scholarly journals DIGITAL WORKFLOWS FOR A 3D SEMANTIC REPRESENTATION OF AN ANCIENT MINING LANDSCAPE

Author(s):  
G. Hiebel ◽  
K. Hanke

The ancient mining landscape of Schwaz/Brixlegg in the Tyrol, Austria witnessed mining from prehistoric times to modern times creating a first order cultural landscape when it comes to one of the most important inventions in human history: the production of metal. In 1991 a part of this landscape was lost due to an enormous landslide that reshaped part of the mountain. With our work we want to propose a digital workflow to create a 3D semantic representation of this ancient mining landscape with its mining structures to preserve it for posterity. First, we define a conceptual model to integrate the data. It is based on the CIDOC CRM ontology and CRMgeo for geometric data. To transform our information sources to a formal representation of the classes and properties of the ontology we applied semantic web technologies and created a knowledge graph in RDF (Resource Description Framework). Through the CRMgeo extension coordinate information of mining features can be integrated into the RDF graph and thus related to the detailed digital elevation model that may be visualized together with the mining structures using Geoinformation systems or 3D visualization tools. The RDF network of the triple store can be queried using the SPARQL query language. We created a snapshot of mining, settlement and burial sites in the Bronze Age. The results of the query were loaded into a Geoinformation system and a visualization of known bronze age sites related to mining, settlement and burial activities was created.

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1822 ◽  
Author(s):  
Ana Claudia Sima ◽  
Christophe Dessimoz ◽  
Kurt Stockinger ◽  
Monique Zahn-Zabal ◽  
Tarcisio Mendes de Farias

The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative analyses, combining information from multiple sources. However, analyzing evolutionary data in RDF is not trivial, due to the steep learning curve required to understand both the data models adopted by different RDF data sources, as well as the SPARQL query language. In this article, we provide a hands-on introduction to querying evolutionary data across multiple sources that publish orthology information in RDF, namely: The Orthologous MAtrix (OMA), the European Bioinformatics Institute (EBI) RDF platform, the Database of Orthologous Groups (OrthoDB) and the Microbial Genome Database (MBGD). We present four protocols in increasing order of complexity. In these protocols, we demonstrate through SPARQL queries how to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups. Finally, we show how orthology information in different sources can be compared, through the use of federated SPARQL queries.


Author(s):  
Reto Gmür ◽  
Donat Agosti

Taxonomic treatments, sections of publications documenting the features or distribution of a related group of organisms (called a “taxon”, plural “taxa”) in ways adhering to highly formalized conventions, and published in scientific journals, shape our understanding of global biodiversity (Catapano 2019). Treatments are the building blocks of the evolving scientific consensus on taxonomic entities. The semantics of these treatments and their relationships are highly structured: taxa are introduced, merged, made obsolete, split, renamed, associated with specimens and so on. Plazi makes this content available in machine-readable form using Resource Description Framework (RDF) . RDF is the standard model for Linked Data and the Semantic Web. RDF can be exchanged in different formats (aka concrete syntaxes) such as RDF/XML or Turtle. The data model describes graph structures and relies on Internationalized Resource Identifiers (IRIs) , ontologies such as Darwin Core basic vocabulary are used to assign meaning to the identifiers. For Synospecies, we unite all treatments into one large knowledge graph, modelling taxonomic knowledge and its evolution with complete references to quotable treatments. However, this knowledge graph expresses much more than any individual treatment could convey because every referenced entity is linked to every other relevant treatment. On synospecies.plazi.org, we provide a user-friendly interface to find the names and treatments related to a taxon. An advanced mode allows execution of queries using the SPARQL query language.


2019 ◽  
Vol 8 (3) ◽  
pp. 1306-1308

Cancer registries are most important to predict and treat the cancer disease. Numerous solutions are available in research to analyze the data in cancer registries. However, there is a lack of well defined data model since there is a link to external web pages. In order to overcome this issue a system is proposed to represent the cancer data using a semantic data model. The data model uses a Resource Description Framework (RDF) format to represent the data from the local cancer databases. It also uses an optimized Querying of the semantically represented data using SPARQL query language. The optimization of the queries is done with the Modified shuffled frog leaping algorithm(MSFL). This helps in treatment of cancer patients in an easy way.


2018 ◽  
Vol 8 (1) ◽  
pp. 18-37 ◽  
Author(s):  
Median Hilal ◽  
Christoph G. Schuetz ◽  
Michael Schrefl

Abstract The foundations for traditional data analysis are Online Analytical Processing (OLAP) systems that operate on multidimensional (MD) data. The Resource Description Framework (RDF) serves as the foundation for the publication of a growing amount of semantic web data still largely untapped by companies for data analysis. Most RDF data sources, however, do not correspond to the MD modeling paradigm and, as a consequence, elude traditional OLAP. The complexity of RDF data in terms of structure, semantics, and query languages renders RDF data analysis challenging for a typical analyst not familiar with the underlying data model or the SPARQL query language. Hence, conducting RDF data analysis is not a straightforward task. We propose an approach for the definition of superimposed MD schemas over arbitrary RDF datasets and show how to represent the superimposed MD schemas using well-known semantic web technologies. On top of that, we introduce OLAP patterns for RDF data analysis, which are recurring, domain-independent elements of data analysis. Analysts may compose queries by instantiating a pattern using only the MD concepts and business terms. Upon pattern instantiation, the corresponding SPARQL query over the source data can be automatically generated, sparing analysts from technical details and fostering self-service capabilities.


2017 ◽  
Vol 1 (2) ◽  
pp. 692-699 ◽  
Author(s):  
Gerald Hiebel ◽  
Klaus Hanke ◽  
Gert Goldenberg ◽  
Markus Staudt ◽  
Caroline Grutsch

The integration of information sources is a fundamental step to advance research and knowledge about the ancient mining landscape of Schwaz/Brixlegg in the Tyrol / Austria. The approach is applied for the localization, identification and interpretation of mining structures within the area. We want to show the use of the CIDOC CRM ontology with extensions in combination with a thesaurus to integrate data on a conceptual level. To implement this integration, we applied semantic web technologies to create a knowledge graph in RDF (Resource Description Framework) that currently represents the available information of seven different information sources in a network structure. More sources will be integrated using the same methodology. These are geochemical analysis of artefacts, onomastic research on names related to mining and archaeological information of other mining areas to research the spread of prehistoric mining activities and technologies.The RDF network can be queried for research, cultural or emergency response questions and the results can be displayed using Geoinformation systems. An exemplary archaeological research question is the location of mining, settlement and burial sites in the Bronze Age, differentiating between ore extraction, ore processing and smelting activities. For emergency forces the names and exact locations of mines are essential in case of an accident within an old mine. Different questions require a subset of the created knowledge graph. The results of queries to retrieve specific information can be visualised using appropriate tools.


2013 ◽  
Vol 07 (04) ◽  
pp. 455-477 ◽  
Author(s):  
EDGARD MARX ◽  
TOMMASO SORU ◽  
SAEEDEH SHEKARPOUR ◽  
SÖREN AUER ◽  
AXEL-CYRILLE NGONGA NGOMO ◽  
...  

Over the last years, a considerable amount of structured data has been published on the Web as Linked Open Data (LOD). Despite recent advances, consuming and using Linked Open Data within an organization is still a substantial challenge. Many of the LOD datasets are quite large and despite progress in Resource Description Framework (RDF) data management their loading and querying within a triple store is extremely time-consuming and resource-demanding. To overcome this consumption obstacle, we propose a process inspired by the classical Extract-Transform-Load (ETL) paradigm. In this article, we focus particularly on the selection and extraction steps of this process. We devise a fragment of SPARQL Protocol and RDF Query Language (SPARQL) dubbed SliceSPARQL, which enables the selection of well-defined slices of datasets fulfilling typical information needs. SliceSPARQL supports graph patterns for which each connected subgraph pattern involves a maximum of one variable or Internationalized resource identifier (IRI) in its join conditions. This restriction guarantees the efficient processing of the query against a sequential dataset dump stream. Furthermore, we evaluate our slicing approach on three different optimization strategies. Results show that dataset slices can be generated an order of magnitude faster than by using the conventional approach of loading the whole dataset into a triple store.


F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 1822
Author(s):  
Ana Claudia Sima ◽  
Christophe Dessimoz ◽  
Kurt Stockinger ◽  
Monique Zahn-Zabal ◽  
Tarcisio Mendes de Farias

The increasing use of Semantic Web technologies in the life sciences, in particular the use of the Resource Description Framework (RDF) and the RDF query language SPARQL, opens the path for novel integrative analyses, combining information from multiple data sources. However, analyzing evolutionary data in RDF is not trivial, due to the steep learning curve required to understand both the data models adopted by different RDF data sources, as well as the equivalent SPARQL constructs required to benefit from this data – in particular, recursive property paths. In this article, we provide a hands-on introduction to querying evolutionary data across several data sources that publish orthology information in RDF, namely: The Orthologous MAtrix (OMA), the European Bioinformatics Institute (EBI) RDF platform, the Database of Orthologous Groups (OrthoDB) and the Microbial Genome Database (MBGD). We present four protocols in increasing order of complexity. In these protocols, we demonstrate through SPARQL queries how to retrieve pairwise orthologs, homologous groups, and hierarchical orthologous groups. Finally, we show how orthology information in different data sources can be compared, through the use of federated SPARQL queries.


Author(s):  
Maarten Trekels ◽  
Matt Woodburn ◽  
Deborah L Paul ◽  
Sharon Grant ◽  
Kate Webbink ◽  
...  

Data standards allow us to aggregate, compare, compute and communicate data from a wide variety of origins. However, for historical reasons, data are most likely to be stored in many different formats and conform to different models. Every data set might contain a huge amount of information, but it becomes tremendously difficult to compare them without a common way to represent the data. That is when standards development jumps in. Developing a standard is a formidable process, often involving many stakeholders. Typically the initial blueprint of a standard is created by a limited number of people who have a clear view of their use cases. However, as development continues, additional stakeholders participate in the process. As a result, conflicting opinions and interests will influence the development of the standard. Compromises need to be made and the standard might look very different from the initial concept. In order to address the needs of the community, a high level of engagement in the development process is encouraged. However, this does not necessarily increase the usability of the standard. To mitigate this, there is a need to test the standard during the early stages of development. In order to facilitate this, we explored the use of Wikibase to create an initial implementation of the standard. Wikibase is the underlying technology that drives Wikidata. The software is open-source and can be customized for creating collaborative knowledge bases. In addition to containing an RDF (Resource Description Framework) triple store under the hood, it provides users with an easy-to-use graphical user interface (see Fig. 1). This facilitates the use of an implementation of a standard by non-technical users. The Wikibase remains fully flexible in the way data are represented and no data model is enforced. This allows users to map their data onto the standard without any restrictions. Retrieving information from RDF data can be done through the SPARQL query language (W3C 2020). The software package has also a built-in SPARQL endpoint, allowing users to extract the relevant information: Does the standard cover all use cases envisioned? Are parts of the standard underdeveloped? Are the controlled vocabularies sufficient to describe the data? Does the standard cover all use cases envisioned? Are parts of the standard underdeveloped? Are the controlled vocabularies sufficient to describe the data? This strategy was applied during the development of the TDWG Collection Description standard. After completing a rough version of the standard, the different terms that were defined in the first version were transferred to a Wikibase instance running on WBStack (Addshore 2020). Initially, collection data were entered manually, which revealed several issues. The Wikibase allowed us to easily define controlled vocabularies and expand them as needed. The feedback reported from users then flowed back to the further development of the standard. Currently we envisage creating automated scripts that will import data en masse from collections. Using the SPARQL query interface, it will then be straightforward to ensure that data can be extracted from the Wikibase to support the envisaged use cases.


Author(s):  
Salvador Lima ◽  
José Moreira

The Web is a crucial means for the dissemination of touristic information. However, most touristic information resources are stored directly in Web pages or in relational databases that are accessible through ad-hoc Web applications, and the use of automated processes to search, extract and interpret information can hardly be implemented. The Semantic Web technologies, aiming at representing the background knowledge about Web resources in a computational way, can be an important contribution to the development of such automated processes. This chapter introduces the concept of touristic object, giving special attention to the representation of temporal, spatial, and thematic knowledge. It also proposes a three-layered architecture for the representation of touristic objects in the Web. The central part is the domain layer, defining a Semantic Model for Tourism (SeMoT) to describe concepts, relationships, and constraints using ontologies. The data layer supports the mapping of touristic information in relational databases into Resource Description Framework (RDF) virtual graphs following the SeMoT specification. The application layer deals with the integration of information from different data sources into a unified knowledge model, offering a common vocabulary to describe touristic information resources. Finally, we also show how to use this framework for planning touristic itineraries.


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