scholarly journals Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies

2018 ◽  
Author(s):  
Sarah M. Alghamdi ◽  
Beth A. Sundberg ◽  
John P. Sundberg ◽  
Paul N. Schofield ◽  
Robert Hoehndorf

ABSTRACTData are increasingly annotated with multiple ontologies to capture rich information about the features of the subject under investigation. Analysis may be performed over each ontology separately, but, recently, there has been a move to combine multiple ontologies to provide more powerful analytical possibilities. However, it is often not clear how to combine ontologies or how to assess or evaluate the potential design patterns available. Here we use a large and well-characterized dataset of anatomic pathology descriptions from a major study of aging mice. We show how different design patterns based on the MPATH and MA ontologies provide orthogonal axes of analysis, and perform differently in over-representation and semantic similarity applications. We discuss how such a data-driven approach might be used generally to generate and evaluate ontology design patterns.

Author(s):  
Julia Chen ◽  
Dennis Foung

This chapter explores the possibility of adopting a data-driven approach to connecting teacher-made assessments with course learning outcomes. The authors begin by describing several key concepts, such as outcome-based education, curriculum alignment, and teacher-made assessments. Then, the context of the research site and the subject in question are described and the use of structural equation modeling (SEM) in this curriculum alignment study is explained. After that, the results of these SEM analyses are presented, and the various models derived from the analyses are discussed. In particular, the authors highlight how a data-driven curriculum model can benefit from input by curriculum leaders and how SEM provides insights into course development and enhancement. The chapter concludes with recommendations for curriculum leaders and front-line teachers to improve the quality of teacher-made assessments.


2019 ◽  
Vol 11 (9) ◽  
pp. 2717
Author(s):  
Fátima L. Vieira ◽  
Paulo A. Vieira ◽  
Denis A. Coelho

This paper proposes a data-driven approach to develop a taxonomy in a data structure on list for triple bottom line (TBL) metrics. The approach is built from the authors reflection on the subject and review of the literature about TBL. The envisaged taxonomy framework grid to be developed through this approach will enable existing metrics to be classified, grouped, and standardized, as well as detect the need for further metrics development in uncovered domains and applications. The approach reported aims at developing a taxonomy structure that can be seen as a bi-dimensional table focusing on feature interrogations and characterizing answers, which will be the basis on which the taxonomy can then be developed. The interrogations column is designed as the stack of the TBL metrics features: What type of metric is it (qualitative, quantitative, or hybrid)? What is the level of complexity of the problems where it is used? What standards does it follow? How is the measurement made, and what are the techniques that it uses? In what kinds of problems, subjects, and domains is the metric used? How is the metric validated? What is the method used in its calculation? The column of characterizing answers results from a categorization of the range of types of answers to the feature interrogations. The approach reported in this paper is based on a screening tool that searches and analyzes information both within abstracts and full-text journal papers. The vision for this future taxonomy is that it will enable locating for any specific context, discern what TBL metrics are used in that context or similar contexts, or whether there is a lack of developed metrics. This meta knowledge will enable a conscious decision to be made between creating a new metric or using one of those that already exists. In this latter case, it would also make it possible to choose, among several metrics, the one that is most appropriate to the context at hand. In addition, this future framework will ease new future literature revisions, when these are viewed as updates of this envisaged taxonomy. This would allow creating a dynamic taxonomy for TBL metrics. This paper presents a computational approach to develop such taxonomy, and reports on the initial steps taken in that direction, by creating a taxonomy framework grid with a computational approach.


2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sarah M. Alghamdi ◽  
Beth A. Sundberg ◽  
John P. Sundberg ◽  
Paul N. Schofield ◽  
Robert Hoehndorf

ReCALL ◽  
1997 ◽  
Vol 9 (2) ◽  
pp. 8-16 ◽  
Author(s):  
Tony McEnery ◽  
Andrew Wilson ◽  
Paul Barker

In this paper we consider how corpora may be of use in the teaching of grammar of the pre-tertiary level. Corpora are becoming well established in teaching in Universities. Corpora also have a role to play in secondary education, in that they can help decide how and what to teach, as well as changing the way in which puplis learn and providing the possibility of open-ended machine-aided tuition. Corpora also seem to provide what UK goverment sponsored reports on teaching grammar have called for – a data-driven approach to the subject.


Semantic Web ◽  
2021 ◽  
pp. 1-19
Author(s):  
Edna Ruckhaus ◽  
Adolfo Anton-Bravo ◽  
Mario Scrocca ◽  
Oscar Corcho

We present an ontology that describes the domain of Public Transport by bus, which is common in cities around the world. This ontology is aligned to Transmodel, a reference model which is available as a UML specification and which was developed to foster interoperability of data about transport systems across Europe. The alignment with this non-ontological resource required the adaptation of the Linked Open Terms (LOT) methodology, which has been used by our team as the methodological framework for the development of many ontologies used for the publication of open city data. The ontology is structured into three main modules: (1) agencies, operators and the lines that they manage, (2) lines, routes, stops and journey patterns, and (3) planned vehicle journeys with their timetables and service calendars. Besides reusing Transmodel concepts, the ontology also reuses common ontology design patterns from GeoSPARQL and the SOSA ontology. As part of the LOT data-driven validation stage, RDF data has been generated taking as input the GTFS feeds (General Transit Feed Specification) provided by the Madrid public bus transport provider (EMT). Mapping rules from structured data sources to RDF were developed using the RDF Mapping Language (RML) to generate RDF data, and queries corresponding to competency questions were tested.


2020 ◽  
Vol 7 ◽  
pp. 237428952095978
Author(s):  
John H. Sinard

The recent COVID pandemic has had a major effect on anatomic pathology specimen volumes across the country. The effect of this pandemic on a subspecialty academic practice is presented. We used a data-driven approach to monitor the changing workloads in a granular fashion and dynamically adjust the scheduling of faculty and histology staff accordingly to minimize the number of people present on-site. At the peak of the pandemic locally, the main hospital in our health system had 450 COVID-positive inpatients. The surgical pathology specimen volume dropped to 13% of the pre-pandemic levels, and this occurred about 2 weeks before the peak of the inpatient census; cytology specimens (the majority of which are outreach gynecological) dropped to approximately 5% of the pre-pandemic volume, 4 weeks before the peak inpatient census. All of the surgical subspecialty services showed a significant decrease in volume, with hematopathology being the least affected (dropped to 30% of the pre-pandemic level). The genitourinary surgical subspecialty service (predominantly prostate and bladder biopsies) was the most affected (dropped to 1% of the pre-pandemic level) but was fastest to return as clinical operations began to return to normal. The only specimen type which showed a significant increase in turnaround time during the pandemic was our gynecologic cytology specimens and that occurred as the specimen volume returned. This was due to stay-at-home directives for the cytotechnologists and the fact that some of them were retasked to participate in our SARS-CoV-2 testing.


2019 ◽  
Vol 8 (9) ◽  
pp. 385 ◽  
Author(s):  
Emmanuel Papadakis ◽  
Song Gao ◽  
George Baryannis

The problem of discovering regions that support particular functionalities in an urban setting has been approached in literature using two general methodologies: top-down, encoding expert knowledge on urban planning and design and discovering regions that conform to that knowledge; and bottom-up, using data to train machine learning models, which can discover similar regions. Both methodologies face limitations, with knowledge-based approaches being criticized for scalability and transferability issues and data-driven approaches for lacking interpretability and depending heavily on data quality. To mitigate these disadvantages, we propose a novel framework that fuses a knowledge-based approach using design patterns and a data-driven approach using latent Dirichlet allocation (LDA) topic modeling in three different ways: Functional regions discovered using either approach are evaluated against each other to identify cases of significant agreement or disagreement; knowledge from patterns is used to adjust topic probabilities in the learning model; and topic probabilities are used to adjust pattern-based results. The proposed methodologies are demonstrated through the use case of identifying shopping-related regions in the Los Angeles metropolitan area. Results show that the combination of pattern-based discovery and topic modeling extraction helps uncover discrepancies between the two approaches and smooth inaccuracies caused by the limitations of each approach.


Linguistics ◽  
2016 ◽  
Vol 54 (1) ◽  
Author(s):  
Florent Perek

AbstractThis paper investigates syntactic productivity in diachrony with a data-driven approach. Previous research indicates that syntactic productivity (the property of grammatical constructions to attract new lexical fillers) is largely driven by semantics, which calls for an operationalization of lexical meaning in the context of empirical studies. It is suggested that distributional semantics can fulfill this role by providing a measure of semantic similarity between words that is derived from lexical co-occurrences in large text corpora. On the basis of a case study of the construction “V


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