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Euler/X: A Toolkit for Logic-based Taxonomy Integration [article]

Mingmin Chen, Shizhuo Yu, Nico Franz, Shawn Bowers, Bertram Lu'́asher
2014 arXiv   pre-print
We introduce Euler/X, a toolkit for logic-based taxonomy integration.  ...  Given two taxonomies and a set of alignment constraints between them, Euler/X provides tools for detecting, explaining, and reconciling inconsistencies; finding all possible merges between (consistent)  ...  We thank the anonymous reviewers for their helpful comments. Work supported in part by NSF awards IIS-1118088 and DBI-1147273.  ... 
arXiv:1402.1992v1 fatcat:yzogcxuawvhsfixkkjjcbtutji

Agreeing to disagree: Reconciling conflicting taxonomic views using a logic-based approach

Yi-Yun Cheng, Nico Franz, Jodi Schneider, Shizhuo Yu, Thomas Rodenhausen, Bertram Ludäscher
2017 Proceedings of the Association for Information Science and Technology  
Taxonomy alignment is a way to integrate two or more taxonomies.  ...  We have implemented these case studies with an open source tool called Euler/X which has been applied primarily for solving complex alignment problems in biological classification.  ...  The authors thank Professor Kathryn La Barre for her comments and suggestions. We would also like to thank Dr. Laetitia Navarro and Jeff Terstriep for help with creating map overlays in QGIS.  ... 
doi:10.1002/pra2.2017.14505401006 dblp:conf/asist/ChengFSYRL17 fatcat:xtthqnhupvfetnwokwjgl7fc74

Controlling the taxonomic variable: Taxonomic concept resolution for a southeastern United States herbarium portal

Nico Franz, Edward Gilbert, Bertram Ludäscher, Alan Weakley
2016 Research Ideas and Outcomes  
We will leverage RCC-5 data from the Weakley Flora and further development of the Euler/X logic reasoning toolkit to provide comprehensive genus-to variety-level concept alignments for at least 10 major  ...  A unique constellation of prior effortsincluding the powerful Symbiota collections software platform, the Euler/X multi-taxonomy alignment toolkit, and the "Weakley Flora" which entails 7,000 concepts  ...  This acknowledgment need not imply that the collaborators are responsible for the overall goals and content of the proposal.  ... 
doi:10.3897/rio.2.e10610 fatcat:zatj4qmqzbd2hm4sq2ufds3pce

Names are not good enough: Reasoning over taxonomic change in the Andropogon complex1

Nico M. Franz, Mingmin Chen, Parisa Kianmajd, Shizhuo Yu, Shawn Bowers, Alan S. Weakley, Bertram Ludäscher, Krysztof Janowicz, Benjamin Adams, Birgitta König-Ries, Deborah McGuinness, Mark Schildhauer
2016 Semantic Web Journal  
We present a novel, logic-based solution to the challenge of reconciling the meanings of taxonomic names across multiple biological taxonomies.  ...  We discuss the applicability of the RCC-5 alignment approach in the context of achieving logic-based integration of non-/congruent taxonomic concept hierarchies in dynamic biodiversity data environments  ...  Introduction We present a novel, logic-based solution to the challenge of integrating the meanings of taxonomic names across multiple biological taxonomies.  ... 
doi:10.3233/sw-160220 fatcat:j2ecsk2iyvhanairvixhd5fymy

Taxonomic Provenance: Two Influential Primate Classifications Logically Aligned [article]

Nico M. Franz, Naomi M. Pier, DeAnn M. Reeder, Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Shawn Bowers, Bertram Ludaescher
2014 arXiv   pre-print
We conclude with an optimistic outlook for logic-based provenance tools in next-generation biodiversity and phylogeny data platforms.  ...  Using 402 concept-to-concept input articulations, the reasoning process yields a single, consistent alignment, and infers 153,111 Maximally Informative Relations that constitute a comprehensive provenance  ...  METHODS Reasoning Toolkit and Workflow The Euler/X software toolkit consists of a set of programming scripts, multiple logic reasoners, and a tree graph visualization system (Thau et al. 2009; Chen  ... 
arXiv:1412.1025v2 fatcat:rbsnamycznaotb22q67imgffjq

Reasoning over Taxonomic Change: Exploring Alignments for the Perelleschus Use Case

Nico M. Franz, Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Shawn Bowers, Bertram Ludäscher, Robert Guralnick
2015 PLoS ONE  
To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners.  ...  An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations.  ...  Acknowledgments The authors thank Charles O'Brien and Juliana Cardona-Duque for their taxonomic contributions to the Perelleschus use case.  ... 
doi:10.1371/journal.pone.0118247 pmid:25700173 pmcid:PMC4336294 fatcat:llv7uurf7nbqjp7fjnzkcgar7i

Two Influential Primate Classifications Logically Aligned

Nico M. Franz, Naomi M. Pier, Deeann M. Reeder, Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Shawn Bowers, Bertram Ludäscher
2016 Systematic Biology  
Using 402 RCC-5 input articulations, the reasoning process yields a single, consistent alignment and 153,111 Maximally Informative Relations that constitute a comprehensive meaning resolution map for every  ...  to infer and visualize logically consistent alignments of these input constraints.  ...  ACKNOWLEDGMENTS The authors thank three anonymous reviewers and the editors for insightful comments that have significantly improved the published version of this study.  ... 
doi:10.1093/sysbio/syw023 pmid:27009895 pmcid:PMC4911943 fatcat:o6du6yvfivatzciavfids6ngvi

A logic approach to modeling nomenclatural change [article]

Nico Franz, Chao Zhang, Joohyung Lee
2016 bioRxiv   pre-print
The results provide a foundation for further developing logic-based nomenclatural change optimization and compliance verification services, which could be applied in globally coordinated nomenclatural  ...  More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and thus may inform the design  ...  Bertram Ludäscher, Parisa Kianmajd, and Shizuo Yu provide support for the Euler/X toolkit.  ... 
doi:10.1101/058834 fatcat:r5o47lpumvfzvo7h342kkyoyie

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion [article]

Nico Franz, Lukas Musher, Joseph Brown, Shizhuo Yu, Bertram Ludaescher
2017 biorxiv/medrxiv   pre-print
Here we develop a novel solution to the conflict verbalization challenge, based on a logic representation and reasoning approach that utilizes the language of Region Connection Calculus (RCC-5) to produce  ...  Because the RCC-5 alignments fundamentally reflect the trained, logic-enabled judgments of systematic experts, future designs for such environments need to promote a culture where experts routinely assess  ...  We are grateful to Hilmar Lapp and one anonymous reviewer for extensive and constrictive criticism of the original manuscript submission. Ludäscher. Author Contributions  ... 
doi:10.1101/233973 fatcat:defl5a6jfncdta5xcesxw74qfm

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion

Nico M. Franz, Lukas J. Musher, Joseph W. Brown, Shizhuo Yu, Bertram Ludäscher, Sergei L. Kosakovsky Pond
2019 PLoS Computational Biology  
knowledge bases for reliable integration and re-use [11, 13, 22, 23, 24] .  ...  It is an extension of prior "concept taxonomy" research [14, 25, 26] , and deploys logic reasoning to align tree hierarchies based on Region Connection Calculus (RCC-5) assertions of node congruence [27  ...  We are grateful to Hilmar Lapp and one anonymous reviewer for extensive and constrictive criticism of the original manuscript submission. Ludäscher. Author Contributions  ... 
doi:10.1371/journal.pcbi.1006493 fatcat:5cvxrsc3trhm7ozcuekwvgnexy

Taxonomy for Humans or Computers? Cognitive Pragmatics for Big Data

Beckett Sterner, Nico M. Franz
2017 Biological Theory  
We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing  ...  A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data.  ...  Acknowledgements The authors are grateful to Hong Cui, Bertram Ludäscher, and Jonathan Rees for helpful feedback on this subject.  ... 
doi:10.1007/s13752-017-0259-5 fatcat:fzabyk3s3jf35ktvjjzelxju4m

Three new species of entimine weevils in Early Miocene amber from the Dominican Republic (Coleoptera: Curculionidae)

Nico Franz, Guanyang Zhang
2017 Biodiversity Data Journal  
Engel (University of Kansas) for granting access to the herein analyzed fossil specimens (along with Conrad C.  ...  Labandeira of the United States National Museum), and also for sharing an earlier, independently generated, and unpublished manuscript in which two of these were described and imaged, although without  ...  as well as integrate evolving taxonomic knowledge over time, where much of the integration work is facilitated at scale by logic-based services (Franz et al. 2016b , Franz et al. 2016c , Franz et al.  ... 
doi:10.3897/bdj.5.e10469 pmid:28325975 pmcid:PMC5345054 fatcat:pexvcnmv7nh7pkar7l4m4zfdie

Phylogenetic revision of Minyomerus Horn, 1876 sec. Jansen & Franz, 2015 (Coleoptera, Curculionidae) using taxonomic concept annotations and alignments

Michael Andrew Jansen, Nico M. Franz
2015 ZooKeys  
A cladistic analysis using 46 morphological characters of 22 terminal taxa (5/17 outgroup/ingroup) yielded a single most-parsimonious cladogram (L = 82, CI = 65, RI = 82).  ...  Articulations among these concepts and pairwise, logically consistent alignments of original and revisionary classifications are also provided, in addition to conventional nomenclatural provenance information  ...  The alignments and visualizations were produced using the Euler/X toolkit for concept Taxonomy, as detailed in Franz et al. (2015a Franz et al. ( , 2015b .  ... 
doi:10.3897/zookeys.528.6001 pmid:26692791 pmcid:PMC4668883 fatcat:f3bmawcj25hi7axqwp4u7ntr2q