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Querying NeXtProt Nanopublications and Their Value for Insights on Sequence Variants and Tissue Expression

Christine Chichester, Pascale Gaudet, Oliver Karch, Paul Groth, Lydie Lane, Amos Bairoch, Barend Mons, Antonis Loizou
2014 Social Science Research Network  
Our work demonstrates for the first time how semantic technologies can be used to address these challenges using the nanopublication model applied to the neXtProt data set, a curated knowledgebase of information  ...  We show by the way of use cases using sequence variations, post-translational modifications (PTMs) and tissue expression, that querying the neXtProt nanopublication implementation is a credible approach  ...  The data set in neXtProt is complemented by the whole corpus of manually curated annotations extracted from UniProtKB/Swiss-Prot [12] and in an e↵ort to increase interoperability with other datasets  ... 
doi:10.2139/ssrn.3199138 fatcat:qg2k2ldsgzellcg7jt4bvjueiy

Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression

Christine Chichester, Pascale Gaudet, Oliver Karch, Paul Groth, Lydie Lane, Amos Bairoch, Barend Mons, Antonis Loizou
2014 Journal of Web Semantics  
Our work demonstrates for the first time how semantic technologies can be used to address these challenges using the nanopublication model applied to the neXtProt data set, a curated knowledgebase of information  ...  We show by the way of use cases using sequence variations, post-translational modifications (PTMs) and tissue expression, that querying the neXtProt nanopublication implementation is a credible approach  ...  The data set in neXtProt is complemented by the whole corpus of manually curated annotations extracted from UniProtKB/Swiss-Prot [12] and in an e↵ort to increase interoperability with other datasets  ... 
doi:10.1016/j.websem.2014.05.001 fatcat:5s7em2vmvbanhfq5fmozvfjfau

Nanopublications for exposing experimental data in the life-sciences: a Huntington's Disease case study

Eleni Mina, Mark Thompson, Rajaram Kaliyaperumal, Jun Zhao, Eelke van der Horst, Zuotian Tatum, Kristina M Hettne, Erik A Schultes, Barend Mons, Marco Roos
2015 Journal of Biomedical Semantics  
Here, we use the nanopublication model to make scientific assertions that were concluded from a workflow analysis of Huntington's Disease data machine-readable, interoperable, and citable.  ...  These results indicate that nanopublications can provide an incentive for researchers to expose data that is interoperable and machine-readable for future use and preservation for which they can get credits  ...  Such an approach can be complex and time-consuming, while the resulting code and data is not necessarily re-usable to answer other research questions.  ... 
doi:10.1186/2041-1480-6-5 pmid:26464783 pmcid:PMC4603842 fatcat:ness72giubdffb4tmaw2cx65qa

Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked Data [article]

Tobias Kuhn, Albert Meroño-Peñuela, Alexander Malic, Jorrit H. Poelen, Allen H. Hurlbert, Emilio Centeno Ortiz, Laura I. Furlong, Núria Queralt-Rosinach, Christine Chichester, Juan M. Banda, Egon Willighagen, Friederike Ehrhart, Chris Evelo (+2 others)
2018 arXiv   pre-print
In contrast to the common Linked Data publishing practice, nanopublications work at the granular level of atomic information snippets and provide a consistent container format to attach provenance and  ...  We provide here an overview of this combined nanopublication dataset, show the results of some overarching analyses, and describe how it can be accessed and queried.  ...  Linked Data approaches directly tackle the interoperability challenge, and the Linked Open Data cloud [6] has come to contain large amounts of scientifically relevant structured data.  ... 
arXiv:1809.06532v1 fatcat:sv73nev7jvdhjpbiztof3grj2i

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana (+64 others)
2019 F1000Research  
Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize the syntactic and semantic interoperability of open data in life sciences.  ...  The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining.  ...  Acknowledgements BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience  ... 
doi:10.12688/f1000research.18238.1 fatcat:mdt6bijqlveanplh4bmca5towu

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information

Marco Masseroli, Barend Mons, Erik Bongcam-Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frederique Lisacek, Paolo Romano
2014 BMC Bioinformatics  
First, relevance of using data and software models for the management and analysis of biological data is stressed.  ...  Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences.  ...  List of abbreviations used Acknowledgements Authors wish to thank all researchers who participated in the lively discussions held in Como during the NETTAB 2012 Workshop.  ... 
doi:10.1186/1471-2105-15-s1-s2 pmid:24564249 pmcid:PMC4015876 fatcat:xv4pyzwxtnfnjhquglv4j4lpna

Semantically enabling a genome-wide association study database

Tim Beck, Robert C Free, Gudmundur A Thorisson, Anthony J Brookes
2012 Journal of Biomedical Semantics  
The annotations are used to assist with cross-species genotype and phenotype comparisons.  ...  Building on the rich semantic phenotype annotation layer, we are able to make cross-species phenotype comparisons and publish a core subset of GWAS data as RDF nanopublications.  ...  Acknowledgements We thank the curation team of Robert Hastings, Sirisha Gollapudi and Raheleh Rahbari for providing the high-quality phenotype annotations within GWAS Central.  ... 
doi:10.1186/2041-1480-3-9 pmid:23244533 pmcid:PMC3579732 fatcat:nepqhbjc5rblpd3ckwriiaw7ge

Structuring research methods and data with the research object model: genomics workflows as a case study

Kristina M Hettne, Harish Dharuri, Jun Zhao, Katherine Wolstencroft, Khalid Belhajjame, Stian Soiland-Reyes, Eleni Mina, Mark Thompson, Don Cruickshank, Lourdes Verdes-Montenegro, Julian Garrido, David de Roure (+7 others)
2014 Journal of Biomedical Semantics  
Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results  ...  One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms.  ...  Case study: genome wide association studies As real-world example we aggregate and describe the research data, methods and metadata of a computational experiment in the context of studies of genetic variation  ... 
doi:10.1186/2041-1480-5-41 pmid:25276335 pmcid:PMC4177597 fatcat:ejlb76ytordqvh57q4ho6xtev4

Getting Ready for the Human Phenome Project: The 2012 Forum of the Human Variome Project

William S. Oetting, Peter N. Robinson, Marc S. Greenblatt, Richard G. Cotton, Tim Beck, John C. Carey, Sandra C. Doelken, Marta Girdea, Tudor Groza, Carol M. Hamilton, Ada Hamosh, Berit Kerner (+11 others)
2013 Human Mutation  
Acknowledgments The 2012 Meeting of the Human Variome Project was chaired by Peter Robinson from Charité Universitätsmedizin Berlin.  ...  information to be used in genome analysis.  ...  The goal of nanopublications is to incentivize the placement of data (that would otherwise be impossible to formally publish in a journal) into the public domain while providing linkage of the data to  ... 
doi:10.1002/humu.22293 pmid:23401191 pmcid:PMC4130157 fatcat:olvqoha4mrcstgbq23cpufuhka

MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases

Gillian S. Townend, Friederike Ehrhart, Henk J. van Kranen, Mark Wilkinson, Annika Jacobsen, Marco Roos, Egon L. Willighagen, David van Enckevort, Chris T. Evelo, Leopold M. G. Curfs
2018 Human Mutation  
genome sequencing data into databases and improvement of interoperability, similar to that offered by the Beacon project in relation to genomic data.  ...  It includes a pipeline to harmonize variant annotation of rare disease genomes (Laurie et al., 2016) To support both clinicians and researchers, we present in this article an overview of a number of  ... 
doi:10.1002/humu.23542 pmid:29704307 pmcid:PMC6033003 fatcat:zv56lxpeezbb7noynqjt7bqzme

Open PHACTS: semantic interoperability for drug discovery

Antony J. Williams, Lee Harland, Paul Groth, Stephen Pettifer, Christine Chichester, Egon L. Willighagen, Chris T. Evelo, Niklas Blomberg, Gerhard Ecker, Carole Goble, Barend Mons
2012 Drug Discovery Today  
The goal of the project is to deliver and sustain an 'open pharmacological space' using and enhancing state-of-the-art semantic web standards and technologies.  ...  OPS is intended to facilitate improvements in drug discovery in academia and industry and to support open innovation and in-house non-public drug discovery research.  ...  We acknowledge all of the collaborators for their contributions to Open PHACTS.  ... 
doi:10.1016/j.drudis.2012.05.016 pmid:22683805 fatcat:qnqlnrdv3zbijesyhdat2knoeu

FAIR Science for Social Machines: Let's Share Metadata Knowlets in the Internet of FAIR Data and Services

Barend Mons
2019 Data Intelligence  
The scalable and transparent routing of data, tools and compute (to run the tools on) is a key central feature of the envisioned Internet of FAIR Data and Services (IFDS). be findable for their major uses  ...  With a tendency to make good data stewardship the norm, a very significant new market for distributed data analytics and learning is opening and a plethora of tools and reusable data objects are being  ...  Two approaches can be used to achieve that.  ... 
doi:10.1162/dint_a_00002 dblp:journals/dint/Mons19 fatcat:63ni7tywufdq5azwm7mexgudt4

Extracting and Measuring Uncertain Biomedical Knowledge from Scientific Statements [article]

Xin Guo, Yuming Chen, Jian Du, Erdan Dong
2021 arXiv   pre-print
Purpose: This study aims to develop a novel approach to extracting and measuring uncertain biomedical knowledge from scientific statements.  ...  Practical implications: Our approach identified major uncertain knowledge areas, such as diagnostic biomarkers, genetic characteristics, and pharmacologic therapies surrounding cardiovascular diseases  ...  They proposed a rule-based, compositional approach that uses lexical and syntactic information to, and compared this approach to a supervised machine learning method that uses a rich feature set based  ... 
arXiv:2112.02570v1 fatcat:62y2phfihzgp7gwbrdwrvfacba

The Implicitome: A Resource for Rationalizing Gene-Disease Associations

Kristina M. Hettne, Mark Thompson, Herman H. H. B. M. van Haagen, Eelke van der Horst, Rajaram Kaliyaperumal, Eleni Mina, Zuotian Tatum, Jeroen F. J. Laros, Erik M. van Mulligen, Martijn Schuemie, Emmelien Aten, Tong Shu Li (+11 others)
2016 PLoS ONE  
Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease  ...  High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases  ...  We would like to thank Tobias Messemaker and Yu Sun for their expert advice on the Seckel Syndrome case study, and Jaap van den Herik of the Leiden Center for Data Science for carefully reading the manuscript  ... 
doi:10.1371/journal.pone.0149621 pmid:26919047 pmcid:PMC4769089 fatcat:dru6ynlspfaf7dsrfj6ojiqg74

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I. Furlong
2016 Nucleic Acids Research  
DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies.  ...  However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome.  ...  ACKNOWLEDGEMENTS The authors would like to thank the Exome Aggregation Consortium and the groups that provided exome variant data for comparison.  ... 
doi:10.1093/nar/gkw943 pmid:27924018 pmcid:PMC5210640 fatcat:5lwyn7r5hnd6bbmbesjjomtmm4
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