Robust Integration of Biodiversity Data by Process- and State-based Representation of Object Histories and Modular Application Architecture

Biodiversity data is obtained by a variety of methodological approaches—including observation surveys, environmental sampling and biological object collection—employing diverse sample processing protocols and data transformations. While complete and accurate accounts of these data-generating processes are important to enable integration and informed reuse of data, the structure and content of published biodiversity data currently are often shaped by specific application goals. For example, data publishers that export specimen-based data from collection management systems for inclusion in aggregations like those in the Global Biodiversity Information Facility (GBIF) must frequently relax their internal models and produce unnatural joins to fit GBIF’s occurrences-based data structure. Third-party assertions over these aggregated data therefore assume the risk of irreproducibility or concept drift. Here we introduce process- and state-based representation of object histories as the main organizing principle for data about specimens and samples in Digital Information System for Natural History Data (DINA, Glöckler et al. 2020)-compliant collection management software (Fig. 1). Specimens, samples and objects in general are subjected to a variety of processes, including planned actions involving the object, e.g., collecting, preparing, subsampling, loaning. Object states are any particular mode of being of an object at a certain point in time. For example, any one intermediate step in preparing a collected specimen for long-term conservation in a collection would constitute an individual object state. An object’s history is the entire chain of these interrelated processes and states. We argue that using object histories as main conceptual modeling paradigm in DINA offers the generality required to accommodate a diverse, open set of use cases in biodiversity data representation, yet also offers the versatility to serve as basis for use-case specific data aggregation and presentation. Specifically, a representation based on object histories provides a coherent structure for documenting individual processes and states for any given object and for linking this documentation (e.g., textual descriptions or images pertaining to a given process or state), a natural representational structure of the real-world sequence of processes an object participates in and for the data generated in these processes (e.g., a DNA-extraction procedure and sequence information generated on its basis), a straightforward structure to link data about related objects (e.g., tissue samples, the biological specimen a bone is derived from) in a network of connected object histories. a coherent structure for documenting individual processes and states for any given object and for linking this documentation (e.g., textual descriptions or images pertaining to a given process or state), a natural representational structure of the real-world sequence of processes an object participates in and for the data generated in these processes (e.g., a DNA-extraction procedure and sequence information generated on its basis), a straightforward structure to link data about related objects (e.g., tissue samples, the biological specimen a bone is derived from) in a network of connected object histories. The approach is designed to be embedded in DINA’s modular application architecture, so that information on object histories can be accessed via corresponding APIs either through its own interfaces (Fig. 2) or by integration with external web services (Fig. 3). Viewing collection management tasks as part of object histories also informs delineation of modules to support these tasks with specialized functions and interfaces. It also admits the use of persistent, dereferencable identifiers for individual processes and states in object histories and for linking their representations to elements in ontologies and controlled vocabularies. In this contribution to the symposium, DINA's object histories as a main organizing principle for collection object data will be discussed and the utility of using it in the context of modular application architecture, data federation, and data integration in projects like BiCIKL will be illustrated.

Research on Enterprise Competitive Information Management Based on Co-Occurrence Analysis

Link data source lack has seriously hampered the research development of competitive information for enterprises based on co-link analysis in recent years, and exploring application and innovation of the new method of URL co-occurrence analysis in enterprises competitive information research is very important to make up for current inadequacy. And exploration on problems such as whether Jaccard handling needs to be conducted on collected data and how the effect is to conduct information research in different methods for data in different handling ways is meaningful to theoretical perfection of competitive information research of enterprises. Non-Jaccard data and Jaccard data are compared with examples of Chinese representative banks based on new methods of URL co-occurrence analysis, and competitive information research of enterprises is conducted in the multidimensional scaling method and social network analysis method; and comprehensive exploration and analysis are conducted from multiperspectives such as gradient grading analysis, recognition of main competitors, and competitive landscape analysis of fine grit. Innovative research competitive information for enterprises based on URL co-occurrence analysis in this thesis effectively makes up for current inadequacy due to link data source lack, and it expands new spaces for competitive information research of enterprises; it is also in research in this thesis that analysis result based on non-Jaccard data is far better than analysis result based on Jaccard data when multidimensional scaling analysis is conducted; analysis result based on non-Jaccard data and analysis result based on Jaccard data uncover competitive information of related enterprises when social network analysis is conducted, and above conclusions in this thesis are all verified and analyzed through example data.

SOEP-RV: Linking German Socio-Economic Panel Data to Pension Records

The aim of the project SOEP-RV is to link data from participants in the German Socio-Economic Panel (SOEP) survey to their individual Deutsche Rentenversicherung (German Pension Insurance) records. For all SOEP respondents who give explicit consent to record linkage, SOEP-RV creates a linked dataset that combines the comprehensive multi-topic SOEP data with detailed cross-sectional and longitudinal data on social security pension records covering the individual’s entire insurance history. This article provides an overview of the record linkage project, highlights potentials for analysis of the linked data, compares key SOEP and pension insurance variables, and suggests a re-weighting procedure that corrects for selectivity. It concludes with details on the process of obtaining the data for scientific use.

Assessment of COVID-19 vaccine hesitancy among undergraduate medical students of a tertiary care teaching hospital, Surat: a source of profound concern

Background: The discussion around COVID-19 vaccines has been in the limelight ever since the announcement was made for mass vaccination campaign in India. Less is known about undergraduate medical students’ perception and willingness towards getting COVID-19 vaccination. The aim of the study was to assess reasons for the apprehension if present towards taking the COVID-19 vaccines among medical students and to spread awareness about the ongoing issue.Methods: This was a prospective, cross sectional, survey-based study which was conducted at Surat Municipal Institute of Medical Education and Research (SMIMER), Surat, Gujarat, India. Questionnaire was distributed among medical students during lectures and exam going students were sent Google form link. Data collection was done from February to March 2021, and 550 students submitted the forms.Results: While 34.9% students had taken the vaccine voluntarily, category I (acceptance group); 18.2% students were initially hesitant to take the vaccine, but later took it, category II (hesitant group); the frequency increased to 46.9% students who are still hesitant and have not taken the vaccine, category III (refusal group). Top reasons for hesitancy were: concern regarding adverse events (69%), safety (60%) and lack of scientific data (27%) provided for the vaccines.Conclusions: This study revealed that there was lack of knowledge and positive attitude towards the COVID-19 vaccines among the non-vaccinated students. This evaluation has guided the importance and the need of targeted educational program to address the knowledge gap.

Predictors of ophthalmology career success (POCS) study

ObjectiveOphthalmology is the busiest outpatient specialty with demand predicted to rise over 40% in the next 20 years. A significant increase in the number of trainee ophthalmologists is required to fill currently vacant consultant posts and meet the UK’s workforce demands by 2038. Our aim was to understand what determines success in ophthalmology training, in order to inform future ophthalmologists, refine recruitment and facilitate workforce planning.Methods and AnalysisThis was a retrospective longitudinal cohort study using routinely collected data available from UK Medical Education Database (UKMED) (https://www.ukmed.ac.uk/). Data were analysed on 1350 candidates who had applied for ophthalmology specialty training (OST) between 2012 and 2018, as well as 495 candidates who had attempted Fellow of the Royal College of Ophthalmologists (FRCOphth) Part 1 between 2013 and 2018. Participants who had not obtained their primary medical qualification from the UK medical schools were excluded. Primary outcome measures included gaining a place on the OST programme and passing the FRCOphth Part 1 examination on first attempt.ResultsHigher education performance measure decile scores at medical school are strongly predictive in securing an OST post and passing the part 1 examination first time (p<0.001). Candidates who attempt FRCOphth Part 1 prior to their ST1 application are more likely to get a place on OST on first attempt. Socioeconomic factors, gender and ethnicity do not influence success in OST entry. Male trainees are more likely to pass FRCOphth Part 1 on their first attempt.ConclusionThis study is the first quantitative assessment of the factors that determine success in OST recruitment and ophthalmology postgraduate examinations in the UK. Similar studies should be undertaken in all other medical and surgical specialties to understand what factors predict success.

The Role of Adaptive Surveillance as a Core Intervention to Achieve Malaria Elimination

Adaptive surveillance systems are essential for national programmes to achieve their malaria elimination goals. Core principles of surveillance systems including accurate diagnosis and reporting of malaria cases, integration of health data across administrative levels and the need to link data to a response are well defined by international guidelines. Nevertheless, while the requirements of surveillance systems along the transmission continuum are clearly documented, the operationalization remains challenging for national programmes. Firstly, because the multi-level increase of surveillance efforts demanding real-time and case-based data as well as the capacity of the health force to trigger locally customized responses, is resource intensive and requires substantial investment. Secondly, because there is a gap in international alignment on best tools and practices on how to operationally implement these requirements. Recently, several initiatives have started to address this gap in international coordination, aiming to establish the operational guidance for elimination programmes to successfully implement adaptive surveillance systems.

Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts

Evolutionary and organismal biology, similar to other fields in biology, have become inundated with data. At the same rate, we are experiencing a surge in broader evolutionary and ecological syntheses for which tree-thinking is the staple for a variety of post-tree analyses. To fully take advantage of this wealth of data to discover and understand large-scale evolutionary and ecological patterns, computational data integration, i.e. the use of machines to link data at large scale by shared entities, is crucial. The most common shared entity by which evolutionary and ecological data need to be linked is the taxon to which they belong. In this paper, we propose a set of requirements that a system for defining such taxa should meet for computational data science: taxon definitions should maintain conceptual consistency, be reproducible via a known algorithm, be computationally automatable, and be applicable across the tree of life. We argue that Linnaean names based in Linnaean taxonomy, by far the most prevalent means of linking data to taxa, fail to meet these requirements due to fundamental theoretical and practical shortfalls. We argue that for the purposes of data-integration we should instead use phylogenetic clade definitions transformed into formal logic expressions. We call such expressions phyloreferences, and argue that, unlike Linnaean names, they meet all requirements for effective data-integration.

Maximizing the Probability of Message Delivery over Ever-changing Communication Scenarios in Tactical Networks

This letter introduces a stochastic model to maximize the probability of message delivery over ever-changing communication scenarios in tactical networks. Our model improves modern tactical systems implementing store-and-forward mechanisms organized in a hierarchy of layers for messages, IP packets and radios. The goal is to compute close to optimal parameters for a transport protocol by computing the optimum redundancy for the user data-flow to overcome packet loss during changes in the link data rate, including disconnections. Experiments in a VHF network illustrate the numerical results from our model using messages with different sizes over two patterns of data rate change.

Maximizing the Probability of Message Delivery over Ever-changing Communication Scenarios in Tactical Networks

This letter introduces a stochastic model to maximize the probability of message delivery over ever-changing communication scenarios in tactical networks. Our model improves modern tactical systems implementing store-and-forward mechanisms organized in a hierarchy of layers for messages, IP packets and radios. The goal is to compute close to optimal parameters for a transport protocol by computing the optimum redundancy for the user data-flow to overcome packet loss during changes in the link data rate, including disconnections. Experiments in a VHF network illustrate the numerical results from our model using messages with different sizes over two patterns of data rate change.