title: Current stewardship practices in invasion biology limit the value and secondary use of genomic data

authors: Vaughan, Amy L.

subjects: biological invasion

abstract: Invasive species threaten native biota, putting fragile ecosystems at risk and having a large-scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole-genome sequences lies an opportunity for cross-species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole-genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field-collected samples. Seventy-six assemblies (38%) reported an ‘undescribed’ sample origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field-collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% (n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large-scale consortia tended to provide the most complete metadata submissions in our analysis—such cross-institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.

text: Current stewardship practices in invasion biology limit the value and secondary use of genomic data Invasive species threaten native biota, putting fragile ecosystems at risk and having a large-scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole-genome sequences lies an opportunity for cross-species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole-genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field-collected samples. Seventy-six assemblies (38%) reported an ‘undescribed’ sample origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field-collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% (n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large-scale consortia tended to provide the most complete metadata submissions in our analysis—such cross-institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.

year: 2023

title: A review of user interface adaption in current semantic web browsers

authors: Turner, Emmanuel King

subjects: computer science

abstract: The semantic web is an example of an innumerable corpus because it contains innumerable subjects expressed using innumerable ontologies. This paper reviews current semantic web browsers to see if they can adaptively show meaningful data presentations to users. The paper also seeks to discover if current semantic web browsers provide a rich enough set of capabilities for future user interface work to be built upon.

text: A review of user interface adaption in current semantic web browsers The semantic web is an example of an innumerable corpus because it contains innumerable subjects expressed using innumerable ontologies. This paper reviews current semantic web browsers to see if they can adaptively show meaningful data presentations to users. The paper also seeks to discover if current semantic web browsers provide a rich enough set of capabilities for future user interface work to be built upon.

year: 2011-02-08

title: “This is not a riot, it is a protest”: A discourse analysis of prison violence in New Zealand news media

authors: Membery, Liam

subjects: Prison Violence

abstract: This thesis examines the discourses of prison violence in the New Zealand news media. Prison violence is a pressing social issue that harms those involved and has permeating consequences for the institution. Prison riots, specifically, involve serious instances of disorder and violence that incur physical, psychological, social and economic harm. Despite prisons being private institutions, prison riots are public events that amass large social responses through news media coverage. The public often use news media to co-construct their perceptions of social phenomena, and policymakers use both public opinion and the news media to guide their decisions when shaping policy. Subsequently, the ways in which the news media discursively construct prison riots will have direct consequences for public attitudes and policy relating to prison violence, a phenomenon that exists outside of the public eye. However, there is currently no research that has examined discourses of prison violence and, further, what the consequences of these discourses may be. Therefore, using a Foucauldian approach to discourse analysis, this study examined the discourses in the news media representations of the large-scale prison violence at the Spring Hill Corrections Facility (2013) and Waikeria Prison (2020-2021). The results uncovered three discourses: the riot discourse, the gang discourse, and the protest discourse. The riot discourse was identified as dominant and constructed prison violence as an individualised issue perpetrated by inherently violent prisoners. The gang discourse worked in conjunction with the riot discourse, constructing prison violence as an individualised issue perpetrated by gang members. The protest discourse was identified as a counter-discourse and constructed the unrest at both facilities as protests against living conditions and inhumane treatment. Each discourse has consequences for public attitudes and in turn, penal policy and practice.

text: “This is not a riot, it is a protest”: A discourse analysis of prison violence in New Zealand news media This thesis examines the discourses of prison violence in the New Zealand news media. Prison violence is a pressing social issue that harms those involved and has permeating consequences for the institution. Prison riots, specifically, involve serious instances of disorder and violence that incur physical, psychological, social and economic harm. Despite prisons being private institutions, prison riots are public events that amass large social responses through news media coverage. The public often use news media to co-construct their perceptions of social phenomena, and policymakers use both public opinion and the news media to guide their decisions when shaping policy. Subsequently, the ways in which the news media discursively construct prison riots will have direct consequences for public attitudes and policy relating to prison violence, a phenomenon that exists outside of the public eye. However, there is currently no research that has examined discourses of prison violence and, further, what the consequences of these discourses may be. Therefore, using a Foucauldian approach to discourse analysis, this study examined the discourses in the news media representations of the large-scale prison violence at the Spring Hill Corrections Facility (2013) and Waikeria Prison (2020-2021). The results uncovered three discourses: the riot discourse, the gang discourse, and the protest discourse. The riot discourse was identified as dominant and constructed prison violence as an individualised issue perpetrated by inherently violent prisoners. The gang discourse worked in conjunction with the riot discourse, constructing prison violence as an individualised issue perpetrated by gang members. The protest discourse was identified as a counter-discourse and constructed the unrest at both facilities as protests against living conditions and inhumane treatment. Each discourse has consequences for public attitudes and in turn, penal policy and practice.

year: 2022