The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.

Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achieving
the goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, _Nature Preceedings_, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals

Internet based molecular collaborative and publishing tools

The scientific electronic publishing model has hitherto been an Internet based delivery of electronic articles that are essentially replicas of their paper counterparts. They contain little in the way of added semantics that may better expose the science, assist the peer review process and facilitate follow on collaborations, even though the enabling technologies have been around for some time and are mature. This thesis will examine the evolution of chemical electronic publishing over the past 15 years. It will illustrate, which the help of two frameworks, how publishers should be exploiting technologies to improve the semantics of chemical journal articles, namely their value added features and relationships with other chemical resources on the Web. The first framework is an early exemplar of structured and scalable electronic publishing where a Web content management system and a molecular database are integrated. It employs a test bed of articles from several RSC journals and supporting molecular coordinate and connectivity information. The value of converting 3D molecular expressions in chemical file formats, such as the MOL file, into more generic 3D graphics formats, such as Web3D, is assessed. This exemplar highlights the use of metadata management for bidirectional hyperlink maintenance in electronic publishing. The second framework repurposes this metadata management concept into a Semantic Web application called SemanticEye. SemanticEye demonstrates how relationships between chemical electronic articles and other chemical resources are established. It adapts the successful semantic model used for digital music metadata management by popular applications such as iTunes. Globally unique identifiers enable relationships to be established between articles and other resources on the Web and SemanticEye implements two: the Document Object Identifier (DOI) for articles and the IUPAC International Chemical Identifier (InChI) for molecules. SemanticEye’s potential as a framework for seeding collaborations between researchers, who have hitherto never met, is explored using FOAF, the friend-of-a-friend Semantic Web standard for social networks

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

Studies on User Intent Analysis and Mining

Predicting the goals of users can be extremely useful in e-commerce, online entertainment, information retrieval, and many other online services and applications. In this thesis, we study the task of user intent understanding, trying to bridge the gap between user expressions to online services and their goals behind it. As far as we know, most of the existing user intent studies are focusing on web search and social media domain. Studies on other areas are not enough. For example, as people more and more rely our daily life on cellphone, our information needs expressing to mobile devices and related services are increasing dramatically. Studies of user intent mining on mobile devices are not much. And the intentions of using mobile devices are different from the ones we use web search engine or social network. So we cannot directly apply the existing user intention to this area. Besides, user's intents are not stable but changing over time. And different interests will impact each other. Modeling such kind of dynamic user interests can help accurately understand and predict user's intent. But there're few existing works in this area. Moreover, user intent could be explicitly or implicitly expressed by users. The implicit intent expression is more close to human's natural language and also have great value to recognize and mine. To make further studies of these challenges, we first try to answer the question of “What is the user intent?” By referring amount of previous studies, we give our definition of user intent as “User intent is a task-specific, predefined or latent concept, topic or knowledge-base that is under an expression from a user who is trying to express his goal of information or service need.“ Then, we focus on the driving scenario when a user using cellphone and study the user intent in this domain. As far as we know, it is the first time of user intent analysis and categorization in this domain. And we also build a dataset of user input and related intent category and attributes by crowdsourcing and carefully handcraft. With the user intent taxonomy and dataset in hand, we conduct a user intent classification and user intent attribute recognition by supervised machine learning models. To classify the user intent for a user intent query, we use a convolutional neural network model to build a multi-class classifier. And then we use a sequential labeling method to recognize the intent attribute in the query. The experiment results show that our proposed method outperforms several baseline models in precision, recall, and F-score. In addition, we study the implicit user intent mining method through web search log data. By using a Restricted Boltzmann Machine, we make use of the correlation of query and click information to learn the latent intent behind a user web search. We propose a user intent prediction model on online discussion forum using Multivariate Hawkes Process. It dynamically models user intentions change and interact over time.The method models both of the internal and external factors of user's online forum response motivations, and also integrated the time decay fact of user's interests. We also present a data visualization method, using an enriched domain ontology to highlight the domain-specific words and entity relations within an article.Ph.D., Information Studies -- Drexel University, 201

Self-organizing distributed digital library supporting audio-video

The StreamOnTheFly network combines peer-to-peer networking and open-archive principles for community radio channels and TV stations in Europe. StreamOnTheFly demonstrates new methods of archive management and personalization technologies for both audio and video. It also provides a collaboration platform for community purposes that suits the flexible activity patterns of these kinds of broadcaster communities