17 papers · ranked by Valyu relevance
Jaclyn Smith, Michael Benedikt, Miloš Nikolić, Amir Shaikhha
While large-scale distributed data processing platforms have become an attractive target for query processing, these systems are problematic for applications that deal with nested collections. Programmers are forced either to perform nontrivial translations of collection programs or to employ automated flattening…
Ulrich Matter
The rise of the programmable web offers new opportunities for the empirically driven social sciences. The access, compilation and preparation of data from the programmable web for statistical analysis can, however, involve substantial up-front costs for the practical researcher. The R-package RWebData provides a…
Jeroen Ooms
A naive realization of JSON data in R maps JSON arrays to an unnamed list, and JSON objects to a named list. However, in practice a list is an awkward, inefficient type to store and manipulate data. Most statistical applications work with (homogeneous) vectors, matrices or data frames. Therefore JSON packages in R…
Stephen J. Beckett, Chris A. Boulton, Hywel T. P. Williams
Nestedness is a statistical measure used to interpret bipartite interaction data in several ecological and evolutionary contexts, e.g. biogeography (species-site relationships) and species interactions (plant-pollinator and host-parasite networks). Multiple methods have been used to evaluate nestedness, which differ in…
Laura K. Wiley, R. Michael Sivley, William S. Bush
Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the…
Alan Geoffrey Hall, Michel Wermelinger, Tony Hirst, Santi Phithakkitnukoon
'Santi Phithakkitnukoon'] A spreadsheet is remarkably flexible in representing various forms of structured data, but the individual cells have no knowledge of the larger structures of which they may form a part. This can hamper comprehension and increase formula replication, increasing the risk of error on both scores.…
Phillip P. A. Staniczenko, Debabrata Panja
Nestedness is a common property of communication, finance, trade, and ecological networks. In networks with high levels of nestedness, the link positions of low-degree nodes (those with few links) form nested subsets of the link positions of high-degree nodes (those with many links), leading to matrix representations…
Ana M. Martín González, Diego P. Vázquez, Rodrigo Ramos-Jiliberto, Sang Hoon Lee + 1 more
The calculation of nestedness has become a routine analysis in the study of ecological networks, as it is commonly associated with community resilience, robustness and species persistence. While meaningful in species distributional patterns, for an interaction matrix to be nested, specialist species must interact with…
Rafael Barros Pereira Pinheiro, Carsten F. Dormann, Gabriel Moreira Félix Ferreira, Marco Aurelio Ribeiro Mello
Nestedness is a common pattern in metacommunities and interaction networks, whose causes are still subject to investigation. Nestedness inference is challenging because, beyond calculating an index, we need to compare observed and expected values using null models. There are many different null models and the choice…
Nick Pullen, Richard J. Morris, Simon Rogers
Inferring parameters for models of biological processes is a current challenge in systems biology, as is the related problem of comparing competing models that explain the data. In this work we apply Skilling's nested sampling to address both of these problems. Nested sampling is a Bayesian method for exploring…
Clàudia Payrató Borrás, Laura Hernández, Yamir Moreno
Mutualistic interactions, which are beneficial for both interacting species, are recurrently present in ecosystems. Observations of natural systems showed that, if we draw mutualistic relationships as binary links between species, the resulting bipartite network of interactions displays a widespread particular ordering…
Alexandr Savinov
The plethora of existing data models and specific data modeling techniques is not only confusing but leads to complex, eclectic and inefficient designs of systems for data management and analytics. The main goal of this paper is to describe a unified approach to data modeling, called the concept-oriented model (COM)…
Christoph Hoeppke, Benno I. Simmons
Nestedness is a widespread pattern in mutualistic networks that has high ecological and evolutionary importance due to its role in enhancing species persistence and community stability. Nestedness measures tend to be correlated with fundamental properties of networks, such as size and connectance, and so nestedness…
Alexandr Savinov
We describe a new logical data model, called the conceptoriented model (COM). It uses mathematical functions as firstclass constructs for data representation and data processing as opposed to using exclusively sets in conventional set-oriented models. Functions and function composition are used as primary semantic…
Alisa Bokulich, Wendy Parker
We critically engage two traditional views of scientific data and outline a novel philosophical view that we call the pragmatic-representational (PR) view of data. On the PR view, data are representations that are the product of a process of inquiry, and they should be evaluated in terms of their adequacy or fitness…
John Kratz, Carly Strasser
The movement to bring datasets into the scholarly record as first class research products (validated, preserved, cited, and credited) has been inching forward for some time, but now the pace is quickening. As data publication venues proliferate, significant debate continues over formats, processes, and terminology.…
Authors not listed
The nanosafety domain has seen significant advancements in data generation and sharing, yet challenges remain in ensuring data interoperability and reuse. This article focuses on developing a semantic interoperability framework for nanosafety data to maximize the FAIRness (Findability, Accessibility, Interoperability…