Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

Abstract. Existing MapReduce systems support relational style join operators which translate multi-join query plans into several Map-Reduce cycles. This leads to high I/O and communication costs due to the multiple data transfer steps between map and reduce phases. SPARQL graph pattern matching is dominated by join operations, and is unlikely to be efficiently processed using existing techniques. This cost is prohibitive for RDF graph pattern matching queries which typically involve several join operations. In this paper, we propose an approach for optimizing graph pattern matching by reinterpreting certain join tree structures as grouping operations. This enables a greater degree of parallelism in join processing resulting in more "bushy" like query execution plans with fewer MapReduce cycles. This approach requires that the intermediate results are managed as sets of groups of triples or TripleGroups. We therefore propose a data model and algebra -Nested TripleGroup Algebra for capturing and manipulating TripleGroups. The relationship with the traditional relational style algebra used in Apache Pig is discussed. A comparative performance evaluation of the traditional Pig approach and RAPID+ (Pig extended with NTGA) for graph pattern matching queries on the BSBM benchmark dataset is presented. Results show up to 60% performance improvement of our approach over traditional Pig for some tasks.

Similar to managing software packages, managing the ontology life cycle involves multiple complex workflows such as preparing releases, continuous quality control checking and dependency management. To manage these processes, a diverse set of tools is required, from command-line utilities to powerful ontology-engineering environmentsr. Particularly in the biomedical domain, which has developed a set of highly diverse yet inter-dependent ontologies, standardizing release practices and metadata and establishing shared quality standards are crucial to enable interoperability. The Ontology Development Kit (ODK) provides a set of standardized, customizable and automatically executable workflows, and packages all required tooling in a single Docker image. In this paper, we provide an overview of how the ODK works, show how it is used in practice and describe how we envision it driving standardization efforts in our community. Database URL: https://github.com/INCATools/ontology-development-kit

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Recently, the number and size of RDF data collections has increased rapidly making the issue of scalable processing techniques crucial. The MapReduce model has become a de facto standard for large scale data processing using a cluster of machines in the cloud. Generally, RDF query processing creates join-intensive workloads, resulting in lengthy MapReduce workflows with expensive I/O, data transfer, and sorting costs. However, the MapReduce computation model provides limited static optimization techniques used in relational databases (e.g., indexing and cost-based optimization). Consequently, dynamic optimization techniques for such joinintensive tasks on MapReduce need to be investigated. In some previous efforts, we propose a Nested TripleGroup data model and Algebra (NTGA) for efficient graph pattern query processing in the cloud. Here, we extend this work with a scansharing technique that is used to optimize the processing of graph patterns with repeated properties. Specifically, our scansharing technique eliminates the need for repeated scanning of input relations when properties are used repeatedly in graph patterns. A formal foundation underlying this scan sharing technique is discussed as well as an implementation strategy that has been integrated in the Apache Pig framework is presented. We also present a comprehensive evaluation demonstrating performance benefits of our NTGA plus scansharing approach.