Biological taxonomy and ontology development: scope and limitations

The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. We briefly such how such integration may proceed based on an initial expert alignment of concept relationship and subsequent use of first-order logic algorithms to maximize consistency, reveal implied relationships, and ultimately merge taxonomies.
 In light of the aforementioned obstacles, we suggest that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies. We furthermore suggest that the prospects of developing successful ontologies for taxonomy will largely depend on the ability of the taxonomic expert community to present their phylogenies and classifications in a way that is more compatible with ontological reasoning than concurrent practice. Minimally, this means (1) adopting rigorous standards for linking new core taxonomies to relevant peripheral taxonomies through comprehensive alignments so that their ontological/taxonomic connections are transparent; (2) using lineage-specific ontological standards for phenotype-based accounts of taxa while taking into account the phylogenetic contextuality of phenotypic descriptors; (3) presenting all nomenclatural and taxonomic novelties in an explicit, ontology-compatible format, including intensional and ostensive definitions; and (4) offering comprehensive intensional/ostensive alignments to entities in relevant preceding taxonomies

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

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

Taxonomy alignment is a way to integrate two or more taxonomies. Semantic interoperability between datasets, information systems, and knowledge bases is facilitated by combining the different input taxonomies into merged taxonomies that reconcile apparent differences or conflicts. We show how alignment problems can be solved with a logic-based region connection calculus (RCC-5) approach, using five base relations to compare concepts: congruence, inclusion, inverse inclusion, overlap, and disjointness. To illustrate this method, we use different “geo-taxonomies”, which organize the United States into several, apparently conflicting, geospatial hierarchies. 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. Using these case studies, we show how this logic-based approach can reconcile conflicts between 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. In this paper, we demonstrate the feasibility and broad applicability of this approach to other domains and alignment problems in support of semantic interoperability.DEB- 1155984DBI-1342595DBI-1643002Ope

BIOLOGICAL TAXONOMY AND ONTOLOGY DEVELOPMENT: SCOPE AND LIMITATIONS

The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are critically reviewed. The common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy is contrasted with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. It is suggested that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies

Kiel Declarative Programming Days 2013

This report contains the papers presented at the Kiel Declarative Programming Days 2013, held in Kiel (Germany) during September 11-13, 2013. The Kiel Declarative Programming Days 2013 unified the following events: * 20th International Conference on Applications of Declarative Programming and Knowledge Management (INAP 2013) * 22nd International Workshop on Functional and (Constraint) Logic Programming (WFLP 2013) * 27th Workshop on Logic Programming (WLP 2013) All these events are centered around declarative programming, an advanced paradigm for the modeling and solving of complex problems. These specification and implementation methods attracted increasing attention over the last decades, e.g., in the domains of databases and natural language processing, for modeling and processing combinatorial problems, and for high-level programming of complex, in particular, knowledge-based systems

Building high-quality merged ontologies from multiple sources with requirements customization

Ontologies are the prime way of organizing data in the Semantic Web. Often, it is necessary to combine several, independently developed ontologies to obtain a knowledge graph fully representing a domain of interest. Existing approaches scale rather poorly to the merging of multiple ontologies due to using a binary merge strategy. Thus, we aim to investigate the extent to which the n-ary strategy can solve the scalability problem. This thesis contributes to the following important aspects: 1. Our n-ary merge strategy takes as input a set of source ontologies and their mappings and generates a merged ontology. For efficient processing, rather than successively merging complete ontologies pairwise, we group related concepts across ontologies into partitions and merge first within and then across those partitions. 2. We take a step towards parameterizable merge methods. We have identified a set of Generic Merge Requirements (GMRs) that merged ontologies might be expected to meet. We have investigated and developed compatibilities of the GMRs by a graph-based method. 3. When multiple ontologies are merged, inconsistencies can occur due to different world views encoded in the source ontologies To this end, we propose a novel Subjective Logic-based method to handling the inconsistency occurring while merging ontologies. We apply this logic to rank and estimate the trustworthiness of conflicting axioms that cause inconsistencies within a merged ontology. 4. To assess the quality of the merged ontologies systematically, we provide a comprehensive set of criteria in an evaluation framework. The proposed criteria cover a variety of characteristics of each individual aspect of the merged ontology in structural, functional, and usability dimensions. 5. The final contribution of this research is the development of the CoMerger tool that implements all aforementioned aspects accessible via a unified interface

Merging Taxonomies under RCC-5 Algebraic Articulations ∗

Taxonomies are widely used to classify information, and multiple (possibly competing) taxonomies often exist for the same domain. Given a set of correspondences between two taxonomies, it is often necessary to “merge ” the taxonomies, thereby creating a unified taxonomy (e.g., that can then be used by data integration and discovery applications). We present an algorithm for merging taxonomies that have been related using articulations given as RCC-5 constraints. Two taxa N and M can be related using (disjunctions of) the five base relations in RCC-5: N ≡ M; N � M; N �; N ⊕ M (partial overlap of N and M); and N! M (disjointness: N ∩ M = ∅). RCC-5 is increasingly being adopted by scientists to specify mappings between large species taxonomies. We discuss the properties of the proposed merge algorithm and evaluate our approach using real-world biological taxonomies. Categories and Subject Descriptor

Soft Robotics: Design for Simplicity, Performance, and Robustness of Robots for Interaction with Humans.

This thesis deals with the design possibilities concerning the next generation of advanced Robots. Aim of the work is to study, analyse and realise artificial systems that are essentially simple, performing and robust and can live and coexist with humans. The main design guideline followed in doing so is the Soft Robotics Approach, that implies the design of systems with intrinsic mechanical compliance in their architecture. The first part of the thesis addresses design of new soft robotics actuators, or robotic muscles. At the beginning are provided information about what a robotic muscle is and what is needed to realise it. A possible classification of these systems is analysed and some criteria useful for their comparison are explained. After, a set of functional specifications and parameters is identified and defined, to characterise a specific subset of this kind of actuators, called Variable Stiffness Actuators. The selected parameters converge in a data-sheet that easily defines performance and abilities of the robotic system. A complete strategy for the design and realisation of this kind of system is provided, which takes into account their me- chanical morphology and architecture. As consequence of this, some new actuators are developed, validated and employed in the execution of complex experimental tasks. In particular the actuator VSA-Cube and its add-on, a Variable Damper, are developed as the main com- ponents of a robotics low-cost platform, called VSA-CubeBot, that v can be used as an exploratory platform for multi degrees of freedom experiments. Experimental validations and mathematical models of the system employed in multi degrees of freedom tasks (bimanual as- sembly and drawing on an uneven surface), are reported. The second part of the thesis is about the design of multi fingered hands for robots. In this part of the work the Pisa-IIT SoftHand is introduced. It is a novel robot hand prototype designed with the purpose of being as easily usable, robust and simple as an industrial gripper, while exhibiting a level of grasping versatility and an aspect comparable to that of the human hand. In the thesis the main theo- retical tool used to enable such simplification, i.e. the neuroscience– based notion of soft synergies, are briefly reviewed. The approach proposed rests on ideas coming from underactuated hand design. A synthesis method to realize a desired set of soft synergies through the principled design of adaptive underactuated mechanisms, which is called the method of adaptive synergies, is discussed. This ap- proach leads to the design of hands accommodating in principle an arbitrary number of soft synergies, as demonstrated in grasping and manipulation simulations and experiments with a prototype. As a particular instance of application of the method of adaptive syner- gies, the Pisa–IIT SoftHand is then described in detail. The design and implementation of the prototype hand are shown and its effec- tiveness demonstrated through grasping experiments. Finally, control of the Pisa/IIT Hand is considered. Few different control strategies are adopted, including an experimental setup with the use of surface Electromyographic signals

Minimising mathematical anxiety in teaching mathematics and assessing student’s work

This paper builds up a theoretical perspective and supports a possibility of creating a special assessment environment for students, where mathematical knowledge and understanding can be assessed with a reduced number of external psychological factors that may affect such assessment. A concept of a zone with minimal effect of anxiety is introduced and described. Students’ successful work on extending the zone by means of a carefully selected chain of questions, where some questions only are part of a real assessment, allows students to reconsider their attitudes towards mathematics and assist teachers to identify some students’ main learning difficulties as of psychological character. Further suggestions about developing and investigating special assessment environments are outlined and discussed