Semantic web-based document: editing and browsing in AktiveDoc

This paper presents a tool for supporting sharing and reuse of knowledge in document creation (writing) and use (reading). Semantic Web technologies are used to support the production of ontology based annotations while the document is written. Free text annotations (comments) can be added to integrate the knowledge in the document. In addition the tool uses external services (e.g. a Semantic Web harvester) to propose relevant content to writing user, enabling easy knowledge reuse. Similar facilities are provided for readers when their task does not coincide with the author’s one. The tool is specifically designed for Knowledge Management in organisations. In this paper we present and discuss how Semantic Web technologies are designed and integrated in the system

Toward an interactive article: integrating journals and biological databases.

BACKGROUND: Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. RESULTS: We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases. CONCLUSIONS: Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Introduction: Modeling, Learning and Processing of Text-Technological Data Structures

Researchers in many disciplines, sometimes working in close cooperation, have been concerned with modeling textual data in order to account for texts as the prime information unit of written communication. The list of disciplines includes computer science and linguistics as well as more specialized disciplines like computational linguistics and text technology. What many of these efforts have in common is the aim to model textual data by means of abstract data types or data structures that support at least the semi-automatic processing of texts in any area of written communication

Augmenting automatic speech recognition and search models for spoken content retrieval

Spoken content retrieval (SCR) is a process to provide a user with spoken documents in which the user is potentially interested. Unlike textual documents, searching through speech is not trivial due to its representation. Generally, automatic speech recognition (ASR) is used to transcribe spoken content such as user-generated videos and podcast episodes into transcripts before search operations are performed. Despite recent improvements in ASR, transcription errors can still be present in automatic transcripts. This is in particular when ASR is applied to out-of-domain data or speech with background noise. This thesis explores improvement of ASR systems and search models for enhanced SCR on user-generated spoken content. There are three topics explored in this thesis. Firstly, the use of multimodal signals for ASR is investigated. This is motivated to integrate background contexts of spoken content into ASR. Integration of visual signals and document metadata into ASR is hypothesised to produce transcripts more aligned to background contexts of speech. Secondly, the use of semi-supervised training and content genre information from metadata are exploited for ASR. This approach is motivated to mitigate the transcription errors caused by recognition of out-of-domain speech. Thirdly, the use of neural models and the model extension using N-best ASR transcripts are investigated. Using ASR N-best transcripts instead of 1-best for search models is motivated because "key terms" missed in 1-best can be present in the N-best transcripts. A series of experiments are conducted to examine those approaches to improvement of ASR systems and search models. The findings suggest that semi-supervised training bring practical improvement of ASR systems for SCR and the use of neural ranking models in particular with N-best transcripts improve the result of known-item search over the baseline BM25 model

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery