A graph database for persistent identifiers

The Handle Software manages references to resources of information. However, it does not support a search functionality. A prior implementation with Elasticsearch could not efficiently capture the complex structure of our dataset, especially the relationships between handles. In this paper, we apply a graph database together with Elasticsearch to provide more search capabilities to users. In addition, the graph can efficiently store meta-data provided during handle creation. Further use cases for this graph include redundancy detection (two or more handles pointing to the same URL), or bibliographic network analysis

Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers

Theory and Practice of Data Citation

Citations are the cornerstone of knowledge propagation and the primary means of assessing the quality of research, as well as directing investments in science. Science is increasingly becoming "data-intensive", where large volumes of data are collected and analyzed to discover complex patterns through simulations and experiments, and most scientific reference works have been replaced by online curated datasets. Yet, given a dataset, there is no quantitative, consistent and established way of knowing how it has been used over time, who contributed to its curation, what results have been yielded or what value it has. The development of a theory and practice of data citation is fundamental for considering data as first-class research objects with the same relevance and centrality of traditional scientific products. Many works in recent years have discussed data citation from different viewpoints: illustrating why data citation is needed, defining the principles and outlining recommendations for data citation systems, and providing computational methods for addressing specific issues of data citation. The current panorama is many-faceted and an overall view that brings together diverse aspects of this topic is still missing. Therefore, this paper aims to describe the lay of the land for data citation, both from the theoretical (the why and what) and the practical (the how) angle.Comment: 24 pages, 2 tables, pre-print accepted in Journal of the Association for Information Science and Technology (JASIST), 201

Compensation methods to support generic graph editing: A case study in automated verification of schema requirements for an advanced transaction model

Compensation plays an important role in advanced transaction models, cooperative work, and workflow systems. However, compensation operations are often simply written as a^−1 in transaction model literature. This notation ignores any operation parameters, results, and side effects. A schema designer intending to use an advanced transaction model is expected (required) to write correct method code. However, in the days of cut-and-paste, this is much easier said than done. In this paper, we demonstrate the feasibility of using an off-the-shelf theorem prover (also called a proof assistant) to perform automated verification of compensation requirements for an OODB schema. We report on the results of a case study in verification for a particular advanced transaction model that supports cooperative applications. The case study is based on an OODB schema that provides generic graph editing functionality for the creation, insertion, and manipulation of nodes and links