbread, Peter Midford


  • SB: tdwg
  • KC: eol
  • CG:tolkin
  • JC: natl ani health network
  • HL: cyberinfrastructure, phyloWS (querying)
  • SM: tol, gmod,
  • PM: phenoscape, onto alignment
  • EP: CDAO
  • JR: science commons
  • GW: systems to support nomenclature
  • RT: vert ontogeny & phylogeny
  • MS: nceas, data interop, SONNet
  • JS: spire
  • AS: cyberinfrastructure, comparative analysis, CDAO,
  • RS: crop ontology,
  • DT: data integration, aligning taxonomies, TDWG, regnum
  • JW: taxonomy, darwincore
  • MW: exposing web services on the semantic web

Questions about VoCamp

  1. Mark S: Should we look for spontaneous collaborations or delve deeply into pre-existing projects?
    • HL: take advantage of opportunities for unique collaborations is preferable
  2. What are some examples of products of a VoCamp?
    • not many to go on
  3. Mark S: OK to organize before-hand?
    • yes
    • organizers act as participants during the event
  4. Joel S: why vocamp instead of hackathon?
  5. Mark S: PATO?
    • Peter, Hilmar

Training and boot camps We need to identify needs for training and information (e.g., how to use Protege, what is PhyloCode, what is CDAO, etc). Stay tuned for further communications on this topic.