scholarly journals Best Practices in Manual Annotation with the Gene Ontology

Author(s):  
Sylvain Poux ◽  
Pascale Gaudet
Database ◽  
2013 ◽  
Vol 2013 (0) ◽  
pp. bat054-bat054 ◽  
Author(s):  
R. Balakrishnan ◽  
M. A. Harris ◽  
R. Huntley ◽  
K. Van Auken ◽  
J. M. Cherry

2018 ◽  
Vol 25 (2) ◽  
pp. 229-258 ◽  
Author(s):  
Matteo Fuoli

Abstract Despite a growing awareness of methodological issues, the literature on appraisal has not so far provided adequate answers to some of the key challenges involved in reliably identifying and classifying evaluative language expressions. This article presents a stepwise method for the manual annotation of appraisal in text that is designed to optimize reliability, replicability and transparency. The procedure consists of seven steps, from the creation of a context-specific annotation manual to the statistical analysis of the quantitative data derived from the manually-performed annotations. By presenting this method, the article pursues the twofold purpose of (i) providing a practical tool that can facilitate more reliable, replicable and transparent analyses, and (ii) fostering a discussion of the best practices that should be observed when manually annotating appraisal.


2014 ◽  
Vol 24 (1) ◽  
pp. 38
Author(s):  
Shuheng Wu ◽  
Besiki Stvilia

The Gene Ontology (GO) is one of the most widely used and successful bio-ontologies in biomedicine and molecular biology. What is special about GO as a knowledge organization (KO) system is its collaborative development and maintenance practices, involving diverse communities in collectively developing the Ontology and controlling its quality. Guided by Activity Theory and a theoretical Information Quality Assessment Framework, this study conducts qualitative content analysis of GO’s curation discussions. The study found that GO has developed various tools and mechanisms to gain expert feedback and engage various communities in developing and maintaining the Ontology in an efficient and less expensive way. The findings of this study can inform KO system designers, curators, and ontologists in establishing functional requirements and quality assurance infrastructure for bioontologies and formulating best practices for ontology development.


2020 ◽  
Vol 20 (S10) ◽  
Author(s):  
Francisco Abad-Navarro ◽  
Manuel Quesada-Martínez ◽  
Astrid Duque-Ramos ◽  
Jesualdo Tomás Fernández-Breis

Abstract Background The increasing adoption of ontologies in biomedical research and the growing number of ontologies available have made it necessary to assure the quality of these resources. Most of the well-established ontologies, such as the Gene Ontology or SNOMED CT, have their own quality assurance processes. These have demonstrated their usefulness for the maintenance of the resources but are unable to detect all of the modelling flaws in the ontologies. Consequently, the development of efficient and effective quality assurance methods is needed. Methods Here, we propose a series of quantitative metrics based on the processing of the lexical regularities existing in the content of the ontology, to analyse readability and structural accuracy. The readability metrics account for the ratio of labels, descriptions, and synonyms associated with the ontology entities. The structural accuracy metrics evaluate how two ontology modelling best practices are followed: (1) lexically suggest locally define (LSLD), that is, if what is expressed in natural language for humans is available as logical axioms for machines; and (2) systematic naming, which accounts for the amount of label content of the classes in a given taxonomy shared. Results We applied the metrics to different versions of SNOMED CT. Both readability and structural accuracy metrics remained stable in time but could capture some changes in the modelling decisions in SNOMED CT. The value of the LSLD metric increased from 0.27 to 0.31, and the value of the systematic naming metric was around 0.17. We analysed the readability and structural accuracy in the SNOMED CT July 2019 release. The results showed that the fulfilment of the structural accuracy criteria varied among the SNOMED CT hierarchies. The value of the metrics for the hierarchies was in the range of 0–0.92 (LSLD) and 0.08–1 (systematic naming). We also identified the cases that did not meet the best practices. Conclusions We generated useful information about the engineering of the ontology, making the following contributions: (1) a set of readability metrics, (2) the use of lexical regularities to define structural accuracy metrics, and (3) the generation of quality assurance information for SNOMED CT.


Author(s):  
Kristen Izaryk ◽  
Robin Edge ◽  
Dawn Lechwar

Purpose The purpose of this article is to explore and describe the approaches and specific assessment tools that speech-language pathologists are currently using to assess social communication disorders (SCDs) in children, in relation to current best practices. Method Ninety-four speech-language pathologists completed an online survey asking them to identify which of the following approaches they use to assess children with SCD: parent/teacher report, naturalistic observation, formal assessment, language sample analysis, interviews, semistructured tasks, and peer/self-report. Participants were also asked to identify specific assessment tools they use within each approach. Results Participants most commonly assess SCDs by combining interviews, naturalistic observation, language sampling, parent/teacher report, and formal assessment. Semistructured tasks and peer/self-report tools were less frequently utilized. Several established parent/teacher report and formal assessment tools were commonly identified for assessing SCDs. Most participants use an informal approach for interviews, language sampling, and naturalistic observations in their SCD assessment process. Conclusions Generally, participants follow best practices for assessing SCDs by combining several different approaches. Some considerations for future assessment are identified, including the use of established protocols in the place of informal approaches in order to make the assessment of SCDs more systematic. Future directions for research are discussed.


Author(s):  
Elena Dukhovny ◽  
E. Betsy Kelly

According to the 2010 U.S. Census, over 20% of Americans speak a language other than English in the home, with Spanish, Chinese, and French being the languages most commonly spoken, aside from English. However, few augmentative and alternative communication (AAC) systems offer multilingual support for individuals with limited functional speech. There has been much discussion in the AAC community about best practices in AAC system design and intervention strategies, but limited resources exist to help us provide robust, flexible systems for users who speak languages other than English. We must provide services that take into consideration the unique needs of culturally and linguistically diverse users of AAC and help them reach their full communication potential. This article outlines basic guidelines for best practices in AAC design and selection, and presents practical applications of these best practices to multilingual/multicultural clients.


2009 ◽  
Vol 18 (4) ◽  
pp. 137-145 ◽  
Author(s):  
Samuel Sennott ◽  
Adam Bowker

People with ASD often need to access AAC in situations where a tabletop digital device is not practical. Recent advancements have made more powerful, portable, and affordable communication technologies available to these individuals. Proloquo2Go is a new portable augmentative and alternative communication system that runs on an iPhone or iPod touch and can be used to meet the diverse needs of individuals with autism spectrum disorders (ASD) who are ambulatory and have difficulty using speech to meet their full daily communication needs. This article examines Proloquo2Go in light of the best practices in AAC for individuals with ASD such as symbols, visual supports, voice output, and inclusion.


2016 ◽  
Vol 1 (6) ◽  
pp. 47-54 ◽  
Author(s):  
Jeffrey J. DiGiovanni ◽  
Travis L. Riffle

The search for best practices in hearing aid fittings and aural rehabilitation has generally used the audiogram and function stemming from peripheral sensitivity. In recent years, however, we have learned that individuals respond differently to various hearing aid and aural rehabilitation techniques based on cognitive abilities. In this paper, we review basic concepts of working memory and the literature driving our knowledge in newer concepts of hearing aid fitting and aural rehabilitation.


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