scholarly journals COMBINE Archive Specification Version 1

2015 ◽  
Vol 12 (2) ◽  
pp. 104-118 ◽  
Author(s):  
Frank T. Bergmann ◽  
Nicolas Rodriguez ◽  
Nicolas Le Novère

Summary Several standard formats have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result.The Open Modeling EXchange format (OMEX) supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, an optional metadata file, and the files describing the model. The manifest is an XML file listing all files included in the archive and their type. The metadata file provides additional information about the archive and its content. Although any format can be used, we recommend an XML serialization of the Resource Description Framework.Together with the other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails.

2015 ◽  
Vol 3 (2) ◽  
pp. 122-135 ◽  
Author(s):  
Ashleigh Faith ◽  
Michelle Chrzanowski

Libraries have struggled with connecting a plethora of content and the metadata stored in catalogs to patrons. Adding more value to catalogs, more tools for reference librarians, and enriched patron search, linked data is a means to connect more people with more relevant information. With the recent transition to the Resource Description and Access (RDA) cataloging standard within libraries, linking data in library databases has become a much easier project to tackle, largely because of another standard called Resource Description Framework (RDF). Both focus on resource description and both are components of linked data within the library. Tying them together is the Functional Requirements for Bibliographic Records (FRBR) conceptual framework. Acknowledging that linked data components are most likely new to many librarians, this article seeks to explain what linked data is, how RDA and RDF are connected by FRBR, and how knowledge maps may improve information access.


Author(s):  
Ala Djeddai ◽  
Hassina Seridi-Bouchelaghem ◽  
Med Tarek Khadir

Regardless of the knowledge structure lack about Resource Description Framework (RDF) data, difficulties, principally, occur in specifying and answering queries. Approximate querying is the solution to find relevant information by getting a set of sub structures (e.g. sub graphs) matching the query. Approaches based on the structure and others based on semantic, marginalized the common meaning between concepts in its computing. In this paper in order to improve the approximation by introducing the meaning similarity between components in the query and RDF components is proposed, getting better need satisfaction. The meaning similarity measure can be calculated using WordNet and used in all steps of the query answering process. In addition, other important properties in the approximation level calculation between query paths and RDF paths are considered; besides indexing and optimizations strategies are performed. Answers are a set of sub graphs ranked in decreasing order on its matching degree. Experiments are conducted within real RDF dataset.


Author(s):  
Andrés Baena-Raya ◽  
Manuel A. Rodríguez-Pérez ◽  
Pedro Jiménez-Reyes ◽  
Alberto Soriano-Maldonado

Sprint running and change of direction (COD) present similar mechanical demands, involving an acceleration phase in which athletes need to produce and apply substantial horizontal external force. Assessing the mechanical properties underpinning individual sprint acceleration might add relevant information about COD performance in addition to that obtained through sprint time alone. The present technical report uses a case series of three athletes with nearly identical 20 m sprint times but with different mechanical properties and COD performances. This makes it possible to illustrate, for the first time, a potential rationale for why the sprint force-velocity (FV) profile (i.e., theoretical maximal force (F0), velocity (V0), maximal power output (Pmax), ratio of effective horizontal component (RFpeak) and index of force application technique (DRF)) provides key information about COD performance (i.e., further to that derived from simple sprint time), which can be used to individualize training. This technical report provides practitioners with a justification to assess the FV profile in addition to sprint time when the aim is to enhance sprint acceleration and COD performance; practical interpretations and advice on how training interventions could be individualized based on the athletes’ differential sprint mechanical properties are also specified.


Author(s):  
Gwendolyn Rehrig ◽  
Reese A. Cullimore ◽  
John M. Henderson ◽  
Fernanda Ferreira

Abstract According to the Gricean Maxim of Quantity, speakers provide the amount of information listeners require to correctly interpret an utterance, and no more (Grice in Logic and conversation, 1975). However, speakers do tend to violate the Maxim of Quantity often, especially when the redundant information improves reference precision (Degen et al. in Psychol Rev 127(4):591–621, 2020). Redundant (non-contrastive) information may facilitate real-world search if it narrows the spatial scope under consideration, or improves target template specificity. The current study investigated whether non-contrastive modifiers that improve reference precision facilitate visual search in real-world scenes. In two visual search experiments, we compared search performance when perceptually relevant, but non-contrastive modifiers were included in the search instruction. Participants (NExp. 1 = 48, NExp. 2 = 48) searched for a unique target object following a search instruction that contained either no modifier, a location modifier (Experiment 1: on the top left, Experiment 2: on the shelf), or a color modifier (the black lamp). In Experiment 1 only, the target was located faster when the verbal instruction included either modifier, and there was an overall benefit of color modifiers in a combined analysis for scenes and conditions common to both experiments. The results suggest that violations of the Maxim of Quantity can facilitate search when the violations include task-relevant information that either augments the target template or constrains the search space, and when at least one modifier provides a highly reliable cue. Consistent with Degen et al. (2020), we conclude that listeners benefit from non-contrastive information that improves reference precision, and engage in rational reference comprehension. Significance statement This study investigated whether providing more information than someone needs to find an object in a photograph helps them to find that object more easily, even though it means they need to interpret a more complicated sentence. Before searching a scene, participants were either given information about where the object would be located in the scene, what color the object was, or were only told what object to search for. The results showed that providing additional information helped participants locate an object in an image more easily only when at least one piece of information communicated what part of the scene the object was in, which suggests that more information can be beneficial as long as that information is specific and helps the recipient achieve a goal. We conclude that people will pay attention to redundant information when it supports their task. In practice, our results suggest that instructions in other contexts (e.g., real-world navigation, using a smartphone app, prescription instructions, etc.) can benefit from the inclusion of what appears to be redundant information.


2021 ◽  
Vol 10 (4) ◽  
pp. 1-27
Author(s):  
Shengxin Jia ◽  
Veronica J. Santos

The sense of touch is essential for locating buried objects when vision-based approaches are limited. We present an approach for tactile perception when sensorized robot fingertips are used to directly interact with granular media particles in teleoperated systems. We evaluate the effects of linear and nonlinear classifier model architectures and three tactile sensor modalities (vibration, internal fluid pressure, fingerpad deformation) on the accuracy of estimates of fingertip contact state. We propose an architecture called the Sparse-Fusion Recurrent Neural Network (SF-RNN) in which sparse features are autonomously extracted prior to fusing multimodal tactile data in a fully connected RNN input layer. The multimodal SF-RNN model achieved 98.7% test accuracy and was robust to modest variations in granular media type and particle size, fingertip orientation, fingertip speed, and object location. Fingerpad deformation was the most informative modality for haptic exploration within granular media while vibration and internal fluid pressure provided additional information with appropriate signal processing. We introduce a real-time visualization of tactile percepts for remote exploration by constructing a belief map that combines probabilistic contact state estimates and fingertip location. The belief map visualizes the probability of an object being buried in the search region and could be used for planning.


Libri ◽  
2021 ◽  
Vol 71 (4) ◽  
pp. 375-387
Author(s):  
Seungmin Lee

Abstract A pidgin metadata framework based on the concept of pidgin metadata is proposed to complement the limitations of existing approaches to metadata interoperability and to achieve more reliable metadata interoperability. The framework consists of three layers, with a hierarchical structure, and reflects the semantic and structural characteristics of various metadata. Layer 1 performs both an external function, serving as an anchor for semantic association between metadata elements, and an internal function, providing semantic categories that can encompass detailed elements. Layer 2 is an arbitrary layer composed of substantial elements from existing metadata and performs a function in which different metadata elements describing the same or similar aspects of information resources are associated with the semantic categories of Layer 1. Layer 3 implements the semantic relationships between Layer 1 and Layer 2 through the Resource Description Framework syntax. With this structure, the pidgin metadata framework can establish the criteria for semantic connection between different elements and fully reflect the complexity and heterogeneity among various metadata. Additionally, it is expected to provide a bibliographic environment that can achieve more reliable metadata interoperability than existing approaches by securing the communication between metadata.


2012 ◽  
Vol 03 (02) ◽  
pp. 1250007 ◽  
Author(s):  
JÜRGEN EICHBERGER ◽  
ANI GUERDJIKOVA

We present a model of technological adaptation in response to a change in climate conditions. The main feature of the model is that new technologies are not just risky, but also ambiguous. Pessimistic agents are thus averse to adopting a new technology. Learning is induced by optimists, who are willing to try out technologies about which there is little evidence available. We show that both optimists and pessimists are crucial for a successful adaptation. While optimists provide the public good of information which gives pessimists an incentive to innovate, pessimists choose the new technology persistently in the long-run which increases the average returns for the society. Hence, the optimal share of optimists in the society is strictly positive. When the share of optimists in the society is too low, innovation is slow and the obtained steady-state is inefficient. We discuss two policies which can potentially alleviate this inefficiency: Subsidies and provision of additional information. We show that if precise and relevant information is available, pessimists would be willing to pay for it and consequently adopt the new technology. Hence, providing information might be a more efficient policy, which is both self-financing and results in better social outcomes.


Author(s):  
Christian Bizer ◽  
Maria-Esther Vidal ◽  
Michael Weiss

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