Gremlin (programming language)

Abstract: Both the notion of Property Graphs (PG) and the Resource Description Framework (RDF) are commonly used models for representing graph-shaped data. While there exist some system-specific solutions to convert data from one model to the other, these solutions are not entirely compatible with one another and none of them appears to be based on a formal foundation. In fact, for the PG model, there does not even exist a commonly agreed-upon formal definition. The aim of this document is to reconcile both models formally. To this end, the document proposes a formalization of the PG model and introduces well-defined transformations between PGs and RDF. As a result, the document provides a basis for the following two innovations: On one hand, by implementing the RDF-to-PG transformations defined in this document, PG-based systems can enable their users to load RDF data and make it accessible in a compatible, system-independent manner using, e.g., the graph traversal language Gremlin or the declarative graph query language Cypher. On the other hand, the PG-to-RDF transformation in this document enables RDF data management systems to support compatible, system-independent queries over the content of Property Graphs by using the standard RDF query language SPARQL. Additionally, this document represents a foundation for systematic research on relationships between the two models and between their query languages.

Abstract: In this work we present, apply, and evaluate a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. To support both global trend analysis and local feature detection, this model enables explorations continuously scaled from the high-level, complete genome perspective, down to the low-level, structural rearrangement view, while preserving global context at all times. We have implemented these techniques in Gremlin, a genomic rearrangement explorer with multi-scale, linked interactions, which we apply to four human cancer genome data sets for evaluation. Using an insight-based evaluation methodology, we compare Gremlin to Circos, the state-of-the-art in genomic rearrangement visualization, through a small user study with computational biologists working in rearrangement analysis. Results from user study evaluations demonstrate that this visualization model enables more total insights, more insights per minute, and more complex insights than the current state-of-the-art for visual analysis and exploration of genome rearrangements.

Abstract: While Model Driven Engineering is gaining more industrial interest, scalability issues when managing large models have become a major problem in current modeling frameworks. Scalable model persistence has been achieved by using NoSQL backends for model storage, but existing modeling framework APIs have not evolved accordingly, limiting NoSQL query performance benefits. In this paper we present the Mogwai, a scalable and efficient model query framework based on a direct translation of OCL queries to Gremlin, a query language supported by several NoSQL databases. Generated Gremlin expressions are computed inside the database itself, bypassing limitations of existing framework APIs and improving overall performance, as confirmed by our experimental results showing an improvement of execution time up to a factor of 20 and a reduction of the memory overhead up to a factor of 75 for large models.

Abstract: More with pride than with petulance, I should like to register the complaint that there seems to be a gremlin playing hob with our research efforts. Since this gremlin seems to function in a systematic way, I shall attempt to describe its behavior, as well as our thoughts on harnessing its energies in treating mental patients. My first experience with this gremlin was in 1956, when our research group was engaged in the statistical treatment of data obtained from a controlled study of certain drugs. 1 We employed at this time a rather complex experimental design, and confounded our variables so successfully that none of the drugs studied was found to have any greater therapeutic value than did the experimental setting. We found that our patients improved without drugs as much as they improved with drugs. At that time we named our gremlin “milieu effect,” for the condition