Selected papers from the 15th Annual Bio-Ontologies special interest group meeting

© 2013 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes

Evolution of statistical analysis in empirical software engineering research: Current state and steps forward

Software engineering research is evolving and papers are increasingly based on empirical data from a multitude of sources, using statistical tests to determine if and to what degree empirical evidence supports their hypotheses. To investigate the practices and trends of statistical analysis in empirical software engineering (ESE), this paper presents a review of a large pool of papers from top-ranked software engineering journals. First, we manually reviewed 161 papers and in the second phase of our method, we conducted a more extensive semi-automatic classification of papers spanning the years 2001--2015 and 5,196 papers. Results from both review steps was used to: i) identify and analyze the predominant practices in ESE (e.g., using t-test or ANOVA), as well as relevant trends in usage of specific statistical methods (e.g., nonparametric tests and effect size measures) and, ii) develop a conceptual model for a statistical analysis workflow with suggestions on how to apply different statistical methods as well as guidelines to avoid pitfalls. Lastly, we confirm existing claims that current ESE practices lack a standard to report practical significance of results. We illustrate how practical significance can be discussed in terms of both the statistical analysis and in the practitioner's context.Comment: journal submission, 34 pages, 8 figure

Desiderata for an Every Citizen Interface to the National Information Infrastructure: Challenges for NLP

In this paper, I provide desiderata for an interface that would enable ordinary people to properly access the capabilities of the NII. I identify some of the technologies that will be needed to achieve these desiderata, and discuss current and future research directions that could lead to the development of such technologies. In particular, I focus on the ways in which theory and techniques from natural language processing could contribute to future interfaces to the NII. Introduction The evolving national information infrastructure (NII) has made available a vast array of on-line services and networked information resources in a variety of forms (text, speech, graphics, images, video). At the same time, advances in computing and telecommunications technology have made it possible for an increasing number of households to own (or lease or use) powerful personal computers that are connected to this resource. Accompanying this progress is the expectation that people will be able to more..

TectoMT – a deep-­linguistic core of the combined Chimera MT system

Chimera is a machine translation system that combines the TectoMT deep-linguistic core with phrase-based MT system Moses. For English–Czech pair it also uses the Depfix post-correction system. All the components run on Unix/Linux platform and are open source (available from Perl repository CPAN and the LINDAT/CLARIN repository). The main website is https://ufal.mff.cuni.cz/tectomt. The development is currently supported by the QTLeap 7th FP project (http://qtleap.eu)

Machine learning computational tools to assist the performance of systematic reviews : A mapping review

Within evidence-based practice (EBP), systematic reviews (SR) are considered the highest level of evidence in that they summarize the best available research and describe the progress in a determined field. Due its methodology, SR require significant time and resources to be performed; they also require repetitive steps that may introduce biases and human errors. Machine learning (ML) algorithms therefore present a promising alternative and a potential game changer to speed up and automate the SR process. This review aims to map the current availability of computational tools that use ML techniques to assist in the performance of SR, and to support authors in the selection of the right software for the performance of evidence synthesis. The mapping review was based on comprehensive searches in electronic databases and software repositories to obtain relevant literature and records, followed by screening for eligibility based on titles, abstracts, and full text by two reviewers. The data extraction consisted of listing and extracting the name and basic characteristics of the included tools, for example a tool's applicability to the various SR stages, pricing options, open-source availability, and type of software. These tools were classified and graphically represented to facilitate the description of our findings. A total of 9653 studies and 585 records were obtained from the structured searches performed on selected bibliometric databases and software repositories respectively. After screening, a total of 119 descriptions from publications and records allowed us to identify 63 tools that assist the SR process using ML techniques. This review provides a high-quality map of currently available ML software to assist the performance of SR. ML algorithms are arguably one of the best techniques at present for the automation of SR. The most promising tools were easily accessible and included a high number of user-friendly features permitting the automation of SR and other kinds of evidence synthesis reviews. The online version contains supplementary material available at 10.1186/s12874-022-01805-4