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            Designing an Exchange Serialization Syntax for Scientific Observations Data and Models: A Workshop of the TDWG Observations Task Group
        
    
        
  
      
      
        
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          jones
        
      
      
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TDWG Observations Task Group  TDWG 2010, Woods Hole, Massachusetts, USA Date: Thursday Sep. 30th, 2010, 8:30 - 11:30 am and 1:00 - 2:30 pm Venue: Room MRC 210 Workshop SummaryA model of scientific observations that is shared and semantically expressive is one of the most promising means to discover, access, aggregate, and analyse on a broad scale scientific data about the earth and the organisms that inhabit it.  To this end, the TDWG Observations Task Group aims to produce a specification for exchanging observational data from scientific disciplines that are relevant to TDWG, including species occurrences, species characteristics, ecological data, and environmental measurements. At this 2010 workshop, the Task Group will examine select observational data models, with the specific purpose to converge on an exchange specification for observational data that can serialize data from those models without losing semantic or quantitative information. The models to initially focus on were chosen for their semantic expressivity, potentially broad scope of data domains, and widespread current application for biodiversity science-relevant data. They include OBOE, the Extensible Observation Ontology, a semantic model originally developed to expose the semantic content of heterogeneous ecological and environmental observations; the OGC Observations and Measurements model, developed to exchange environmental observations as part of the Sensor Web Enablement suite; the Entity-Quality (EQ) model, developed for making descriptive biological observations computable; and Darwin Core, a vocabulary and also an XML format in widespread use to exchange species observations.  The activities planned for the workshop include 1) beginning to define a syntax for the exchange standard using a few alternative approaches (such as XML Schema and RDF), and 2) for each serialization approach, identifying issues in scalability, expressivity, tool compatibility, etc. early on.  Participants will draw upon existing serialization work in observations data modeling, including the use of the OBOE, O+M, and EQ serialization approaches. The development of the exchange specification, and thus this workshop, is coordinated by a partnership of the TDWG Task Group with the NSF-funded Scientific Observations Network (SONet) and the Joint Working Group on Observational Data Models and Semantics. These initiatives have highly synergistic goals regarding the interoperability and semantic richness of observational data, but have a much broader remit. Participation  
Members of the Observations Task Group, SONet, the Joint Working Group on Observational Data Semantics, and othersassume detailed knowledge of 1 or more existing approaches to observations modelingsome may have expertise in OWL, XML Schema, etc.
   Agenda1. Welcome and overview of the Observations Task Group goals (Matthew Jones) (30 mins) (slides)Relationship to other groups (SONet, JWG, etc.)Towards an observational data exchange standard (Hilmar Lapp) Participant Introductions (round the room)
 Approaches to serialization and exchange of observational data (10 mins each) (40 mins total)O+M  (Matt Jones) (slides)OBOE (Mark Schildhauer) (slides)
EQ (Hilmar Lapp) (slides)SERONTO (Kathi Schleidt)Darwin Core (?)
 Working session: needs for an observational data model exchange specification (Lapp moderates) (2 hours)Products: Desiderata for the exchange syntax/modeling language (e.g., effectiveness for expressing ontological concepts, linked data compliance)Requirements for the exchange syntax (e.g., shouldn't massively expand the data size)Brainstorming exercise, consolidation
 Approach to an exchange schema (in XML, or other tech) covering OBOE, EQ, O+MFormat that uses RDF/OWL?
 Goal: recommedations regarding which approach, possibly nascent syntax
 Action items and timeline: (15 mins) (Jones moderates)Create milestones and action items leading to presentation of an observational data exchange standard at 2011 meetingRatificationIdentify action items for community outreach to involve BD and Geospatial groups at TDWG
 Adjourn
 Background reading and informationBalhoff, James P., Wasila M. Dahdul, Cartik R. Kothari, Hilmar Lapp, John G. Lundberg, Paula Mabee, Peter E. Midford, Monte Westerfield, and Todd J. Vision. 2010. Phenex: Ontological Annotation of Phenotypic Diversity. PLoS ONE 5, no. 5: e10500. http://dx.plos.org/10.1371/journal.pone.0010500Extensible Observation Ontology (OBOE), downloadable at https://code.ecoinformatics.org/code/semtools/trunk/dev/oboe/Madin J, S Bowers, M Schildhauer, S Krivov, D Pennington, F Villa. (2007) An ontology for describing and synthesizing ecological observation data. Ecological Informatics 2 (3): 279-296. http://dx.doi.org/doi:10.1016/j.ecoinf.2007.05.004Madin J. S., Bowers S., Schildhauer M., and Jones M. B. 2008. Advancing ecological research with ontologies. Trends in Ecology and Evolution 23 (3): 159-168. http://dx.doi.org/doi:10.1016/j.tree.2007.11.007Mungall, Chris, Georgios Gkoutos, Nicole Washington, and Suzanna Lewis. 2007. Representing phenotypes in OWL. In OWL: Experiences and Directions (OWLED 2007), Innsbruk, Austria. Innsbruck, Austria: Citeseer. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.107.94&rep=rep1&type=pdfObservational Data projects: #OGC Observations and MeasurementsProbst, F. (2006). Ontological Analysis of Observations and Measurements. Lecture Notes in Computer Science, 2006, Volume 4197/2006, 304-320, DOI: 10.1007/11863939_20. http://dx.doi.org/10.1007/978-3-540-79996-2_10 Williams RJ, Martinez ND, Golbeck J. (2006) Ontologies for ecoinformatics. Web Semantics: Science, Services and Agents on the World Wide Web 4: 237–242. http://dx.doi.org/doi:10.1016/j.websem.2006.06.002
   
    
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