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PubMed | TU Dresden, BASF, Transinsight and Scientific Consultancy Animal Welfare
Type: Journal Article | Journal: Toxicology in vitro : an international journal published in association with BIBRA | Year: 2014

The knowledge-based search engine Go3R, www.Go3R.org, has been developed to assist scientists from industry and regulatory authorities in collecting comprehensive toxicological information with a special focus on identifying available alternatives to animal testing. The semantic search paradigm of Go3R makes use of expert knowledge on 3Rs methods and regulatory toxicology, laid down in the ontology, a network of concepts, terms, and synonyms, to recognize the contents of documents. Search results are automatically sorted into a dynamic table of contents presented alongside the list of documents retrieved. This table of contents allows the user to quickly filter the set of documents by topics of interest. Documents containing hazard information are automatically assigned to a user interface following the endpoint-specific IUCLID5 categorization scheme required, e.g. for REACH registration dossiers. For this purpose, complex endpoint-specific search queries were compiled and integrated into the search engine (based upon a gold standard of 310 references that had been assigned manually to the different endpoint categories). Go3R sorts 87% of the references concordantly into the respective IUCLID5 categories. Currently, Go3R searches in the 22 million documents available in the PubMed and TOXNET databases. However, it can be customized to search in other databases including in-house databanks.

Schmidt S.,University of Kiel | Plonka C.,Transinsight | Gotze H.-J.,University of Kiel | Lahmeyer B.,Statoil
Geophysical Prospecting | Year: 2011

Modern geophysical interpretation requires an interdisciplinary approach and software capable of handling multiple geophysical data types such as seismic, full tensor gravity gradiometry, magnetics and magnetotellurics. We use the IGMAS+ (Interactive Gravity and Magnetic Application System) geo-modelling software that is designed for 3D gravity, gravity gradient and magnetic modelling. This paper deals with a special aspect of potential field modelling, combining conventional triangulated model geometries (building polyhedrons) with voxel cubes. The hybrid modelling combines the advantages of both the vector and raster modelling system: both may be used alone (polyhedrons without voxels, voxels without polyhedrons) or simultaneously by superposition of both effects, which provides flexibility towards full interoperability. The key idea of our approach is, on the one hand to use two different, completely independent geometries (vector and raster) and give on the other hand the possibility to link both on demand for either editing the voxel model or to combine a large number of voxel cells under a common physical parameter function - which results in more reliable parameter inversion results. © 2011 European Association of Geoscientists & Engineers.

Alvers M.R.,Transinsight | Lahmeyer B.,Statoil | Plonka C.,Transinsight | Stangeland Karlsen E.,Statoil
76th European Association of Geoscientists and Engineers Conference and Exhibition 2014: Experience the Energy - Incorporating SPE EUROPEC 2014 | Year: 2014

3D interactive inversion of potential field data presents an interesting addition to the toolbox used to find subsurface models being consistent with the measured data and other information like seismic and geology. The concept was presented last year at the EAGE in London (Alvers et al. 2013). In the meantime this concept has been implemented and applied to a realistic case, the SEAM model, representing a complex salt geometry in the GoM (Pangman 2007). Results and learnings of this test will be presented.

Alvers M.R.,Transinsight | Gotze H.J.,University of Kiel | Lahmeyer B.,Statoil | Plonka C.,Transinsight | Schmidt S.,University of Kiel
75th European Association of Geoscientists and Engineers Conference and Exhibition 2013 Incorporating SPE EUROPEC 2013: Changing Frontiers | Year: 2013

We present improved 3D modeling techniques for potential field data. A new 3D-editing concept makes geometry changes in 3D easier, without the risk of creating inconsistent models with crossing boundaries or holes. Based on the new 3D editor the concept of interactive inversion is introduced. Also spherical modeling avoids incorrect calculations for big regional models. In order to guarantee that the improvements above are applicable in an interactive program we present strategies for big performance improvements. All the techniques described are currently tested and will be implemented in IGMAS+. Copyright © (2012) by the European Association of Geoscientists & Engineers All rights reserved.

Gotze H.-J.,Istitut fur Geowissenschaften Kiel | Alvers M.R.,Transinsight | Barrio-Alvers L.,Transinsight | Lahmeyer B.,Statoil | And 2 more authors.
Proceedings of IAMG 2015 - 17th Annual Conference of the International Association for Mathematical Geosciences | Year: 2015

We are describing here a new approach for "joint inversion"': Highly interactive, ideally realtime and topology conserving. These are important ingredients for joint inversion not only for gravity (FTG) and magnetic modelling based on seismic input, but also ingredients toward a true integration of Full Waveform inversion (FWI) and EM methods. We think now we are a bit closer to the dream of treating all geophysical methods in one realistic underground model and aim for fulfilling most of the constraints: measured data and geological plausibility.

Agency: European Commission | Branch: FP7 | Program: CSA | Phase: ICT-2011.4.4 | Award Amount: 1.38M | Year: 2012

BioASQ will push for a solution to the information access problem of biomedical experts by setting up a challenge on biomedical semantic indexing and question answering (QA). Biomedical knowledge is dispersed in hundreds of heterogeneous knowledge sources and databases; many of them are connected on the Linked Open Data cloud. Biomedical experts, on the other hand, are in constant need of highly specialized information, which they cannot easily obtain. To address their needs, an information system needs to ``understand the data and answer efficiently the experts questions. Often, however, experts need responses that cannot be answered by a single information source. To integrate information from disparate sources, semantic indexing of the vast quantities of information is needed to bridge the experts needs with the available data sources. Semantic indexing is currently achieved by manual annotation, and does not scale up. Automating this process requires large-scale classification of data into hierarchically organized concepts. QA methods capable of ``interpreting questions in terms of the same concepts are also needed. BioASQ will push towards improved biomedical semantic indexing and QA via ambitious, yet realistic challenge tasks. The challenge will run in two stages, designed to (a) adapt traditional semantic indexing and QA methods to the needs of biomedical experts, and (b) collect feedback and improve the experimental setting itself. A large computational infrastructure, already available to the consortium, will be used to evaluate competing systems. The required datasets and evaluation measures will be established before the challenge. Biomedical experts will participate in the consortium, both as partners and through a supporting network of third parties.

PubMed | University of Leipzig, Athens University of Economics and Business, Joseph Fourier University, Greek National Center For Scientific Research and 3 more.
Type: | Journal: BMC bioinformatics | Year: 2015

This article provides an overview of the first BIOASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BIOASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies.The 2013 BIOASQ competition comprised two tasks, Task 1a and Task 1b. In Task 1a participants were asked to automatically annotate new PUBMED documents with MESH headings. Twelve teams participated in Task 1a, with a total of 46 system runs submitted, and one of the teams performing consistently better than the MTI indexer used by NLM to suggest MESH headings to curators. Task 1b used benchmark datasets containing 29 development and 282 test English questions, along with gold standard (reference) answers, prepared by a team of biomedical experts from around Europe and participants had to automatically produce answers. Three teams participated in Task 1b, with 11 system runs. The BIOASQ infrastructure, including benchmark datasets, evaluation mechanisms, and the results of the participants and baseline methods, is publicly available.A publicly available evaluation infrastructure for biomedical semantic indexing and QA has been developed, which includes benchmark datasets, and can be used to evaluate systems that: assign MESH headings to published articles or to English questions; retrieve relevant RDF triples from ontologies, relevant articles and snippets from PUBMED Central; produce exact and paragraph-sized ideal answers (summaries). The results of the systems that participated in the 2013 BIOASQ competition are promising. In Task 1a one of the systems performed consistently better from the NLMs MTI indexer. In Task 1b the systems received high scores in the manual evaluation of the ideal answers; hence, they produced high quality summaries as answers. Overall, BIOASQ helped obtain a unified view of how techniques from text classification, semantic indexing, document and passage retrieval, question answering, and text summarization can be combined to allow biomedical experts to obtain concise, user-understandable answers to questions reflecting their real information needs.

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