Deliverables 5.3 Data model and Ontologies Due date of deliverable: month 36 (Nov 2012) Actual submission data: month 48 (Nov2013) WP Leader: Gerry Sutton Coastal & Marine Resource Centre, University College Cork (Partner 8, UCC Cork, Ireland) Author: Stefanos Kavadas Hellenic Centre for Marine Research (Partner 5, HCMR, Greece) Yassine Lassoued Coastal & Marine Resource Centre, University College Cork (Partner 8, UCC, Cork, Ireland) Grant Agreement number: 226661 Project acronym: MESMA Project title: Funding Scheme: Collaborative project Project coordination: IMARES, IJmuiden, the Netherlands Project website: www.mesma.org
MESMA Document Change Record Authors Modification Issue Date Stefanos Kavadas First draft 0.1 20130903 Yassine Lassoued Added Ontologies section and updated summary 0.2 20131126 Gerry Sutton Edits, amendments, formatting, links and TOC 0.3 20131127 The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement n 226661 1
MESMA Deliverable 5.3 Data Model and Ontologies 1
MESMA Executive Summary This report presents deliverable D5.3, Data model and ontologies. It proposes a methodology enabling the construction of data models based on INSPIRE standards. Selected MESMA project thematic units (data themes) are given as examples. The deliverable comprises a) methodological steps needed to establish and expand a data modelling framework (geodatabase) and b) MESMA data modelling in XML format including description of entities and relationships. When imported to ESRI ArcCatalog this schema file automatically generates a complete geodatabase suitable for internal MESMA and general use. This document also introduces the ontologies selected for use in the MESMA project and explains how these are used in practice. In MESMA, ontologies are used as thesauri to control metadata keywords through the provision of standardised terms with their definitions to be used as keyword values. We identified three thesauri suitable for annotating the MESMA datasets, and which therefore were used in the MESMA metadata catalogue. These thesauri are: the INSPIRE spatial data themes, the General Multilingual Environmental Thesaurus (GEMET), and the science and services keywords list from the Global Change Master Directory (GCMD) keywords. The MESMA metadata catalogue was customised such that a keyword selection widget pops up when a user tries to edit a keyword. This widget enables users to first select a thesaurus then one or more keywords from it with which to complete the appropriate metadata fields. The MESMA Geoportal, which allows access to the MESMA metadata, data and maps, uses the INSPIRE spatial data themes as categories for data browsing. 2
MESMA Deliverable 5.3 Data Model and Ontologies Contents Executive Summary... 2 1. Data model and INSPIRE... 4 1.1. Data Models... 4 1.2. INSPIRE... 5 1.3. INSPIRE Architecture and Data Concepts... 6 2. Implementing Methodology Leading from INSPIRE Standard to Data Model (Geodatabase) Creation... 9 2.1 Approach using ESRI Tools... 9 2.2 Using CASE Tools...11 3. Ontologies...16 3.1 INSPIRE Spatial Data Themes...16 3.2 General Multilingual Environmental Thesaurus (GEMET):...17 3.3 NASA Global Change Master Directory (GCMD) Thesaurus...17 3.4 Ontologies in the MESMA metadata catalogue and geoportal...18 References...21 Acronyms...22 3
MESMA 1. Data model and INSPIRE 1.1. Data Models A data model describes the content, properties, data structures, rules and relations between the entities of a data model (Fig. 1.). It is independent of hardware or software constraints. Levels of a data model Reality: real world phenomena Conceptual model: human-oriented model of selected objects and processes in relevance, often partially structured. Logical model: implementation-oriented representation of reality, often expressed in the form of diagrams and lists. Physical model: portrays the actual application in a GIS, often comprises tables stored as files or databases. Fig. 1. Levels of data model (graph by Matthew West and Julian Fowler) The following five steps are routinely followed during the design of a Geodatabase, when progressing through conceptual, logical, and physical phases: 1. modeling the user s view, 2. defining objects and relationships, 3. selecting geographic representations, 4. matching geodatabase elements, 5. organizing the geodatabase structure. 4
MESMA Deliverable 5.3 Data Model and Ontologies 1.2. INSPIRE INSPIRE (Infrastructure for Spatial Information in the European Community) The INSPIRE process is an ambitious initiative intended to build a European Spatial Data Infrastructure (ESDI), to support policy making in issues concerning protection of the environment. INSPIRE is to be based on the National Spatial Data (SDI*) that are -or will be- created and maintained by the EU Member States. Therefore, one of the main tasks of INSPIRE is to enable harmonisation across Europe through interoperable spatial data sets and services. *SDI has evolved to enable geospatial information sharing at a significant scale. INSPIRE is supported by a legal directive, Directive 2007/2/EC of the European Parliament and of the Council of 14 March 2007 establishing an Infrastructure for Spatial Information in the European Community, which was published in the official Journal on the 25th April 2007. The INSPIRE directive entered into force on the 15th May 2007. The Directive sets generic rules for establishing an Infrastructure for Spatial Information in the European Community. To ensure that the national SDI of the Member States are compatible and usable in a Community and trans-boundary context, the Directive requires that common Implementing Rules (IR) are adopted in a number of specific areas. Implementing Rules are adopted as Commission Regulations and are binding in their entirety. As part of the Directive, all public authority organizations that maintain and produce spatial data are required to provide data in a way that conforms to the INSPIRE Implementing Rules. A set of INSPIRE data specifications can be found on the official site (Fig. 2.): http://inspire.ec.europa.eu/index.cfm/pageid/2 Sample data models are provided in the following formats: UML models for Enterprise Architect (EAP, XMI) GML application schemas and code list dictionaries HTML view of UML models Feature catalogue http://inspire.ec.europa.eu/index.cfm/pageid/2/list/datamodels The following Key definitions are provided at this point for clarity as they are essential enablers in the standardization process codelist: An expandable list of valid identifiers of named literal values. Attributes of a codelist type may only take values from this list. enumeration: A fixed list of valid identifiers of named literal values. Attributes of an enumerated type may only take values from this list. 5
MESMA Fig. 2. Set of INSPIRE data specifications. 1.3. INSPIRE Architecture and Data Concepts The data is categorized into a set of data themes, each organized into one of three Annexes (Fig. 3.). Annex I is completed. ANNEX II & ANNEX III are under construction. Changes could be proposed concerning structure and codification system. Every thematic unit is fully documented and can be downloaded from INSPIRE website An example of Species distribution data theme is given in Figure 4, 5. 6
MESMA Deliverable 5.3 Data Model and Ontologies Fig. 3. INSPIRE architecture 7
MESMA Fig. 4. Structure of species distribution data theme Fig. 5. Species distribution data theme: data type and codelist example. 8
MESMA Deliverable 5.3 Data Model and Ontologies 2. Implementing Methodology Leading from INSPIRE Standard to Data Model (Geodatabase) Creation 2.1 Approach using ESRI Tools To design the data model, ESRI tools and guides have been used 1. These tools are now universally used and appreciated by the majority of project partners and geospatial data producers/users internationally as an industry standard. Thus in the context of the MESMA project (and partners capabilities) this approach is considered to provide the most practical common approach to harmonisation at the data set (layer) level. The first step is to design the geodatabase. To create a new geodatabase from scratch, a complete set of tools provided in ArcCatalog can be used to create the schema for feature datasets, tables, geometric networks, relationships, and other items inside the database which are illustrated in (Fig. 6). Fig. 6. ArcCatalog tool 1 http://www.esri.com/products (accessed 271113). 9
MESMA ArcGIS Diagrammer is an alternative productivity tool for GIS professionals to create, edit or analyze the geodatabase schema (Fig. 7). Fig. 7. ArcGIS Diagrammer tool. 10
MESMA Deliverable 5.3 Data Model and Ontologies If data in various formats (shapefiles, coverages, tables) are available, the ArcCatalog import tool can be used to migrate/convert these data into the geodatabase (Fig. 8). Fig. 8. ArcCatalog import tool. Once data have been imported into the geodatabase, ArcCatalog can be used for further modifications such as building geometric networks and establishing subtypes, attribute domains, and so on. 2.2 Using CASE Tools Alternatively CASE (Computer-Aided Software Engineering) tools can also be used to help in building geodatabases. CASE consists of tools and techniques that automate the process of developing software systems and database design. These tools can be used to create new custom objects and generate a geodatabase schema from a UML diagram. Once a geodatabase is designed, any of three methods outlined can be employed to create a new geodatabase (Fig. 9). In practice, a combination of all or some of the methods outlined is often used. Fig. 9. Methods to create a Geodatabase (source: ESRI) 11
MESMA Once a geodatabase is created, the Export tool from ArcCatalog can be used to export the geodatabase to XML Workspace Document (Fig. 10). Fig. 10. Export tool in ArcCatalog. The data or schema only can be saved (Fig. 11). The XML file can be imported into other machines using Import tool from ArcCatalog or from ArcGIS Diagrammer. Fig. 11. Export in XML format, Data or Schema only. In the deliverable XML file, a number of thematic units were selected to be included in the data modelling, plus a number of parametric tables (codelist) to support the referential integrity between spatial data and alphanumeric entities (ie. between geographic entities points/lines/polygons etc. and associated attribute information). The XML file can be accessed here http://mesma.ucc.ie/deliverables/mesma_db_schema.xml Figures 12-14, show examples of a Schema Diagram, a Schema Report and a Data Report that have been produced using the ArcGIS Diagrammer. 12
MESMA Deliverable 5.3 Data Model and Ontologies Fig. 12. Schema Diagram: Habitat & Biotopes. 13
MESMA Fig. 13. Schema Report (produced by ArcGIS diagrammer). 14
MESMA Deliverable 5.3 Data Model and Ontologies Fig. 14. Data Report based on CS7 thematic maps (produced by ArcGIS diagrammer). 15
MESMA 3. Ontologies In MESMA, ontologies (thesauri) are used to control metadata keywords through the provision of standardised terms with their definitions to be used as keyword values. We identified three ontologies suitable for annotating the MESMA datasets, and which therefore were used in the MESMA metadata catalogue. 3.1 INSPIRE Spatial Data Themes As part of the INSPIRE directive the European Commission has specified high level themes for geospatial data cataloguing. The INSPIRE themes are organized into 3 annexes as shown below. Greyed themes are the ones that do not match the MESMA datasets. As per the INSPIRE directive, the use of these themes is mandatory. As some of the MESMA datasets do not fit under any of the INSPIRE themes, we introduced two additional themes, termed MESMA themes: Environmental Health and Safety and Biological resources. Annex I 1. Coordinate reference systems 2. Geographical grid systems 3. Geographical names 4. Administrative units 5. Addresses 6. Cadastral parcels 7. Transport networks 8. Hydrography 9. Protected sites Annex II 1. Elevation 2. Land cover 3. Orthoimagery 4. Geology Annex III 1. Statistical units 2. Buildings 3. Soil 4. Land use 5. Human health and safety 6. Utility and governmental services 7. Environmental monitoring facilities 8. Production and industrial facilities 9. Agricultural and aquaculture facilities 10. Population distribution and demography 11. Area management / restriction / regulation zones & reporting units 12. Natural risk zones 13. Atmospheric conditions 14. Meteorological geographical features 15. Oceanographic geographic features 16. Sea regions 17. Bio-geographical regions 18. Habitat and biotopes 19. Species distribution 20. Energy resources 21. Mineral resources 16
MESMA Deliverable 5.3 Data Model and Ontologies 3.2 General Multilingual Environmental Thesaurus (GEMET)2: The European Environment Information and Observation Network (EIONET) 3 maintains a multilingual thesaurus of environmental themes and terms that cover a wide range of environmental data and applications. Figure 15 shows a screenshot of the GEMET user interface with the high-level themes. More specific terms are also available from the GEMET website and organised both alphabetically and hierarchically. Fig. 15. GEMET High-level Themes 3.3 NASA Global Change Master Directory (GCMD) Thesaurus4 GCMD 5 is an entire data portal as well as a set of descriptors and broader content metadata files. It relies on a thesaurus of scientific themes and terms to annotate the available resources, called GCMD keywords [OMS13]. These keywords are split into 10 lists. The most relevant of these to the MESMA datasets is the Science and Services Keywords list (c.f., snippet below) which was used in the MESMA catalogue. 2 http://www.eionet.europa.eu/gemet (accessed on 25 November 2013) 3 http://www.eionet.europa.eu (accessed on 25 November 2013) 4 http://gcmd.nasa.gov/learn/keywords.html (accessed on 25 November 2013) 5 http://gcmd.nasa.gov (accessed on 25 November 2013) 17
MESMA " EARTH SCI ENCE", " HUMAN DI MENSI ONS", " ", " ", " ", " " " EARTH SCI ENCE", " HUMAN DI MENSI ONS", " BOUNDARI ES", " ", " ", " " " EARTH SCI ENCE", " HUMAN DI MENSI ONS", " BOUNDARI ES", " ADMI NI STRATI VE DI VI SI ONS", " ", " " " EARTH SCI ENCE", " HUMAN DI MENSI ONS", " BOUNDARI ES", " BOUNDARY SURVEYS", " ", " " " EARTH SCI ENCE", " HUMAN DI MENSI ONS", " BOUNDARI ES", " POLI TI CAL DI VI SI ONS", " ", " " " EARTH SCI ENCE", " HUMAN DI MENSI ONS", " ECONOMI C RESOURCES", " ", " ", " " " EARTH SCI ENCE", " OCEANS", " ", " ", " ", " " " EARTH SCI ENCE", " OCEANS", " AQUATI C SCI ENCES", " ", " ", " " " EARTH SCI ENCE", " OCEANS", " AQUATI C SCI ENCES", " AQUACULTURE", " ", " " " EARTH SCI ENCE", " OCEANS", " AQUATI C SCI ENCES", " FI SHERI ES", " ", " " " EARTH SCI ENCE", " OCEANS", " BATHYMETRY/ SEAFLOOR TOPOGRAPHY", " ", " ", " " " EARTH SCI ENCE", " OCEANS", " BATHYMETRY/ SEAFLOOR TOPOGRAPHY", " BATHYMETRY", " ", " " " EARTH SCI ENCE", " OCEANS", " BATHYMETRY/ SEAFLOOR TOPOGRAPHY", " WATER DEPTH", " ", " " " EARTH SCI ENCE", " OCEANS", " COASTAL PROCESSES", " ", " ", " " " EARTH SCI ENCE", " OCEANS", " COASTAL PROCESSES", " BARRI ER I SLANDS", " ", " " " EARTH SCI ENCE", " OCEANS", " COASTAL PROCESSES", " BEACHES", " ", " " " EARTH SCI ENCE", " OCEANS", " COASTAL PROCESSES", " COASTAL ELEVATI ON", " ", " " " EARTH SCI ENCE", " OCEANS", " COASTAL PROCESSES", " CORAL REEFS", " ", " " " EARTH SCI ENCE", " OCEANS", " COASTAL PROCESSES", " DELTAS", " ", " " " EARTH SCI ENCE", " OCEANS", " COASTAL PROCESSES", " DUNES", " ", " " 3.4 Ontologies in the MESMA metadata catalogue and geoportal The MESMA metadata catalogue 6, which is based on the Geonetwork 7 open source catalogue, was configured to popup a keyword selection widget when a user clicks on a metadata keyword field to enter or edit a keyword. This widget, which is shown in the screenshot in Figure 16, displays the list of available thesauri to choose from (INSPIRE themes, GEMET themes and terms thesauri, and GCMD thesaurus). When the user selects a thesaurus, he/she can then select a keyword (term). The keyword selector then fills in the keyword and thesaurus information fields automatically. The keyword selector relies on thesauri encoded in RDF/XML 8 and which are stored and administred through the MESMA Geonetwork. 6 http://mesma.ucc.ie/geonetwork (accessed on 25 November 2013) 7 http://geonetwork-opensource.org (accessed on 25 November 2013) 8 RDF/XML specification: http://www.w3.org/tr/rec-rdf-syntax (accessed on 25 November 2013) 18
MESMA Deliverable 5.3 Data Model and Ontologies Fig. 16. Screenshot of the MESMA Metadata Keyword Selector The INSPIRE themes together with the additional two MESMA themes are used in the MESMA Geoportal 9 for data discovery. As shown in the screenshot of Figure 17 below, when a users selects an INSPIRE or MESMA keyword (left side area of the map), the geoportal displays the list of datasets matching the selected theme (bottom list). 9 http://mesma.ucc.ie/geoportal (accessed on 25 November 2013) 19
MESMA Fig. 17. INSPIRE Keywords-based Data Discovery in the MESMA Geoportal 20
MESMA Deliverable 5.3 Data Model and Ontologies References [OMS13] Olsen, L.M., G. Major, K. Shein, J. Scialdone, S. Ritz, T. Stevens, M. Morahan, A. Aleman, R. Vogel, S. Leicester, H. Weir, M. Meaux, S. Grebas, C.Solomon, M. Holland, T. Northcutt, R. A. Restrepo, R. Bilodeau, 2013. NASA/Global Change Master Directory (GCMD) Earth Science Keywords. Version 8.0.0.0.0. 21
MESMA Acronyms CMRC GCMD GEMET INSPIRE MESMA Coastal and Marine Research Centre Global Change Master Directory General Multilingual Environmental Thesaurus Infrastructure for Spatial Information in Europe 22