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Provenance for Explaining Taxonomy Alignments [chapter]

Mingmin Chen, Shizhuo Yu, Parisa Kianmajd, Nico Franz, Shawn Bowers, Bertram Ludäscher
2015 Lecture Notes in Computer Science  
We study provenance in the application of Euler/X [1], a logic-based toolkit for aligning multiple biological taxonomies.  ...  We propose a combination of approaches to explain both, logical inconsistencies in the input alignment, and the derivation of new facts in the output taxonomies. Taxonomy Alignment.  ...  Fig. 4 . 4 Provenance of f c (depicted as f < c). Lightly colored 3D-boxes are input facts (taxonomies and input alignment). Inferred relations are shown as darker boxes (Color figure online).  ... 
doi:10.1007/978-3-319-16462-5_27 fatcat:qofhwt37tvenjcns6iiyw4vkwi

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
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 introduce Euler/X, a toolkit for logic-based taxonomy integration.  ...  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

Automated assembly of a reference taxonomy for phylogenetic data synthesis

Jonathan Rees, Karen Cranston
2017 Biodiversity Data Journal  
Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity  ...  Citation: Rees J, Cranston K (2017) Automated assembly of a reference taxonomy for phylogenetic data synthesis. Biodiversity Data Journal 5: e12581. https://doi.  ...  questions about source taxonomies; Cody Hinchliff for writing an early version of the assembly code and establishing the general approach to taxonomy combination; and Yan Wong and other users of the Open  ... 
doi:10.3897/bdj.5.e12581 pmid:28765728 pmcid:PMC5515096 fatcat:5tj4fg2gg5bjldmgkyg5zmxqcu

Automated assembly of a reference taxonomy for phylogenetic data synthesis [article]

Jonathan Rees, Karen Ann Cranston
2017 biorxiv/medrxiv   pre-print
Here we describe a system for reproducibly combining several source taxonomies into a synthetic taxonomy, and we discuss the challenges of taxonomic and nomenclatural synthesis for downstream biodiversity  ...  Taxonomy and nomenclature data are critical for any project that synthesizes biodiversity data, as most biodiversity data sets use taxonomic names to identify taxa.  ...  questions about source taxonomies; Cody Hinchliff for writing an early version of the assembly code and establishing the general approach to taxonomy combination; and Yan Wong and other users of the Open  ... 
doi:10.1101/116418 fatcat:334eyrpsczfkxgvi52uqwtrc4a

Foundations of Explainable Knowledge-Enabled Systems [article]

Shruthi Chari, Daniel M. Gruen, Oshani Seneviratne, Deborah L. McGuinness
2020 arXiv   pre-print
Explainability has been an important goal since the early days of Artificial Intelligence. Several approaches for producing explanations have been developed.  ...  With the proliferation of AI-enabled systems in sometimes critical settings, there is a need for them to be explainable to end-users and decision-makers.  ...  Their hope was for future methods to use the taxonomy as a reference to build explainable models.  ... 
arXiv:2003.07520v1 fatcat:pz54e4ag35hf3osr7dfbmhb4ze

Taxonomy - for Computers [article]

Nico Franz, Beckett Sterner
2015 bioRxiv   pre-print
If we expect our virtual comparative information environments to provide logically enabled taxonomic concept provenance services, then we must improve the syntax and semantics of human taxonomy making  ...  - for computers.  ...  Acknowledgments The authors are grateful to Hong Cui, Bertram Ludäscher, and Jonathan Rees for helpful feedback on this subject.  ... 
doi:10.1101/022145 fatcat:tnzu7osblnbv5ovx4iyqvfmzse

Unsupervised cross-lingual matching of product classifications [article]

Denis Gordeev, Alexey Rey, Dmitry Shagarov
2018 arXiv   pre-print
Our work also investigates limitations of unsupervised vector alignment and we also suggest two other techniques for aligning product classifications based on their descriptions: using hierarchical information  ...  Unsupervised cross-lingual embeddings mapping has provided a unique tool for completely unsupervised translation even for languages with different scripts.  ...  However, it seems unlikely that it is possible to directly align categories vectors for national taxonomies because their domains are too different.  ... 
arXiv:1809.07234v1 fatcat:damki7den5dwzgk5wnvzkzsmlm

Reflections on Provenance Ontology Encodings [chapter]

Li Ding, Jie Bao, James R. Michaelis, Jun Zhao, Deborah L. McGuinness
2010 Lecture Notes in Computer Science  
We expect the outcome of this work to provide guidance for understanding, aligning and evolving existing provenance ontologies.  ...  This paper analyzes a selection of popular Semantic Web provenance ontologies such as the Open Provenance Model (OPM), Dublin Core (DC) and the Proof Markup Language (PML).  ...  It consists of three modules: (i) the core module that defines basic concepts for tracking data creation and data access, (ii) a taxonomy specific to Web information transfer and (iii) a taxonomy specific  ... 
doi:10.1007/978-3-642-17819-1_22 fatcat:6larr7iaurffxn5h7b3urwxn5a

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.  ...  For example, we align T CEN , a taxonomy derived from the Census Bureau's regions map, with T NDC , from the National Diversity Council (NDC), and with T TZ , a taxonomy capturing the U.S. time zones.  ...  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

Unsupervised Cross-lingual Matching of Product Classifications

Denis Gordeev, Alexey Rey, Dmitry Shagarov
2018 Zenodo  
Our work also investigates limitations of unsupervised vector alignment and we also suggest two other techniques for aligning product classifications based on their descriptions: using hierarchical information  ...  Unsupervised cross-lingual embeddings mapping has provided a unique tool for completely unsupervised translation even for languages with different scripts.  ...  However, it seems unlikely that it is possible to directly align categories vectors for national taxonomies because their domains are too different.  ... 
doi:10.5281/zenodo.4553685 fatcat:odgsdgntxbcgvdy6jkgiel3264

Cacao, Cocao, or Cocoa?: Reconciliation of Taxonomic Names in Biodiversity Heritage Library [chapter]

Yi-Yun Cheng, Khanh Linh Hoang, Bertram Ludäscher
2020 Knowledge Organization at the Interface  
We demonstrate this by using a logic-based, taxonomy alignment approach to match variations of species and subspecies names of Theobroma cacao from four major biodiversity sources: the Encyclopedia of  ...  Through the use case of Theobroma cacao, commonly known as chocolate plants, this research aims at presenting a framework to reconcile species names in BHL by merging external taxonomies.  ...  Acknowledgement This project is supported by the Center for Informatics Research in Science and Scholarship (CIRSS) at iSchool, University of Illinois at Urbana-Champaign. The first author  ... 
doi:10.5771/9783956507762-88 fatcat:exzpq3fupjhbzolpjzyujm6oga

Reasoning about taxonomies and articulations

David Thau
2008 Proceedings of the 2008 EDBT Ph.D. workshop on - Ph.D. '08  
Critical to this research is the development of a framework for testing logics and support for the development of taxonomies and articulations.  ...  on a given set of taxonomies and articulations and provides a framework for testing assumptions about underspecified taxonomies.  ...  A set of taxonomies and articulations between them is called an alignment. The process of discovering an alignment given a set of taxonomies is called the taxonomy alignment problem.  ... 
doi:10.1145/1387150.1387153 fatcat:irbvmxfqh5fhxbx4miv7tsiwn4

Introducing W.A.T.E.R.S.: a Workflow for the Alignment, Taxonomy, and Ecology of Ribosomal Sequences

Amber L Hartman, Sean Riddle, Timothy McPhillips, Bertram Ludäscher, Jonathan A Eisen
2010 BMC Bioinformatics  
The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools.  ...  One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system.  ...  Acknowledgements We are grateful to Srijak Bhatnagar and Jenna Morgan for assistance with preliminary testing of WATERS.  ... 
doi:10.1186/1471-2105-11-317 pmid:20540779 pmcid:PMC2898799 fatcat:gklvji3cnzg5xjdic2eglyvalu

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

Jennifer Fouquier, Jai Ram Rideout, Evan Bolyen, John Chase, Arron Shiffer, Daniel McDonald, Rob Knight, J Gregory Caporaso, Scott T. Kelley
2016 Microbiome  
distant fungi because the sequences are hard to align accurately.  ...  Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic  ...  Author details 1 Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA. 2 Center for Microbial Genetics and Genomics, Northern Arizona University,  ... 
doi:10.1186/s40168-016-0153-6 pmid:26905735 pmcid:PMC4765138 fatcat:ir4hti56uneavn2wlxifb6h52y

Directions for Explainable Knowledge-Enabled Systems [article]

Shruthi Chari, Daniel M. Gruen, Oshani Seneviratne, Deborah L. McGuinness
2020 arXiv   pre-print
Recently, researchers have been investigating and tackling explainability with a user-centric focus, looking for explanations to consider trustworthiness, comprehensibility, explicit provenance, and context-awareness  ...  Interest in the field of Explainable Artificial Intelligence has been growing for decades and has accelerated recently.  ...  AI model provenance.  ... 
arXiv:2003.07523v1 fatcat:mnsqhmeq6nfttirizkt5mipvwy
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