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Comparison of ontology alignment systems across single matching task via the McNemar's test [article]

Majid Mohammadi, Amir Ahooye Atashin, Wout Hofman, Yao-Hua Tan
2018 arXiv   pre-print
comparison of two ontology alignment systems over one matching task is drawn.The test applies to a 2x2 contingency table which can be constructed in two different ways based on the alignments,each of  ...  scores typically require the identified alignment and a reference containing the underlying actual correspondences of the given ontologies.The current trend in the alignment evaluation is to put forward  ...  Given the source and target ontologies for alignment, a correspondence is defined as the mapping of one concept in the source to one concept in the target ontology.  ... 
arXiv:1704.00045v2 fatcat:hcjvts4dlvbuhelkf6whtjqlsy

Foundational ontologies meet ontology matching: A survey

Cassia Trojahn, Renata Vieira, Daniela Schmidt, Adam Pease, Giancarlo Guizzardi, Jérôme Euzenat
2021 Semantic Web Journal  
The role of foundational ontologies for ontology matching is an important one, as they provide a well-founded reference model that can be shared across domains.  ...  It is multifaceted and with room for development. This paper presents an overview of the different tasks involved in ontology matching that consider foundational ontologies.  ...  Acknowledgement Renata Vieira is funded by the Portuguese Foundation for Science and Technology, project UIDB-00057-2020.  ... 
doi:10.3233/sw-210447 fatcat:mb3jo5cr2bcc5ekckku6klnvvq

Quality Validation through Pattern Detection - A Semantic Web Perspective

David Walsh, Philipp Schugerl, Juergen Rilling, Philippe Charland
2011 2011 IEEE 35th Annual Computer Software and Applications Conference  
We illustrate the flexibility and applicability of our approach through several use cases, including the detection of security and design patterns, violations of secure programming guideline violations  ...  Quality Validation through Pattern Detection -A Semantic Web Perspective David Walsh Given the ongoing trend towards a globalization of software systems, open networks and distributed platforms, validating  ...  For instance, the Java language [23, 32] has a set of guidelines in that matter and tools to support the detection of their violation [29] .  ... 
doi:10.1109/compsac.2011.40 dblp:conf/compsac/WalshSRC11 fatcat:sbbkodvkcfgh7ox7h26wg4lwfq

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis, Roderic Guigó
2008 PLoS Computational Biology  
Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared.  ...  Our results have implications for comparative genomics analyses in any species, including the human.  ...  Nguyen for informatics assistance; David DeCaprio, Jade Vinson, and James Galagan for helpful discussions regarding SMCRFs; and Alexander Stark and Pouya Kheradpour for additional comments and discussions  ... 
doi:10.1371/journal.pcbi.1000067 pmid:18421375 pmcid:PMC2291194 fatcat:j7wjlrrsznblrc4qwq63jsxosa

Linked data schemata: Fixing unsound foundations

Kevin Chekov Feeney, Gavin Mendel Gleason, Rob Brennan, Amrapali Zaveri, Dimitris Kontokostas, Sebastian Hellmann, Jürgen Umbrich, Amrapali Zaveri, Dimitris Kontokostas, Sebastian Hellmann, Jürgen Umbrich
2017 Semantic Web Journal  
In addition to identifying problems, this paper suggests a set of recommendations for linked data ontology design best practice.  ...  This paper describes our tools and method for an evaluation of the practical and logical implications of combining common linked data vocabularies into a single local logical model for the purpose of reasoning  ...  This research has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 644055, the ALIGNED project (www.aligned-project.eu) and from the ADAPT  ... 
doi:10.3233/sw-170271 fatcat:fgpetjjp55brfh52ejycp7vjca

Genome-Wide Polymorphism and Comparative Analyses in the White-Tailed Deer (Odocoileus virginianus): A Model for Conservation Genomics

Christopher M. Seabury, Eric K. Bhattarai, Jeremy F. Taylor, Ganesh G. Viswanathan, Susan M. Cooper, Donald S. Davis, Scot E. Dowd, Mitch L. Lockwood, Paul M. Seabury, Rudy A. Hartskeerl
2011 PLoS ONE  
A SNP validation study designed to test specific classes of putative SNPs provides evidence for as many as 10,476 genome-wide SNPs in the current dataset.  ...  for 10 unique species of Cervidae, and a median joining haplotype network as a putative representation of mitochondrial evolution in O. virginianus.  ...  The contig accessions described in this paper are the first version. Note, 43 contigs were removed by NCBI filtering. A complete mitochondrial genome was deposited in Genbank (Accession HQ332445).  ... 
doi:10.1371/journal.pone.0015811 pmid:21283515 pmcid:PMC3023705 fatcat:wg7jhcwduvbqvoxms2osktuzwi

Functional Annotation of Uncharacterized Protein from Photobacterium damselae subsp. piscicida (Pasteurella piscicida) and Comparison of Drug Target Between Conventional Medicine and Phytochemical Compound Against Disease Treatment in Fish: An In-silico Approach

Sk Injamamul Islam, Mou Moslema Jahan
2022 Genetics of Aquatic Organisms  
Photobacterium damselae is one of the deadliest bacterial pathogens in the world of aquaculture.  ...  The protein-protein interaction network suggested that this uncharacterized protein may serve as a DNA/RNA hydrase and conserved domain search predict two different domains.  ...  Acknowledgements The first author sincerely grateful to the ASEAN and Non-ASEAN scholarship authority at Chulalongkorn University, Thailand as giving financial support for pursuing masters studies.  ... 
doi:10.4194/ga453 fatcat:rerkturez5bmbjplnewfahk66u

Genome-wide identification of conserved regulatory function in diverged sequences

L. Taher, D. M. McGaughey, S. Maragh, I. Aneas, S. L. Bessling, W. Miller, M. A. Nobrega, A. S. McCallion, I. Ovcharenko
2011 Genome Research  
Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element.  ...  We have developed a method that can accurately identify pairs of functional noncoding orthologs at evolutionarily diverged loci by searching for conserved TFBS arrangements.  ...  best available for the purpose.  ... 
doi:10.1101/gr.119016.110 pmid:21628450 pmcid:PMC3129256 fatcat:sac4frij2fgnphyd5s4puxed6q

Hunting for beneficial mutations: conditioning on SIFT scores when estimating the distribution of fitness effect of new mutations

J Chen, T Bataillon, S Glémin, M Lascoux
2021 Genome Biology and Evolution  
SIFT scores are assigned to nucleotide sites based on their level of conservation across a multi species alignment: the more conserved a site, the more likely mutations occurring at this site are deleterious  ...  In the present study, we developed a new measure based on SIFT scores.  ...  Acknowledgments This work was supported by a grant from the Chinese Research Council to J.C. and a grant from the Swedish Research Council to M.L.  ... 
doi:10.1093/gbe/evab151 pmid:34180988 pmcid:PMC8743036 fatcat:dyaovachhneehbwzrjs4ejzyde

Genomics, environment and balancing selection in behaviorally bimodal populations: the caribou case

Maria Cavedon, Chrysoula Goubili, Elizabeth Heppenheimer, Bridgett vonHoldt, Stefano Mariani, Mark Hebblewhite, Troy Hegel, Dave Hervieux, Robert Serrouya, Robin Steenweg, Byron V. Weckworth, Marco Musiani
2019 Molecular Ecology  
For example, NFDS is hypothesized to maintain partial migration, a dimorphic behavioural trait prominent in species where only a fraction of the population seasonally migrates.  ...  We applied a Pool-seq approach and detected selection on alleles associated with environmental variables along a North-South gradient in western North American caribou, a species displaying partially migratory  ...  We are grateful to two anonymous reviewers for their helpful comments on the manuscript.  ... 
doi:10.1111/mec.15039 pmid:30714247 fatcat:b54ltqhvo5b65ghqoka3a3hgcu

From norms to normative configurations: a pragmatist and relational approach to theorizing normativity in IR

Simon Frankel Pratt
2019 International Theory  
I offer a way of conceptualizing and analyzing normativity consistent with these alternative approaches.  ...  Namely, I have brought together a pragmatist theory of action with the social theories of a number of key relational social theorists and philosophers, oriented around a reading of what norms-talk actually  ...  It makes the theoretical goods and themes of the norms research programme ontologically tractable to those working from relational and practice-theoretic approaches, while also introducing the critiques  ... 
doi:10.1017/s1752971919000095 fatcat:t3rys5li5jcvricfi2whsad4a4

Open biomedical pluralism: formalising knowledge about breast cancer phenotypes

Aleksandra Sojic, Oliver Kutz
2012 Journal of Biomedical Semantics  
In order to clarify how the plurality of epistemic motivations can be integrated on a formal level, we give a distinction between six categories of human agents as individuals and groups focused around  ...  circumscription allowing a transparent formal modelling of the normal/ abnormal distinction in phenotypes.  ...  This article has been published as part of Journal of Biomedical Semantics Volume 3 Supplement 2, 2012: Proceedings of Ontologies in Biomedicine and Life Sciences (OBML 2011).  ... 
doi:10.1186/2041-1480-3-s2-s3 pmid:23046572 pmcid:PMC3448532 fatcat:5yrrk3i7j5fbfcylozljjmvkki

The contemporary concepts of homology in biology: A theoretical review

I. Ya. Pavlinov
2012 Biology Bulletin Reviews  
A review of the contemporary theoretical concepts of homology addresses the following issues: the ontological status of homology (nominalistic, realistic, and conceptualistic interpretations); the absolute  ...  or rel ative nature of homology statements; distinguishing between the general categories of taxic and transformational homologies and the methods for assuming homology in each of these categories; homology  ...  The concept of homology is among the most basic concepts in the disciplines based on a comparative (in a broad sense) approach.  ... 
doi:10.1134/s2079086412010057 fatcat:vyibcoi3fzbtne2ifin7vwzvgq

Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases

Shilpa Nadimpalli Kobren, Undiagnosed Diseases Network, Dustin Baldridge, Matt Velinder, Joel B. Krier, Kimberly LeBlanc, Cecilia Esteves, Barbara N. Pusey, Stephan Züchner, Elizabeth Blue, Hane Lee, Alden Huang (+11 others)
2021 Genetics in Medicine  
integration, demonstrating a diversity of approaches for solving the most mysterious undiagnosed cases.  ...  Methods We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network  ...  In the following sections, we delve into the purpose of and tools used in each of these categories.  ... 
doi:10.1038/s41436-020-01084-8 pmid:33580225 pmcid:PMC8187147 fatcat:s4mbmmxe7jhx5bn7fp5mv77iyu

Mathematics via Symmetry [article]

Noson S. Yanofsky, Mark Zelcer
2013 arXiv   pre-print
We state the defining characteristic of mathematics as a type of symmetry where one can change the connotation of a mathematical statement in a certain way when the statement's truth value remains the  ...  We explore the very nature of mathematics and its relationship with natural science from this perspective. This point of view helps clarify some standard problems in the philosophy of mathematics.  ...  A philosophical naturalist's interest in the philosophy of mathematics is the alignment of the ontology, epistemology, and especially methodology of mathematics with those established for science.  ... 
arXiv:1306.4235v1 fatcat:ktohmdb73bg7vmdbm24hyukol4
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