Joint Working Group on Observational Data Semantics: SONet, DataONE, Data Conservancy
(note: consider having lunch sent in?)
(note: was trying to slot about 4 hrs to each session-- but ran out towards end)
Participants
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Shawn Bowers bowers@gonzaga.edu
Corinna Gries cgries@wisc.edu
Philip Dibner pdibner@ogcii.org
Deborah McGuinness dlm@cs.rpi.edu
Matthew B. Jones jones@nceas.ucsb.edu
Mark Schildhauer schild@nceas.ucsb.edu
Dave Vieglais dave.vieglais@gmail.com
Carl Lagoze clagoze@gmail.com
Hilmar Lapp hlapp@nescent.org
Jeff Horsburgh jeff.horsburgh@usu.edu
Margaret O'Brien mob@msi.ucsb.edu
Andrew Maffei amaffei@whoi.edu
Ruth Duerr rduerr@nsidc.org
Stephan Zednik zednis@rpi.edu
Ben Leinfelder leinfelder@nceas.ucsb.edu
Chris Jones cjones@nceas.ucsb.edu
Invited but unable to attend
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Josh Madin jmadin@bio.mq.edu.au - not attending
Steve Kelling stk2@cornell.edu - not attending
Luis Bermudez lbermudez@opengeospatial.org - not attending
Chris Mungall CJMungall@lbl.gov - not attending-- at European mtg
Cam Webb cwebb@oeb.harvard.edu - not attending-- in Indonesian forest
Peter Fox pfox@cs.rpi.edu - not attending
David Tarboton dtarb@usu.edu - not attending
Simon Cox simon.cox@csiro.au- not attending
Peter McCartney pmccartn@nsf.gov - not attending
Cyndy Chandler cchandler@whoi.edu- not attending
Mark Parsons parsonsm@nsidc.org- not attending
Goals:
1. Can we do more integrated ontology development? Incorporate different ontologies together?
Agenda
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Mon, April 18
9AM Overview--- introduce Data Conservancy/DataONE and Joint Working Group; review original mission of SONet and JWG Ithaca meeting--"foster more data-sharing outside of silos"; and provide overview of this meeting's goals (20 mins; Schildhauer)
9:20-9:30 Introductions
9:30-10:30 Demonstrations/descriptions of capabilities of ongoing projects implementing observational data models 20 min. each (15 min + 5 min ques)
SONet-semtools (Bowers/Leinfelder)
Data Conservancy Semantics(Lagoze)
DataONE Semantics (Vieglais?)
10:30-10:45 break
10:45-12:05 20 minute presentations, continued
Phenoscape/EQ (Lapp)
OOI (Maffei-- working with RPI; images
NSIDC (Duerr)
VSTO (Zednik/Fox; alignment of VSTO onts with O&M 2.0)
12:00-1:15 lunch
1:15-2:00 20 minute presentations, continued
HIS (Horsburgh-- O&M?)
SW Darwin Core (Webb/Baskauf-- remote submission)
2:00-2:30 Discussion
Where are there strong partnerships already in place among our projects?
Review proposed sessions for framing further discussion--
need for new/revised topics?
2:30-3:30 Session 1: Observational data ontology co-development
* Product:
-- Should we coordinate observational data ontology development across our projects?
-- If so, how should that be technically and procedurally facilitated?
Details:
* process for submissions; reviews; revisions & versioning; formats & standards; citation;
* OBO curated model vs autonomous communities (simple repository model)
* mechanisms for sustained sharing of information regarding: implementation, capabilities/shortcomings of various models
* need for "framework", process, and tools to enable collaboration--identify and discuss candidates for these?
* establish shared corpus of test data
* establish shared corpus of Use Cases-- already exist? need more refinement?
* establish shared corpus for semantic code?
* are there specific types of ontologies that should be co-developed and shared?
3:30-3:45 Break
3:45-5:00 Session 1: Observational data ontology co-development (continued)
6:30 Dinner together for those interested
Tues, Apr. 19
9:00-10:30 Continue and conclusions for Session 1
10:30-10:45 Break
10:45-12:00 Session 2: Comparative ontology review (better to name something like "Challenges in Domain Ontology alighment"?:
*What relevant ontologies should be included in co-development activities?
* Side-by-side comparisons of favored ontologies: broadstroke-- identify areas of overlap, gaps and dependencies. Identify structural differences, types of constructs used-- e.g. equivalence classes, class vs. instance prevalence, natural language descriptions, partial/complete (some of these more sophistacted topics might better go in the 'semantic capabilities' session)
* Authority-- how are communities going to develop and adopt ontologies? Is there need for "sanctioning"
* How deal with integrating disparate and/or complementary ontologies-- feasibility of referencing multiple namespaces, or need for a fully integrated (monolithic) ontology.
Candidates to review: OBOE-SBC, VSTO, SWEET, ENVO, PATO, PlantOntology (PO), Trait Ontology (TO)
WaterML in O&M?
Semantic Darwin Core
12:00-1:15 Lunch
1:15-3:30 Continue Session 2: Comparative ontology review (better to name something like "Challenges in Domain Ontology alighment"?:
3:30-3:45 Break
3:45-5:00 Continue and conclusions for Session 2
6:30 Joint dinner?
Wed, Apr. 20
Session 4: Semantic capabilities-- Examples of semantic queries enabled by observational data model
* clarifying nesting constructs in data
* clarifying observations associated with same instance
* clarifying primary (direct) from inferred measurements
Session 5: Mechanisms for binding ontologies to raw data (semantic annotation), and storing, retrieving and interpreting semantic annotations.
Data interchange format--v. W3C group on annotations--Annotation Ontology (AO)
LOD
resolving ABox-TBox in scalable solutions
Wed, Apr. 20 1:00-3:00P
Session F: Leaders' meeting-- plan for next working groups; way forward; products; new partnerships and opportunities
Session G: Managing complexity for scientists-users
Session D: (too complex for this meeting-- hold off for more focused meeting) ODPs-- ontology design patterns (especially context; recursion of "entities"; best practice with OWL-- e.g. complete definitions, equivalence classes) for modeling observational data
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Questionnaire:
Shawn suggested we ask participants to fill out a questionnaire asking them about their work; below are some topics we could cover:
Regarding observational data semantics, please concisely address the following questions.
1. What is the main URL where you are reporting on your observational data semantic efforts?
2. What are the 2-3 most useful publications where you are describing your observational data semantic efforts?
3. What are the main informatics or analytical challenges and Use Cases driving your work on observational data and semantics?
4. Do you have a specific corpus of data that you are using to focus your efforts with observational data? If so, are these publicly accessible?
5. What are the primary data types/formats of concern? Is your focus on: data discovery; data integration; analysis and modeling; linking data to publications; linking data to analyses? (URL)
6. What ontologies you are using in your work? What format these are in, what is their stage of maturity, and what are the intended uses for these? (URLs)
Which of these ontologies are you developing in-house, and do they depend on other ontologies?
7. Are you constructing an open Code base for your efforts in observational data semantics? Are you developing and sharing API's, libraries, open-source, etc.? Do you have an over-arching architectural diagram you can share that depicts your work on obserational data semantics?(URL)
8. What standards/specifications, etc., if any, must you conform to in your semantic development on observational data? E.g. compatible with OGC O&M WATERML
9. How much actual workforce is available to advance observational data efforts in your program?
10. What specific semantics capabilities are you expecting will be enabled by adopting an Observational data model?
11. What are the major impediments to progress in semantic tools development for your project?