Concept: Semantic Web
BACKGROUND: Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. RESULTS: With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (www.phylotastic.org), and a server image. CONCLUSIONS: Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.
BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the ‘Semantic Web’, and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.
PubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as an increasingly important approach to distribute and integrate scientific data. Exposing PubChem data to Semantic Web services may help enable automated data integration and management, as well as facilitate interoperable web applications.
Increasingly, scholarly articles contain URI references to “web at large” resources including project web sites, scholarly wikis, ontologies, online debates, presentations, blogs, and videos. Authors reference such resources to provide essential context for the research they report on. A reader who visits a web at large resource by following a URI reference in an article, some time after its publication, is led to believe that the resource’s content is representative of what the author originally referenced. However, due to the dynamic nature of the web, that may very well not be the case. We reuse a dataset from a previous study in which several authors of this paper were involved, and investigate to what extent the textual content of web at large resources referenced in a vast collection of Science, Technology, and Medicine (STM) articles published between 1997 and 2012 has remained stable since the publication of the referencing article. We do so in a two-step approach that relies on various well-established similarity measures to compare textual content. In a first step, we use 19 web archives to find snapshots of referenced web at large resources that have textual content that is representative of the state of the resource around the time of publication of the referencing paper. We find that representative snapshots exist for about 30% of all URI references. In a second step, we compare the textual content of representative snapshots with that of their live web counterparts. We find that for over 75% of references the content has drifted away from what it was when referenced. These results raise significant concerns regarding the long term integrity of the web-based scholarly record and call for the deployment of techniques to combat these problems.
- Proceedings of the National Academy of Sciences of the United States of America
- Published about 5 years ago
The jury trial is a critical point where the state and its citizens come together to define the limits of acceptable behavior. Here we present a large-scale quantitative analysis of trial transcripts from the Old Bailey that reveal a major transition in the nature of this defining moment. By coarse-graining the spoken word testimony into synonym sets and dividing the trials based on indictment, we demonstrate the emergence of semantically distinct violent and nonviolent trial genres. We show that although in the late 18th century the semantic content of trials for violent offenses is functionally indistinguishable from that for nonviolent ones, a long-term, secular trend drives the system toward increasingly clear distinctions between violent and nonviolent acts. We separate this process into the shifting patterns that drive it, determine the relative effects of bureaucratic change and broader cultural shifts, and identify the synonym sets most responsible for the eventual genre distinguishability. This work provides a new window onto the cultural and institutional changes that accompany the monopolization of violence by the state, described in qualitative historical analysis as the civilizing process.
OBJECTIVE: There is a growing realisation that clinical pathways (CPs) are vital for improving the treatment quality of healthcare organisations. However, treatment personalisation is one of the main challenges when implementing CPs, and the inadequate dynamic adaptability restricts the practicality of CPs. The purpose of this study is to improve the practicality of CPs using semantic interoperability between knowledge-based CPs and semantic electronic health records (EHRs). METHODS: Simple protocol and resource description framework query language is used to gather patient information from semantic EHRs. The gathered patient information is entered into the CP ontology represented by web ontology language. Then, after reasoning over rules described by semantic web rule language in the Jena semantic framework, we adjust the standardised CPs to meet different patients' practical needs. RESULTS: A CP for acute appendicitis is used as an example to illustrate how to achieve CP customisation based on the semantic interoperability between knowledge-based CPs and semantic EHRs. A personalised care plan is generated by comprehensively analysing the patient’s personal allergy history and past medical history, which are stored in semantic EHRs. Additionally, by monitoring the patient’s clinical information, an exception is recorded and handled during CP execution. According to execution results of the actual example, the solutions we present are shown to be technically feasible. CONCLUSION: This study contributes towards improving the clinical personalised practicality of standardised CPs. In addition, this study establishes the foundation for future work on the research and development of an independent CP system.
We describe a framework to model visual semantics of liver lesions in CT images in order to predict the visual semantic terms (VST) reported by radiologists in describing these lesions. Computational models of VST are learned from image data using high-order steerable Riesz wavelets and support vector machines (SVM). The organization of scales and directions that are specific to every VST are modeled as linear combinations of directional Riesz wavelets. The models obtained are steerable, which means that any orientation of the model can be synthesized from linear combinations of the basis filters. The latter property is leveraged to model VST independently from their local orientation. In a first step, these models are used to predict the presence of each semantic term that describes liver lesions. In a second step, the distances between all VST models are calculated to establish a non-hierarchical computationally-derived ontology of VST containing inter-term synonymy and complementarity. A preliminary evaluation of the proposed framework was carried out using 74 liver lesions annotated with a set of 18 VSTs from the RadLex ontology. A leave-one-patient-out cross-validation resulted in an average area under the ROC curve of 0.853 for predicting the presence of each VST when using SVMs in a feature space combining the magnitudes of the steered models with CT intensities. Likelihood maps are created for each VST, which enables high transparency of the information modeled. The computationally-derived ontology obtained from the VST models was found to be consistent with the underlying semantics of the visual terms. It was found to be complementary to the RadLex ontology, and constitutes a potential method to link the image content to visual semantics. The proposed framework is expected to foster human-computer synergies for the interpretation of radiological images while using rotation-covariant computational models of VSTs to (1) quantify their local likelihood and (2) explicitly link them with pixel-based image content in the context of a given imaging domain.
- IEEE transactions on neural networks and learning systems
- Published over 4 years ago
Kohonen’s self-organizing map (SOM) is used to map high-dimensional data into a low-dimensional representation (typically a 2-D or 3-D space) while preserving their topological characteristics. A major reason for its application is to be able to visualize data while preserving their relation in the high-dimensional input data space as much as possible. Here, we are seeking to go further by incorporating semantic meaning in the low-dimensional representation. In a conventional SOM, the semantic context of the data, such as class labels, does not have any influence on the formation of the map. As an abstraction of neural function, the SOM models bottom-up self-organization but not feedback modulation which is also ubiquitous in the brain. In this paper, we demonstrate a hierarchical neural network, which learns a topographical map that also reflects the semantic context of the data. Our method combines unsupervised, bottom-up topographical map formation with top-down supervised learning. We discuss the mathematical properties of the proposed hierarchical neural network and demonstrate its abilities with empirical experiments.
Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.