Survey-based naming conventions for use in OBO Foundry ontology development

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data

Missing in translation: Maori language and oral tradition in scientific analyses of traditional ecological knowledge (TEK)

Recent conceptual shifts in ecology towards integration of humans into ecosystems requires all possible sources of ecological knowledge available (Berkes 2004, 2009 this issue). Māori traditional ecological knowledge of natural systems (TEK) can add valuable ecological data to more conventional scientific studies as the former tends to be diachronic, based on a cumulative system of understanding the environment founded on observations and experience (Gadgil et al. 1993; Berkes 2008), while the latter is frequently synchronic, with experiments that may explore causal effects in ecological patterns (Newman & Moller 2005; Moller et al. 2009a). However accessing TEK can be both difficult and time-consuming, as demonstrated by the 14-year research project Kia Mau Te Tītī Mo Ake Tonu Atu (the ‘Keep the Tītī Forever’ research project; Moller et al. 2009a). We argue that oral traditions offer a wealth of information that is frequently overlooked, in part because of a lack of knowledge of te reo Māori (the Māori language) and, further, a lack of recognition of the inextricable link between biological and cultural diversity (Maffi 2005)

Generating natural language specifications from UML class diagrams

Early phases of software development are known to be problematic, difficult to manage and errors occurring during these phases are expensive to correct. Many systems have been developed to aid the transition from informal Natural Language requirements to semistructured or formal specifications. Furthermore, consistency checking is seen by many software engineers as the solution to reduce the number of errors occurring during the software development life cycle and allow early verification and validation of software systems. However, this is confined to the models developed during analysis and design and fails to include the early Natural Language requirements. This excludes proper user involvement and creates a gap between the original requirements and the updated and modified models and implementations of the system. To improve this process, we propose a system that generates Natural Language specifications from UML class diagrams. We first investigate the variation of the input language used in naming the components of a class diagram based on the study of a large number of examples from the literature and then develop rules for removing ambiguities in the subset of Natural Language used within UML. We use WordNet,a linguistic ontology, to disambiguate the lexical structures of the UML string names and generate semantically sound sentences. Our system is developed in Java and is tested on an independent though academic case study

Relating Developers’ Concepts and Artefact Vocabulary in a Financial Software Module

Developers working on unfamiliar systems are challenged to accurately identify where and how high-level concepts are implemented in the source code. Without additional help, concept location can become a tedious, time-consuming and error-prone task. In this paper we study an industrial financial application for which we had access to the user guide, the source code, and some change requests. We compared the relative importance of the domain concepts, as understood by developers, in the user manual and in the source code. We also searched the code for the concepts occurring in change requests, to see if they could point developers to code to be modified. We varied the searches (using exact and stem matching, discarding stop-words, etc.) and present the precision and recall. We discuss the implication of our results for maintenance

Telerehabilitation for aphasia – protocol of a pragmatic, exploratory, pilot randomized controlled trial

Background The Cochrane review on the effectiveness of speech and language therapy for aphasia following stroke suggests intensity of therapy is a key predictor for outcome. Current aphasia services cannot provide intervention at the intensity observed within trial contexts because of resource limitations. Telerehabilitation could widen access to speech-language pathologists (SLPs) in geographically remote contexts and reduce the time spent on travel by the therapist and patient. The current academic literature within this field is in its infancy, with few trials of speech and language therapy (SLT) delivered by videoconference. Our pilot randomized controlled trial (RCT) will explore feasibility aspects and effectiveness of telerehabilitation for aphasia in addition to standard SLT. Method/design Our study is a pragmatic, exploratory, pilot randomized controlled trial, where participants will be randomized to a telerehabilitation group or a control group. Both groups receive standard SLT (usual care) but the telerehabilitation group receives an additional 5 h of telerehabilitation per week over 4 weeks through videoconference. This additional telerehabilitation focuses on spoken language with an emphasis on word naming. We aim to include 40 patients in each group, with inclusion criteria being aphasia any time post stroke. Participants will be assessed blindly at pre-randomization (baseline), and 4 weeks and 4 months after randomization. The primary endpoint is naming ability 3 months after the completed intervention, measured by the Norwegian Basic Aphasia Assessment (NGA) naming subtest. Secondary endpoints include other subtests of the NGA, the VAST (Verb and Sentence Test) subtest sentence production, Communicative Effectiveness Index (CETI) and the Stroke and Aphasia Quality of Life scale (SAQOL-39). Experiences of patients and SLPs with telerehabilitation are assessed using questionnaires and semi-structured interviews. Statistical between group comparisons will be in line with an intention-to-treat analysis. Discussion This pilot RCT of intensive language training by videoconference will contribute new scientific evidence to the field of aphasia telerehabilitation. Here, we describe our trial which will explore the feasibility of telerehabilitation for aphasia as an intervention, our choice of primary and secondary outcome measures and proposed analyses. Our trial will provide information for the development and delivery of future definitive RCTs. Trial registration ClinicalTrials.gov, ID: NCT02768922 . Registered on 11 May 2016. Last updated on 17 November 2017

The Relevance of Rigour for Design Practise

Design is an inverted discipline. The concept of rigour, as understood within the natural sciences, cannot be applied to Design Practice. Rigour for the natural sciences is a quality assurance mechanism ensuring that the knowledge bases of the disciplines are developed to an accepted set of standards. Design’s ontology is not like the natural sciences and as such an understanding of rigour for Design must proceed from an appropriate standpoint about the nature of Design Practice. This paper builds upon Harfield’s [1] ontological assessment of Design, Schön’s [2] [3] work on Reflective Practice and Spencer’s [4] investigation into the experience and practise of designing to develop a standpoint about Design Practice and make a proposition about the relevance of rigour for Design Practise. This paper considers how individual Reflective Practice practitioners, within the context of Design Practice, manage and ensure quality control through the application of care and thoroughness. This paper argues that rigour for Design Practise is the personal and phenomenological quality control of a design inquiry: a process of managing expanding mental chaos and restricting order

Righting Names: The Importance of Native American Philosophies of Naming for Environmental Justice

Controlling the names of places, environments, and species is one way in which settler colonial ontologies delimit the intelligibility of ecological relations, Indigenous peoples, and environmental injustices. To counter this, this article amplifies the voices of Native American scholars and foregrounds a philosophical account of Indigenous naming. First, I explore some central characteristics of Indigenous ontology, epistemic virtue, and ethical responsibility, setting the stage for how Native naming draws these elements together into a complete, robust philosophy. Then I point toward leading but contingent principles of Native naming, foregrounding how Native names emerge from and create communities by situating (rather than individuating) the beings that they name within kinship structures, including human and nonhuman agents. Finally, I outline why and how Indigenous names and the knowledges they contain are crucial for both resisting settler violence and achieving environmental justice, not only for Native Americans, but for their entire animate communities