scholarly journals Incentivising use of structured language in biological descriptions: Author-driven phenotype data and ontology production

2018 ◽  
Vol 6 ◽  
Author(s):  
Hong Cui ◽  
James Macklin ◽  
Joel Sachs ◽  
Anton Reznicek ◽  
Julian Starr ◽  
...  
Keyword(s):  
Large Scale ◽  
Empirical Studies ◽  
Ontology Development ◽  
Free Text ◽  
Great Effort ◽  
Phenotypic Data ◽  
Manual Curation ◽  
Phenotype Data ◽  
The Moment ◽  
The Right

Phenotypes are used for a multitude of purposes such as defining species, reconstructing phylogenies, diagnosing diseases or improving crop and animal productivity, but most of this phenotypic data is published in free-text narratives that are not computable. This means that the complex relationship between the genome, the environment and phenotypes is largely inaccessible to analysis and important questions related to the evolution of organisms, their diseases or their response to climate change cannot be fully addressed. It takes great effort to manually convert free-text narratives to a computable format before they can be used in large-scale analyses. We argue that this manual curation approach is not a sustainable solution to produce computable phenotypic data for three reasons: 1) it does not scale to all of biodiversity; 2) it does not stop the publication of free-text phenotypes that will continue to need manual curation in the future and, most importantly, 3) It does not solve the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other). Our empirical studies have shown that inter-curator variation is as high as 40% even within a single project. With this level of variation, it is difficult to imagine that data integrated from multiple curation projects can be of high quality. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardised vocabularies (ontologies). We argue that the authors describing phenotypes are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project’s semantics and ontology. This will speed up ontology development and improve the semantic clarity of phenotype descriptions from the moment of publication. A proof of concept project on this idea was funded by NSF ABI in July 2017. We seek readers input or critique of the proposed approaches to help achieve community-based computable phenotype data production in the near future. Results from this project will be accessible through https://biosemantics.github.io/author-driven-production.

scholarly journals Workforce experience of the implementation of an advanced clinical practice framework in England: a mixed methods evaluation

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Jessica Lawler ◽  
Katrina Maclaine ◽  
Alison Leary
Keyword(s):  
Clinical Practice ◽  
Large Scale ◽  
Medical Model ◽  
Free Text ◽  
Advanced Practice ◽  
Full Time ◽  
Mixed Methods Evaluation ◽  
Future Direction ◽  
The Right ◽  
Practice Framework

Abstract Background This study aims to understand how the implementation of the advanced clinical practice framework in England (2017) was experienced by the workforce to check assumptions for a national workforce modelling project. The advanced clinical practice framework was introduced in England in 2017 by Health Education England to clarify the role of advanced practice in the National Health Service. Methods As part of a large-scale workforce modelling project, a self-completed questionnaire was distributed via the Association of Advanced Practice Educators UK aimed at those studying to be an Advanced Clinical Practitioner or who are practicing at this level in order to check assumptions. Semi-structured phone interviews were carried out with this same group. Questionnaires were summarised using descriptive statistics in Excel for categorical responses and interviews and survey free-text were analysed using thematic analysis in NVivo 10. Results The questionnaire received over 500 respondents (ten times that expected) and 15 interviews were carried out. Advanced clinical practice was considered by many respondents the only viable clinical career progression. Respondents felt that employers were not clear about what practicing at this level involved or its future direction. 54% (287) thought that ‘ACP’ was the right job title for them. 19% (98) of respondents wanted their origin registered profession to be included in their title. Balancing advanced clinical practice education concurrently with a full-time role was challenging, participants underestimated the workload and expectations of employer’s training. There is an apparent dichotomy that has developed from the implementation of the 2017 framework: that of advanced clinical practice as an advanced level of practice within a profession, and that of Advanced Clinical Practitioner as a new generic role in the medical model. Conclusions Efforts to establish further clarity and structure around advanced clinical practice are needed for both the individuals practising at this level and their employers. A robust evaluation of the introduction of this role should take place.

scholarly journals The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes

2013 ◽  
Author(s):  
Peter E Midford ◽  
T Alex Dececchi ◽  
James P Balhoff ◽  
Wasila M Dahdul ◽  
Nizar Ibrahim ◽  
...  
Keyword(s):  
Large Scale ◽  
Model Organism ◽  
Primary Source ◽  
Semantic Integration ◽  
Biodiversity Data ◽  
Phenotypic Data ◽  
Creative Commons ◽  
Phenotype Data ◽  
Large Scale Integration ◽  
Scale Integration

Background: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. Description: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across the vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,927 taxonomic terms, 23 taxonomic ranks, 104,506 synonyms, and 162,132 taxonomic cross-references. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) replacing subgroups with more authoritative local taxonomies; and (3) automating this process as much as possible to accommodate updates in source taxonomies. Conclusions: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and nonmodel vertebrates. The VTO is useful for crudely inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for different episodes in vertebrate evolution.

scholarly journals The Vertebrate Taxonomy Ontology: A framework for reasoning across model organism and species phenotypes

2013 ◽  
Author(s):  
Peter E Midford ◽  
T Alex Dececchi ◽  
James P Balhoff ◽  
Wasila M Dahdul ◽  
Nizar Ibrahim ◽  
...  
Keyword(s):  
Large Scale ◽  
Model Organism ◽  
Primary Source ◽  
Semantic Integration ◽  
Biodiversity Data ◽  
Phenotypic Data ◽  
Creative Commons ◽  
Phenotype Data ◽  
Large Scale Integration ◽  
Scale Integration

Background: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. Description: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across the vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,927 taxonomic terms, 23 taxonomic ranks, 104,506 synonyms, and 162,132 taxonomic cross-references. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) replacing subgroups with more authoritative local taxonomies; and (3) automating this process as much as possible to accommodate updates in source taxonomies. Conclusions: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and nonmodel vertebrates. The VTO is useful for crudely inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for different episodes in vertebrate evolution.

scholarly journals Workforce experience of the implementation of an advanced clinical practice framework in England: a mixed methods evaluation

2020 ◽  
Author(s):  
Jessica Lawler ◽  
Katrina Maclaine ◽  
Alison Leary
Keyword(s):  
Clinical Practice ◽  
Large Scale ◽  
Medical Model ◽  
Free Text ◽  
Advanced Practice ◽  
Full Time ◽  
Mixed Methods Evaluation ◽  
Future Direction ◽  
The Right ◽  
Practice Framework

Abstract Background This study aims to understand how the implementation of the Advanced Clinical Practice framework in England (2017) was experienced by the workforce to check assumptions for a national workforce modelling project. The Advanced Clinical Practice framework was introduced in England in 2017 by Health Education England to clarify the role of advanced practice in the National Health Service.Methods: As part of a large-scale workforce modelling project, a self-completed questionnaire was distributed via the Association of Advanced Practice Educators UK aimed at those studying to be an Advanced Clinical Practitioner or who are practicing at this level in order to check assumptions. Semi-structured phone interviews were carried out with this same group. Questionnaires were summarised using descriptive statistics in Excel for categorical responses and interviews and survey free-text were analysed using thematic analysis in NVivo 10.Results: The questionnaire received over 500 respondents (ten times that expected) and 15 interviews were carried out. Advanced Clinical Practice was considered by many respondents the only viable clinical career progression. Respondents felt that employers were not clear about what practicing at this level involved or its future direction. 54% (287) thought that ‘ACP’ was the right job title for them. 19% (98) of respondents wanted their origin registered profession to be included in their title. Balancing Advanced Clinical Practice education concurrently with a full-time role was challenging, participants underestimated the workload and expectations of employer’s training. There is an apparent dichotomy that has developed from the implementation of the 2017 framework: that of Advanced Clinical Practice as an advanced level of practice within a profession, and that of Advanced Clinical Practitioner as a new generic role in the medical model.Conclusions: Efforts to establish further clarity and structure around advanced clinicalpractice are needed for both the individuals practising at this level and their employers. A robust evaluation of the introduction of this role should take place.

Why Has There Been No People’s Power Rebellion in North Korea?

2018 ◽  
pp. 1-34
Author(s):  
Andrew Jackson
Keyword(s):  
Rural Areas ◽  
North Korea ◽  
Large Scale ◽  
Political Elite ◽  
Information Control ◽  
Al Jazeera ◽  
The North ◽  
New Information ◽  
Effective System ◽  
The Right

One scenario put forward by researchers, political commentators and journalists for the collapse of North Korea has been a People’s Power (or popular) rebellion. This paper analyses why no popular rebellion has occurred in the DPRK under Kim Jong Un. It challenges the assumption that popular rebellion would happen because of widespread anger caused by a greater awareness of superior economic conditions outside the DPRK. Using Jack Goldstone’s theoretical expla-nations for the outbreak of popular rebellion, and comparisons with the 1989 Romanian and 2010–11 Tunisian transitions, this paper argues that marketi-zation has led to a loosening of state ideological control and to an influx of infor-mation about conditions in the outside world. However, unlike the Tunisian transitions—in which a new information context shaped by social media, the Al-Jazeera network and an experience of protest helped create a sense of pan-Arab solidarity amongst Tunisians resisting their government—there has been no similar ideology unifying North Koreans against their regime. There is evidence of discontent in market unrest in the DPRK, although protests between 2011 and the present have mostly been in defense of the right of people to support themselves through private trade. North Koreans believe this right has been guaranteed, or at least tacitly condoned, by the Kim Jong Un government. There has not been any large-scale explosion of popular anger because the state has not attempted to crush market activities outright under Kim Jong Un. There are other reasons why no popular rebellion has occurred in the North. Unlike Tunisia, the DPRK lacks a dissident political elite capable of leading an opposition movement, and unlike Romania, the DPRK authorities have shown some flexibility in their anti-dissent strategies, taking a more tolerant approach to protests against economic issues. Reduced levels of violence during periods of unrest and an effective system of information control may have helped restrict the expansion of unrest beyond rural areas.

White Backlash

2015 ◽  
Author(s):  
Marisa Abrajano ◽  
Zoltan L. Hajnal
Keyword(s):  
Ethnic Diversity ◽  
Republican Party ◽  
Large Scale ◽  
White Americans ◽  
Political Beliefs ◽  
White Backlash ◽  
Political Spectrum ◽  
Racial Divide ◽  
The Right ◽  
Political Backlash

This book provides an authoritative assessment of how immigration is reshaping American politics. Using an array of data and analysis, it shows that fears about immigration fundamentally influence white Americans' core political identities, policy preferences, and electoral choices, and that these concerns are at the heart of a large-scale defection of whites from the Democratic to the Republican Party. The book demonstrates that this political backlash has disquieting implications for the future of race relations in America. White Americans' concerns about Latinos and immigration have led to support for policies that are less generous and more punitive and that conflict with the preferences of much of the immigrant population. America's growing racial and ethnic diversity is leading to a greater racial divide in politics. As whites move to the right of the political spectrum, racial and ethnic minorities generally support the left. Racial divisions in partisanship and voting, as the book indicates, now outweigh divisions by class, age, gender, and other demographic measures. The book raises critical questions and concerns about how political beliefs and future elections will change the fate of America's immigrants and minorities, and their relationship with the rest of the nation.

Would you Make the Right Decision? – Decision Making Biases in Economy - Related Dilemmas

2018 ◽  
Vol 9 (1) ◽  
pp. 59-66
Author(s):  
Zsuzsanna Gödör ◽  
Georgina Szabó
Keyword(s):  
Decision Making ◽  
Online Survey ◽  
Framing Effect ◽  
Economic Knowledge ◽  
Bank Account ◽  
Financial Decisions ◽  
Hungarian Population ◽  
The Moment ◽  
The Right ◽  
Decision Making Biases

Abstract As they say, money can’t buy happiness. However, the lack of it can make people’s lives much harder. From the moment we open our first bank account, we have to make lots of financial decisions in our life. Should I save some money or should I spend it? Is it a good idea to ask for a loan? How to invest my money? When we make such decisions, unfortunately we sometimes make mistakes, too. In this study, we selected seven common decision making biases - anchoring and adjustment, overconfidence, high optimism, the law of small numbers, framing effect, disposition effect and gambler’s fallacy – and tested them on the Hungarian population via an online survey. In the focus of our study was the question whether the presence of economic knowledge helps people make better decisions? The decision making biases found in literature mostly appeared in the sample as well. It proves that people do apply them when making decisions and in certain cases this could result in serious and costly errors. That’s why it would be absolutely important for people to learn about them, thus increasing their awareness and attention when making decisions. Furthermore, in our research we did find some connection between decisions and the knowledge of economics, people with some knowledge of economics opted for the better solution in bigger proportion

Zeitstrukturen im Jazz

2014 ◽  
Vol 59 (1) ◽  
pp. 79-92
Author(s):  
Alexander Becker
Keyword(s):  
Large Scale ◽  
Large Scale Structure ◽  
Time Frame ◽  
Scale Structure ◽  
Classical Form ◽  
Jazz Music ◽  
The Moment

Wie erlebt der Hörer Jazz? Bei dieser Frage geht es unter anderem um die Art und Weise, wie Jazz die Zeit des Hörens gestaltet. Ein an klassischer Musik geschultes Ohr erwartet von musikalischer Zeitgestaltung, den zeitlichen Rahmen, der durch Anfang und Ende gesetzt ist, von innen heraus zu strukturieren und neu zu konstituieren. Doch das ist keine Erwartung, die dem Jazz gerecht wird. Im Jazz wird der Moment nicht im Hinblick auf ein Ziel gestaltet, das von einer übergeordneten Struktur bereitgestellt wird, sondern so, dass er den Bewegungsimpuls zum nächsten Moment weiterträgt. Wie wirkt sich dieses Prinzip der Zeitgestaltung auf die musikalische Form im Großen aus? Der Aufsatz untersucht diese Frage anhand von Beispielen, an denen sich der Weg der Transformation von einer klassischen zu einer dem Jazz angemessenen Form gut nachverfolgen lässt.<br><br>How do listeners experience Jazz? This is a question also about how Jazz music organizes the listening time. A classically educated listener expects a piece of music to structure, unify and thereby re-constitute the externally given time frame. Such an expectation is foreign to Jazz music which doesn’t relate the moment to a goal provided by a large scale structure. Rather, one moment is carried on to the next, preserving the stimulus potentially ad infinitum. How does such an organization of time affect the large scale form? The paper tries to answer this question by analyzing two examples which permit to trace the transformation of a classical form into a form germane to Jazz music.

JUSTICE AND SOCIAL CHANGE FOR INCLUSIVE EDUCATION IN INDONESIA AND ASEAN FOR DISABLED PERSONS (STUDY ON PEOPLE AFFECTED BY LEPROSY)

2017 ◽  
Vol 1 (1) ◽  
pp. 1-5
Author(s):  
Nuah Perdamenta Tarigan ◽  
Christian Siregar ◽  
Simon Mangatur Tampubolon
Keyword(s):  
Inclusive Education ◽  
Local Governments ◽  
Disabled Persons ◽  
Equal Rights ◽  
Central Java ◽  
The People ◽  
Asean Countries ◽  
The Government ◽  
The Moment ◽  
The Right

Justice that has not existed and is apparent among the disabilities in Indonesia is very large and spread in the archipelago is very large, making the issue of equality is a very important thing especially with the publication of the Disability Act No. 8 of 2016 at the beginning of that year. Only a few provinces that understand properly and well on open and potential issues and issues will affect other areas including the increasingly growing number of elderly people in Indonesia due to the increasing welfare of the people. The government of DKI Jakarta, including the most concerned with disability, from the beginning has set a bold step to defend things related to disability, including local governments in Solo, Bali, Makassar and several other areas. Leprosy belonging to the disability community has a very tough marginalization, the disability that arises from leprosy quite a lot, reaches ten percent more and covers the poor areas of Indonesia, such as Nusa Tenggara Timur, Papua, South Sulawesi Provinces and even East Java and West Java and Central Java Provinces. If we compare again with the ASEAN countries we also do not miss the moment in ratifying the CRPD (Convention of Rights for People with Disability) into the Law of Disability No. 8 of 2016 which, although already published but still get rejections in some sections because do not provide proper empowerment and rights equality. The struggle is long and must be continued to build equal rights in all areas, not only health and welfare but also in the right of the right to receive continuous inclusive education.

Evaluation of Ovaries in Patients with Polycystic Ovary Syndrome using Shear Wave Elastography

2020 ◽  
Vol 16 (5) ◽  
pp. 578-583
Author(s):  
Aysegul Altunkeser ◽  
Zeynep Ozturk Inal ◽  
Nahide Baran
Keyword(s):  
Shear Wave ◽  
Large Scale ◽  
Polycystic Ovary ◽  
Shear Wave Elastography ◽  
Left Ovary ◽  
Control Group ◽  
Tissue Elasticity ◽  
Group I ◽  
Pcos Group ◽  
The Right

Background: Shear wave electrography (SWE) is a novel non-invasive imaging technique which demonstrate tissue elasticity. Recent research evaluating the elasticity properties of normal and pathological tissues emphasize the diagnostic importance of this technique. Aims: Polycystic ovarian syndrome (PCOS), which is characterized by menstrual irregularity, hyperandrogenism, and polycystic overgrowth, may cause infertility. The aim of this study was to evaluate the elasticity of ovaries in patients with PCOS using SWE. Methods: 66 patients diagnosed with PCOS according to the Rotterdam criteria (PCOS = group I) and 72 patients with non-PCOS (Control = group II), were included in the study. Demographic and clinical characteristics of the participants were recorded. Ovarian elasticity was assessed in all patients with SWE, and speed values were obtained from the ovaries. The elasticity of the ovaries was compared between the two groups. Results: While there were statistically significant differences between the groups in body mass index (BMI), right and left ovarian volumes, luteinizing hormone and testosterone levels (p<0.05), no significant differences were found between groups I and II in the velocity (for the right ovary 3.89±1.81 vs. 2.93±0.72, p=0.301; for the left ovary 2.88±0.65 vs. 2.95±0.80, p=0.577) and elastography (for the right ovary 36.62±17.78 vs. 36.79±14.32, p=0.3952; for the left ovary 36.56±14.15 vs. 36.26±15.10, p=0.903) values, respectively. Conclusion: We could not obtain different velocity and elastography values from the ovaries of the patients with PCOS using SWE. Therefore, further large-scale studies are needed to elucidate this issue.

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