Knowledge Organization Systems (KOS) in the Semantic Web: A Multi-Dimensional Review

Since the Simple Knowledge Organization System (SKOS) specification and its SKOS eXtension for Labels (SKOS-XL) became formal W3C recommendations in 2009 a significant number of conventional knowledge organization systems (KOS) (including thesauri, classification schemes, name authorities, and lists of codes and terms, produced before the arrival of the ontology-wave) have made their journeys to join the Semantic Web mainstream. This paper uses "LOD KOS" as an umbrella term to refer to all of the value vocabularies and lightweight ontologies within the Semantic Web framework. The paper provides an overview of what the LOD KOS movement has brought to various communities and users. These are not limited to the colonies of the value vocabulary constructors and providers, nor the catalogers and indexers who have a long history of applying the vocabularies to their products. The LOD dataset producers and LOD service providers, the information architects and interface designers, and researchers in sciences and humanities, are also direct beneficiaries of LOD KOS. The paper examines a set of the collected cases (experimental or in real applications) and aims to find the usages of LOD KOS in order to share the practices and ideas among communities and users. Through the viewpoints of a number of different user groups, the functions of LOD KOS are examined from multiple dimensions. This paper focuses on the LOD dataset producers, vocabulary producers, and researchers (as end-users of KOS).Comment: 31 pages, 12 figures, accepted paper in International Journal on Digital Librarie

Taxonomy for Humans or Computers? Cognitive Pragmatics for Big Data

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision and ambiguity that are key to designing effective solutions for generating big data about biodiversity. 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 meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services

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

abstract: Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.The article is published at http://journals.plos.org/plosone/article?id=10.1371/journal.pone.011824

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

Classifications and phylogenetic inferences of organismal groups change in light of new insights. Over time these changes can result in an imperfect tracking of taxonomic perspectives through the re-/use of Code-compliant or informal names. To mitigate these limitations, we introduce a novel approach for aligning taxonomies through the interaction of human experts and logic reasoners. We explore the performance of this approach with the Perelleschus use case of Franz & Cardona-Duque (2013). The use case includes six taxonomies published from 1936 to 2013, 54 taxonomic concepts (i.e., circumscriptions of names individuated according to their respective source publications), and 75 expert-asserted Region Connection Calculus articulations (e.g., congruence, proper inclusion, overlap, or exclusion). An Open Source reasoning toolkit is used to analyze 13 paired Perelleschus taxonomy alignments under heterogeneous constraints and interpretations. The reasoning workflow optimizes the logical consistency and expressiveness of the input and infers the set of maximally informative relations among the entailed taxonomic concepts. The latter are then used to produce merge visualizations that represent all congruent and non-congruent taxonomic elements among the aligned input trees. In this small use case with 6-53 input concepts per alignment, the information gained through the reasoning process is on average one order of magnitude greater than in the input. The approach offers scalable solutions for tracking provenance among succeeding taxonomic perspectives that may have differential biases in naming conventions, phylogenetic resolution, ingroup and outgroup sampling, or ostensive (member-referencing) versus intensional (property-referencing) concepts and articulations.Comment: 30 pages, 16 figure

Modeling and Publishing Finnish Person Names as a Linked Open Data Ontology

Online workshop.Peer reviewe

Pemanfaatan Layanan Web Keanekaragaman untuk Pengelolaan Informasi Tumbuhan Obat Indonesia

Penelitian ini mengusulkan pemanfaatan layanan web keanekaragaman hayati untuk pengelolaan informasi tumbuhan obat Indonesia. Penyedia layanan web keanekaragaman hayati yang digunakan adalah Global Biodiversity Information Facility (GBIF) dan Encyclopedia of Life (EOL). Layanan web tersebut dimanfaatkan untuk melengkapi informasi tumbuhan obat Indonesia. Penyedia layanan web keanekaragaman hayati tersebut memiliki fasilitas untuk membagikan informasi yang dimilikinya. Fasilitas yang disediakan adalah application programming interface (API). Parameter utama yang digunakan untuk mendapatkan informasi-informasi yang diinginkan adalah nama spesies tumbuhan. Hasil penelitian menunjukkan bahwa GBIF dan EOL dapat dijadikan sebagai sumber infomasi tumbuhan obat Indonesia. Integrasi antara GBIF dan EOL dapat menghasilkan informasi tumbuhan obat menjadi lebih banyak dan beragam

En busca de un horizonte común para la Biblioteca digital de arqueología náutica (NADL). Reflexiones sobre ciencia, método, teoría y plantillas

[EN] Data sharing is a fundamental process for the advancement of both natural and social sciences. Starting from the idea that computers and the internet have drastically changed the world in the last decades, this paper advocates for the creation of a space where archaeologists from around the world can share information about maritime history and exchange data with colleagues. Following the principles of open access, we argue that raw data publication is necessary and significant for the development and democratization of the discipline. This study explains the fundamental aspects of the Nautical Archaeology Digital Library (NADL) and its efforts to standardize information collection for shipwrecks and related sites, so that scholars can create a community to disseminate both raw data and complete information in the field of maritime archaeology. To achieve this, our purpose is to facilitate the development of common-ground methodology and terminology that promotes an intelligible dialogue within the global community of nautical archaeologists. This paper addresses some considerations on terminology and systematization in scientific disciplines and discusses the theoretical and methodological issues linked to the process of making a template for recording shipwrecks. Furthermore, this article analyses some of the problems related to the standardization of description processes and the necessity to create a flexible system that accounts for data diversity. The third section discusses how science is greatly enhanced by publishing information in open access platforms.Highlights:Standardization of data allows robust comparative and inter-subjective analysis of coastal and maritime projects, shipwrecks and nautical technology.Research is strongly benefited by sharing information underlying publications and raw data generated within a project in open source platforms.Digital databases such as NADL enhance cooperative research, as well as teaching and outreach strategies.[ES] Compartir información es un proceso fundamental para el desarrollo de las ciencias naturales y sociales. Partiendo de la idea de que las computadoras e Internet han cambiado drásticamente el mundo en las últimas décadas, este trabajo aboga por la creación de un espacio en el que arqueólogos de alrededor del mundo puedan compartir información sobre historia marítima e intercambiar datos con otros colegas. Siguiendo los principios del libre acceso, sostenemos que la publicación de datos en bruto es necesaria y significativa para el desarrollo y democratización de la disciplina. Este artículo explica los fundamentos de la Biblioteca Digital de Arqueología Náutica (NADL: https://nadl.tamu.edu/) y sus esfuerzos por estandarizar el registro de la información sobre naufragios y sitios relacionados, para que los investigadores puedan crear una comunidad de divulgación, tanto de datos primarios como de información completa en el campo de la arqueología marítima. Para lograrlo, nuestro propósito es contribuir al desarrollo de una metodología y terminología común que promueva un diálogo inteligible entre la comunidad global de arqueólogos náuticos. En este artículo presentamos algunas consideraciones sobre la terminología y la sistematización en las disciplinas científicas y discutimos los problemas teóricos y metodológicos vinculados al proceso de creación de una plantilla para el registro de naufragios. Además, reflexionamos sobre algunos de los problemas relacionados con la estandarización de los procesos descriptivos y la necesidad de crear un sistema flexible que refleje la diversidad de los datos. Finalmente, discutimos cómo la ciencia se ve enormemente favorecida por la publicación de información en plataformas de libre acceso.This paper is a result of a T3 Texas A&M University grant. We want to thank the NADL community for their input. This paper is based on extensive discussions among the community. We would also like to thank Prof. José Luis Lerma, the editorial team of VAR and the reviewers for their insightful comments.Borrero L., R.; Schwindingera, P.; Castelli, A.; Ciarlo, NC.; Torres, R.; Manders, M.; Castro, F.... (2021). Seeking a common ground for the Nautical Archaeology Digital Library (NADL). Reflections on science, method, theory and templates. Virtual Archaeology Review. 12(24):11-24. https://doi.org/10.4995/var.2021.14331OJS11241224Adams, J. (2001). Ships and Boats as Archaeological Source Material. World Archaeology, 32(3), 292-310. https://doi.org/10.1080/00438240120048644Bailey, G. (2007). Time perspectives, palimpsests, and the archaeology of time. Journal of Anthropological Archaeology, 26(2), 198-223. https://doi.org/10.1016/j.jaa.2006.08.002Berkeley, G. (1998). A Treatise Concerning the Principles of Human Knowledge. Oxford University Press.Campbell, R. N. (2009). What is Science? London: Cornell University Library.Castro, F., Bendig, C., Bérubé, M., Borrero, R., Budsberg, N., Dostal, C., Monteiro, A., Smith, C., Torres, R., & Yamafune, K. (2018). Recording, Publishing, and Reconstructing Wooden Shipwrecks. Journal of Maritime Archaeology, 13(1), 55-66. https://doi.org/10.1007/s11457-017-9185-8Coseriu, E. (1977). Principios de semántica structural. Madrid: Gredos.Doerr, M., Bekiari, C., Bruseker, G., Ore, C-E., Stead, & Velios, S. T. (Eds.). (2020). Definition of the CIDOC Conceptual Reference Model. Volume A. ICOM/CIDOC Documentation Standards Group and CRM Special Interest Group. Version 7.1, October 2020. Retrieved 28th October, 2020, from: http://www.cidoc-crm.org/sites/default/files/CIDOC%20CRM_v.7.0.1_%2018-10-2020.pdfEerkens, J. W. & Bettinger, R. L. (2001). Techniques for Assessing Standardization in Artifact Assemblages: Can we Scale Material Variability? American Antiquity, 66(3), 493 -504. https://doi.org/10.2307/2694247Eiteljorg, H. (2004). Computing for Archaeologists. In S. Schreibman, R. & J. Unsworth, A companion to digital humanities (pp. 20-30). Oxford: Blackwell Publishing.Frege, F. L. G. (1903). Grundgesetze der Arithmetik, Vol. 2. Jena: Verlag Hermann Pohle.Ford, B. (Ed.) (2011). The Archaeology of Maritime Landscapes. New York: Springer. https://doi.org/10.1007/978-1-4419-8210-0Furuta, R., Monroy, C., & Castro, F. (2007a). Ancient Technical Manuscripts: the Case of 17th-century Portuguese Shipbuilding Treatises. In S. Schmidt, R. Siemens, A. Kumar & J. Unsworth (Eds.), Digital Humanities 2007 Conference Proceedings (pp.67-69). Urbana-Champagne: University of Illinois.Furuta, R., Monroy, C., & Castro, F. (2007b). A Multilingual Approach to Technical Manuscripts: 16th and 17th-century Portuguese Shipbuilding Treatises. In E. Rasmussen (Chair), Proceedings of ACM/IEEE Joint Conference on Digital Libraries (pp.413-414). Vancouver, BC, Canada.Hill, R., (1994). A Dynamic Context Recording and Modeling System for Archaeology. International Journal of Nautical Archaeology, 23(2), 141-145. https://doi.org/10.1111/j.1095-9270.1994.tb00453.xHuggett, J. (2012a). Lost in information? Ways of knowing and modes of representation in e-archaeology. World Archaeology, 44(4), 538-552. https://doi.org/10.1080/00438243.2012.736274Huggett, J. (2012b). Core or periphery? Digital Humanities from an archaeological perspective. Historische Sozialforschung, 37 (3), 86-105. https://doi.org/10.12759/hsr.37.2012.3.86-105Klimovsky, G. (2005). Las desventuras del conocimiento científico. Buenos Aires: A-Z Editora.Kuhn, T. S. (1977). La tensión esencial: tradición e innovación en la investigación científica. In T. Kuhn (Ed.), La tensión esencial. Estudios selectos sobre la tradición y el cambio en el ámbito de la ciencia (pp. 248-262). México, D.F.: Fondo de Cultura Económica.Lock, G. (2003). Using computers in Archaeology: Towards virtual pasts. Routledge, New York. https://doi.org/10.1080/00665983.2003.11078213Lock, G., & Molyneaux, B. (Eds.) (2006). Confronting Scale in Archaeology. Springer, New York. https://doi.org/10.1007/0-387-32773-8Losee, J. (1981). Introducción histórica a la filosofía de la ciencia. Madrid: Alianza. Translation of the 1st Edition.Mach, E., (1959). The Analysis of Sensations. New York: Dover Publications.Manders, M., Oosting, R., & Brouwers, W. (2009). MACHU Final Report Nr. 3. Rotterdam: Educom Publishers B.V.Menéndez, E. (1999). Uso y desuso de conceptos: ¿dónde quedaron los olvidos? Alteridades, 9(17): 147-164.Mill, J. S. (2002). A System of Logic. Honolulu: University Press of the Pacific.Monroy, C., Parks, N., Furuta, R., & Castro, F. (2006). The Nautical Archaeology Digital Library. In Gonzalo et al. (Eds.), European Conference on Digital Libraries 2006 LNCS 4172 (pp. 544-547). Berlin and Heidelberg: Springer-Verlag.Monroy, C., Furuta, R., & Castro, F., (2007). Texts, Illustrations, and Physical Objects: The Case of Ancient Shipbuilding Treatises. 11th European Conference on Research and Advanced Technology for Digital Libraries ECDL, Budapest, Hungary.Monroy, C., Furuta, R., & Castro, F. (2009). Ask Not What Your Text Can do For You. Ask What You Can do For Your Text (a Dictionary's perspective). Digital Humanities. University of Maryland, MD: College Park. 344-347.Monroy, C., Furuta, R., & Castro, F. (2010). "Using an Ontology and a Multilingual Glossary for Enhancing the Nautical Archaeology Digital Library". Joint Conference on Digital Libraries JCDL, Queensland, Australia, 259-262.Muckleroy, K. (1976). The integration of historical and archaeological data concerning an historic wreck site: The 'Kennemerland'. World Archaeology, 7(3), 280-289. https://doi.org/10.1080/00438243.1976.9979641Muckleroy, K. (1978). Maritime Archaeology. Cambridge University Press.Nagel, E. (1961). The Structure of Science: Problems in the Logic of Scientific Explanation. New York, NY: Harcourt.Nieto Prieto, X. (1997). Le commerce de cabotage et de redistribution. In P. Pomey (Ed.), La navigation dans l'Antiquité (pp. 146-159). Aix-en-Provence: Edisud.Pomey, P. (2011). Defining a Ship: Architecture, Function, and Human Space. In A. Catsambis, B. Ford & D. L. Hamilton (Eds.), The Oxford Handbook of Maritime Archaeology (pp. 25-46). Oxford: Oxford University Press. https://doi.org/10.1093/oxfordhb/9780199336005.001.0001Popper, K. (1959). The Logic of Scientific Discovery. New York: Basic Books. https://doi.org/10.1063/1.3060577Sautu, R. (2005). Todo es teoría. Objetivos y métodos de investigación. Buenos Aires: Lumiere.Schiffer, M. B. (1972). Archaeological Context and Systemic Context. American Antiquity, 37(2), 156-165. https://doi.org/10.2307/278203Schiffer, M. B. (1987). Formation Processes of the Archaeological Record. Albuquerque: University of New Mexico Press.Shanks, M. & McGuire, R. H. (1996). The craft of archaeology. American Antiquity, 61(1), 75-88. https://doi.org/10.1017/S0002731600050046Steffy, J. (1990). Problems and Progress in Dating Ancient Vessels by their Construction Features. In H. Tzalas, (Ed.), Tropis II, Proceedings of the 2nd International Symposium on Ship Construction in Antiquity (pp.315-320). Athens.Steffy, J. (1995). Ancient Scantlings: The Projection and Control of Ancient Hull Shapes. In H. Tzalas, (Ed.), Tropis III, Proceedings of the 3rd International Symposium on Ship Construction in Antiquity (pp.417-428). Athens.Thomas, J. (2015). Why 'The Death of Archaeological Theory'?. In C. Hillerdal & J. Siapkas (Eds.), Debating Archaeological Empiricism: The Ambiguity of Material Evidence (pp. 11-31). London: Routledge.Tudhope, D., Binding, C., Jeffrey, S., May, K., & Vlachidis, A. (2011). A STELLAR role for knowledge organization systems in digital archaeology. Bulletin of the Association for Information Science and Technology, 43(5), 15-18. https://doi.org/10.1002/bult.2011.1720370405Torres, R. (2017). Arqueologia Histórica na Era Digital. Revista Latino-Americana de Arqueología Histórica, 11(1), 7-19. https://doi.org/10.31239/vtg.v11i1.10547Weitz, M. (1977). The Opening Mind. A Philosophical Study of Humanistic Concepts. London: University of Chicago Press.Westerdahl, C. (1992). The Maritime Landscape. International Journal of Nautical Archaeology, 21(1), 5-14. https://doi.org/10.1111/j.1095-9270.1992.tb00336.xWittgenstein, L. (2006). Sobre la certeza. Barcelona: Editorial Gedisa, S.A.Vidal Torres Caballero, J. (1994). Reflexiones sobre la terminología lingüístico-gramatical. Cauce: Revista de filología y su didáctica, 17, 83-106.Zeltwanger, H. (2015). A short history of standardization and CAN. Control Engineering, Digital Edition, February 16. Retrieved July 29th, 2020, from: https://www.controleng.com/Zubrow, E. (2006). Digital Archaeology. A historical context. In T. Evans and P. Daly (Eds.), Digital Archaeology. Bridging method and theory (pp. 8-26). London: Routledge

A Semantic Framework for Declarative and Procedural Knowledge

In any scientic domain, the full set of data and programs has reached an-ome status, i.e. it has grown massively. The original article on the Semantic Web describes the evolution of a Web of actionable information, i.e.\ud information derived from data through a semantic theory for interpreting the symbols. In a Semantic Web, methodologies are studied for describing, managing and analyzing both resources (domain knowledge) and applications (operational knowledge) - without any restriction on what and where they\ud are respectively suitable and available in the Web - as well as for realizing automatic and semantic-driven work\ud ows of Web applications elaborating Web resources.\ud This thesis attempts to provide a synthesis among Semantic Web technologies, Ontology Research, Knowledge and Work\ud ow Management. Such a synthesis is represented by Resourceome, a Web-based framework consisting of two components which strictly interact with each other: an ontology-based and domain-independent knowledge manager system (Resourceome KMS) - relying on a knowledge model where resource and operational knowledge are contextualized in any domain - and a semantic-driven work ow editor, manager and agent-based execution system (Resourceome WMS).\ud The Resourceome KMS and the Resourceome WMS are exploited in order to realize semantic-driven formulations of work\ud ows, where activities are semantically linked to any involved resource. In the whole, combining the use of domain ontologies and work ow techniques, Resourceome provides a exible domain and operational knowledge organization, a powerful engine for semantic-driven work\ud ow composition, and a distributed, automatic and\ud transparent environment for work ow execution