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

Development of Computer Science Disciplines - A Social Network Analysis Approach

In contrast to many other scientific disciplines, computer science considers conference publications. Conferences have the advantage of providing fast publication of papers and of bringing researchers together to present and discuss the paper with peers. Previous work on knowledge mapping focused on the map of all sciences or a particular domain based on ISI published JCR (Journal Citation Report). Although this data covers most of important journals, it lacks computer science conference and workshop proceedings. That results in an imprecise and incomplete analysis of the computer science knowledge. This paper presents an analysis on the computer science knowledge network constructed from all types of publications, aiming at providing a complete view of computer science research. Based on the combination of two important digital libraries (DBLP and CiteSeerX), we study the knowledge network created at journal/conference level using citation linkage, to identify the development of sub-disciplines. We investigate the collaborative and citation behavior of journals/conferences by analyzing the properties of their co-authorship and citation subgraphs. The paper draws several important conclusions. First, conferences constitute social structures that shape the computer science knowledge. Second, computer science is becoming more interdisciplinary. Third, experts are the key success factor for sustainability of journals/conferences

The Homeostasis Protocol: Avoiding Transaction Coordination Through Program Analysis

Datastores today rely on distribution and replication to achieve improved performance and fault-tolerance. But correctness of many applications depends on strong consistency properties - something that can impose substantial overheads, since it requires coordinating the behavior of multiple nodes. This paper describes a new approach to achieving strong consistency in distributed systems while minimizing communication between nodes. The key insight is to allow the state of the system to be inconsistent during execution, as long as this inconsistency is bounded and does not affect transaction correctness. In contrast to previous work, our approach uses program analysis to extract semantic information about permissible levels of inconsistency and is fully automated. We then employ a novel homeostasis protocol to allow sites to operate independently, without communicating, as long as any inconsistency is governed by appropriate treaties between the nodes. We discuss mechanisms for optimizing treaties based on workload characteristics to minimize communication, as well as a prototype implementation and experiments that demonstrate the benefits of our approach on common transactional benchmarks

Private Information Retrieval Schemes for Coded Data with Arbitrary Collusion Patterns

In Private Information Retrieval (PIR), one wants to download a file from a database without revealing to the database which file is being downloaded. Much attention has been paid to the case of the database being encoded across several servers, subsets of which can collude to attempt to deduce the requested file. With the goal of studying the achievable PIR rates in realistic scenarios, we generalize results for coded data from the case of all subsets of servers of size $t$ colluding, to arbitrary subsets of the servers. We investigate the effectiveness of previous strategies in this new scenario, and present new results in the case where the servers are partitioned into disjoint colluding groups.Comment: Updated with a corrected statement of Theorem

Evolving NoSQL Databases Without Downtime

NoSQL databases like Redis, Cassandra, and MongoDB are increasingly popular because they are flexible, lightweight, and easy to work with. Applications that use these databases will evolve over time, sometimes necessitating (or preferring) a change to the format or organization of the data. The problem we address in this paper is: How can we support the evolution of high-availability applications and their NoSQL data online, without excessive delays or interruptions, even in the presence of backward-incompatible data format changes? We present KVolve, an extension to the popular Redis NoSQL database, as a solution to this problem. KVolve permits a developer to submit an upgrade specification that defines how to transform existing data to the newest version. This transformation is applied lazily as applications interact with the database, thus avoiding long pause times. We demonstrate that KVolve is expressive enough to support substantial practical updates, including format changes to RedisFS, a Redis-backed file system, while imposing essentially no overhead in general use and minimal pause times during updates.Comment: Update to writing/structur