scholarly journals Whip: Communicate and Test What to Expect from Data

2018 ◽  
Vol 2 ◽  
pp. e25317
Author(s):  
Stijn Van Hoey ◽  
Peter Desmet
Keyword(s):  
Data Quality ◽  
Controlled Vocabulary ◽  
Published Data ◽  
Data Set ◽  
Data Publication ◽  
Use Of Data ◽  
Maximum Utility ◽  
Group 2 ◽  
Publication Guidelines ◽  
Available Information

The ability to communicate and assess the quality and fitness for use of data is crucial to ensure maximum utility and re-use. Data consumers have certain requirements for the data they seek and need to be able to check if a data set conforms with these requirements. Data publishers aim to provide data with the highest possible quality and need to be able to identify potential errors that can be addressed with the available information at hand. The development and adoption of data publication guidelines is one approach to define and meet those requirements. However, the use of a guideline, the mapping decisions, and the requirements a dataset is expected to meet, are generally not communicated with the provided data. Moreover, these guidelines are typically intended for humans only. In this talk, we will present 'whip': a proposed syntax for data specifications. With whip, one can define column-based constraints for tabular (tidy) data using a number of rules, e.g. how data is structured following Darwin Core, how a term uses controlled vocabulary values, or what the expected minimum and maximum values are. These rules are human- and machine-readable, which communicates the specifications, and allows to automatically validate those in pipelines for data publication and quality assessment, such as Kurator. Whip can be formatted as a (yaml) text file that can be provided with the published data, communicating the specifications a dataset is expected to meet. The scope of these specifications can be specific to a dataset, but can also be used to express expected data quality and fitness for use of a publisher, consumer or community, allowing bottom-up and top-down adoption. As such, these specifications are complementary to the core set of data quality tests as currently under development by the TDWG Biodiversity Data Quality Task 2 Group 2. Whip rules are currently generic, but more specific ones can be defined to address requirements for biodiversity information.

Improving Data Quality: Actors, Incentives, and Capabilities

2007 ◽  
Vol 15 (4) ◽  
pp. 365-386 ◽  
Author(s):  
Yoshiko M. Herrera ◽  
Devesh Kapur
Keyword(s):  
Data Quality ◽  
International Organizations ◽  
Data Sets ◽  
Data Set ◽  
The Core ◽  
Use Of Data ◽  
Private Organizations ◽  
Assess Data Quality ◽  
Existing Data ◽  
Shape Data

This paper examines the construction and use of data sets in political science. We focus on three interrelated questions: How might we assess data quality? What factors shape data quality? and How can these factors be addressed to improve data quality? We first outline some problems with existing data set quality, including issues of validity, coverage, and accuracy, and we discuss some ways of identifying problems as well as some consequences of data quality problems. The core of the paper addresses the second question by analyzing the incentives and capabilities facing four key actors in a data supply chain: respondents, data collection agencies (including state bureaucracies and private organizations), international organizations, and finally, academic scholars. We conclude by making some suggestions for improving the use and construction of data sets.It is a capital mistake, Watson, to theorise before you have all the evidence. It biases the judgment.—Sherlock Holmes in “A Study in Scarlet”Statistics make officials, and officials make statistics.”—Chinese proverb

Reproducibility and efficiency in handling complex neurophysiological data

Neuroforum ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michael Denker ◽  
Sonja Grün ◽  
Thomas Wachtler ◽  
Hansjörg Scherberger
Keyword(s):  
Best Practices ◽  
Data Management ◽  
Data Integrity ◽  
Behavioral Neuroscience ◽  
Data Set ◽  
Data Publication ◽  
Electrophysiological Data ◽  
Data Formats ◽  
Neurophysiological Data ◽  
Community Effort

Abstract Preparing a neurophysiological data set with the aim of sharing and publishing is hard. Many of the available tools and services to provide a smooth workflow for data publication are still in their maturing stages and not well integrated. Also, best practices and concrete examples of how to create a rigorous and complete package of an electrophysiology experiment are still lacking. Given the heterogeneity of the field, such unifying guidelines and processes can only be formulated together as a community effort. One of the goals of the NFDI-Neuro consortium initiative is to build such a community for systems and behavioral neuroscience. NFDI-Neuro aims to address the needs of the community to make data management easier and to tackle these challenges in collaboration with various international initiatives (e.g., INCF, EBRAINS). This will give scientists the opportunity to spend more time analyzing the wealth of electrophysiological data they leverage, rather than dealing with data formats and data integrity.

scholarly journals A System for Phenotype Harmonization in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program

2021 ◽  
Author(s):  
Adrienne M Stilp ◽  
Leslie S Emery ◽  
Jai G Broome ◽  
Erin J Buth ◽  
Alyna T Khan ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Association Studies ◽  
Controlled Vocabulary ◽  
National Institutes Of Health ◽  
Design Data ◽  
Data Set ◽  
Data Repositories ◽  
Phenotype Data ◽  
National Heart Lung ◽  
Centralized System

Abstract Genotype-phenotype association studies often combine phenotype data from multiple studies to increase power. Harmonization of the data usually requires substantial effort due to heterogeneity in phenotype definitions, study design, data collection procedures, and data set organization. Here we describe a centralized system for phenotype harmonization that includes input from phenotype domain and study experts, quality control, documentation, reproducible results, and data sharing mechanisms. This system was developed for the National Heart, Lung and Blood Institute’s Trans-Omics for Precision Medicine program, which is generating genomic and other omics data for >80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants from up to 17 studies per phenotype (participants recruited 1948-2012). We discuss challenges in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled-access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include (1) the code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify or extend these harmonizations to additional studies; and (2) results of labeling thousands of phenotype variables with controlled vocabulary terms.

Estimating performance from capabilities in business process improvement

2016 ◽  
Vol 22 (6) ◽  
pp. 1099-1117 ◽  
Author(s):  
Boyd A. Nicholds ◽  
John P.T. Mo
Keyword(s):  
Process Improvement ◽  
Business Process ◽  
Expected Improvement ◽  
Management Decision ◽  
Published Data ◽  
Performance Gain ◽  
Data Set ◽  
Business Process Improvement ◽  
Improvement Project ◽  
Content Type

Purpose The research indicates there is a positive link between the improvement capability of an organisation and the intensity of effort applied to a business process improvement (BPI) project or initiative. While a degree of stochastic variation in applied effort to any particular improvement project may be expected there is a clear need to quantify the causal relationship, to assist management decision, and to enhance the chance of achieving and sustaining the expected improvement targets. The paper aims to discuss these issues. Design/methodology/approach The paper presents a method to obtain the function that estimates the range of applicable effort an organisation can expect to be able to apply based on their current improvement capability. The method used analysed published data as well as regression analysis of new data points obtained from completed process improvement projects. Findings The level of effort available to be applied to a process improvement project can be expressed as a regression function expressing the possible range of achievable BPI performance within 90 per cent confidence limits. Research limitations/implications The data set applied by this research is limited due to constraints during the research project. A more accurate function can be obtained with more industry data. Practical implications When the described function is combined with a separate non-linear function of performance gain vs effort a model of performance gain for a process improvement project as a function of organisational improvement capability is obtained. The probability of success in achieving performance targets may be estimated for a process improvement project. Originality/value The method developed in this research is novel and unique and has the potential to be applied to assessing an organisation’s capability to manage change.

Relative testis size and mating systems in anurans: large testis in multiple-male mating in foam-nesting frogs

2011 ◽  
Vol 61 (2) ◽  
pp. 225-238 ◽  
Author(s):  
Wen Bo Liao ◽  
Zhi Ping Mi ◽  
Cai Quan Zhou ◽  
Ling Jin ◽  
Xian Han ◽  
...  
Keyword(s):  
Sperm Competition ◽  
Published Data ◽  
Male Mating ◽  
Data Sets ◽  
Testis Size ◽  
Data Set ◽  
Monogamous Species ◽  
Large Testis ◽  
Testes Size ◽  
Testis Mass

AbstractComparative studies of the relative testes size in animals show that promiscuous species have relatively larger testes than monogamous species. Sperm competition favours the evolution of larger ejaculates in many animals – they give bigger testes. In the view, we presented data on relative testis mass for 17 Chinese species including 3 polyandrous species. We analyzed relative testis mass within the Chinese data set and combining those data with published data sets on Japanese and African frogs. We found that polyandrous foam nesting species have relatively large testes, suggesting that sperm competition was an important factor affecting the evolution of relative testes size. For 4 polyandrous species testes mass is positively correlated with intensity (males/mating) but not with risk (frequency of polyandrous matings) of sperm competition.

Application of Machine Learning for Lithology-on-Bit Prediction using Drilling Data in Real-Time

2021 ◽  
Author(s):  
Temirlan Zhekenov ◽  
Artem Nechaev ◽  
Kamilla Chettykbayeva ◽  
Alexey Zinovyev ◽  
German Sardarov ◽  
...  
Keyword(s):  
Machine Learning ◽  
Data Quality ◽  
Real Time ◽  
Hybrid Modeling ◽  
Data Set ◽  
Drilling Parameters ◽  
Drilling Data ◽  
Stable Solutions ◽  
Mud Logging

SUMMARY Researchers base their analysis on basic drilling parameters obtained during mud logging and demonstrate impressive results. However, due to limitations imposed by data quality often present during drilling, those solutions often tend to lose their stability and high levels of predictivity. In this work, the concept of hybrid modeling was introduced which allows to integrate the analytical correlations with algorithms of machine learning for obtaining stable solutions consistent from one data set to another.

Effects of genotype and lactation number on health and reproductive problems in dairy cows

1997 ◽  
Vol 1997 ◽  
pp. 143-143
Author(s):  
B.L. Nielsen ◽  
R.F. Veerkamp ◽  
J.E. Pryce ◽  
G. Simm ◽  
J.D. Oldham
Keyword(s):  
Dairy Cows ◽  
Large Data ◽  
Large Data Sets ◽  
Data Sets ◽  
Variation Analysis ◽  
Genetic Line ◽  
Data Set ◽  
Health Events ◽  
Use Of Data ◽  
Low Incidence

High producing dairy cows have been found to be more susceptible to disease (Jones et al., 1994; Göhn et al., 1995) raising concerns about the welfare of the modern dairy cow. Genotype and number of lactations may affect various health problems differently, and their relative importance may vary. The categorical nature and low incidence of health events necessitates large data-sets, but the use of data collected across herds may introduce unwanted variation. Analysis of a comprehensive data-set from a single herd was carried out to investigate the effects of genetic line and lactation number on the incidence of various health and reproductive problems.

scholarly journals Children with 5′-end NF1 gene mutations are more likely to have glioma

2017 ◽  
Vol 3 (5) ◽  
pp. e192 ◽  
Author(s):  
Corina Anastasaki ◽  
Stephanie M. Morris ◽  
Feng Gao ◽  
David H. Gutmann
Keyword(s):  
Gene Mutation ◽  
Statistical Significance ◽  
Gene Mutations ◽  
Neurofibromatosis Type ◽  
Published Data ◽  
Data Sets ◽  
Nonsense Mutations ◽  
Data Set ◽  
Nf1 Gene ◽  
The Relationship

Objective:To ascertain the relationship between the germline NF1 gene mutation and glioma development in patients with neurofibromatosis type 1 (NF1).Methods:The relationship between the type and location of the germline NF1 mutation and the presence of a glioma was analyzed in 37 participants with NF1 from one institution (Washington University School of Medicine [WUSM]) with a clinical diagnosis of NF1. Odds ratios (ORs) were calculated using both unadjusted and weighted analyses of this data set in combination with 4 previously published data sets.Results:While no statistical significance was observed between the location and type of the NF1 mutation and glioma in the WUSM cohort, power calculations revealed that a sample size of 307 participants would be required to determine the predictive value of the position or type of the NF1 gene mutation. Combining our data set with 4 previously published data sets (n = 310), children with glioma were found to be more likely to harbor 5′-end gene mutations (OR = 2; p = 0.006). Moreover, while not clinically predictive due to insufficient sensitivity and specificity, this association with glioma was stronger for participants with 5′-end truncating (OR = 2.32; p = 0.005) or 5′-end nonsense (OR = 3.93; p = 0.005) mutations relative to those without glioma.Conclusions:Individuals with NF1 and glioma are more likely to harbor nonsense mutations in the 5′ end of the NF1 gene, suggesting that the NF1 mutation may be one predictive factor for glioma in this at-risk population.

scholarly journals Data Quality Task Group 2: Tests and Assertions

2018 ◽  
Vol 2 ◽  
pp. e25608 ◽  
Author(s):  
Lee Belbin ◽  
Arthur Chapman ◽  
John Wieczorek ◽  
Paula Zermoglio ◽  
Alex Thompson ◽  
...  
Keyword(s):  
Data Quality ◽  
Task Group ◽  
Global Biodiversity Information Facility ◽  
Unique Identifier ◽  
Project Completion ◽  
Darwin Core ◽  
Resource Type ◽  
Valuable Product ◽  
Group 2 ◽  
Validation Tests

Task Group 2 of the TDWG Data Quality Interest Group aims to provide a standard suite of tests and resulting assertions that can assist with filtering occurrence records for as many applications as possible. Currently ‘data aggregators’ such as the Global Biodiversity Information Facility (GBIF), the Atlas of Living Australia (ALA) and iDigBio run their own suite of tests over records received and report the results of these tests (the assertions): there is, however, no standard reporting mechanisms. We reasoned that the availability of an internationally agreed set of tests would encourage implementations by the aggregators, and at the data sources (museums, herbaria and others) so that issues could be detected and corrected early in the process. All the tests are limited to Darwin Core terms. The ~95 tests refined from over 250 in use around the world, were classified into four output types: validations, notifications, amendments and measures. Validations test one of more Darwin Core terms, for example, that dwc:decimalLatitude is in a valid range (i.e. between -90 and +90 inclusive). Notifications report a status that a user of the record should know about, for example, if there is a user-annotation associated with the record. Amendments are made to one or more Darwin Core terms when the information across the record can be improved, for example, if there is no value for dwc:scientificName, it can be filled in from a valid dwc:taxonID. Measures report values that may be useful for assessing the overall quality of a record, for example, the number of validation tests passed. Evaluation of the tests was complex and time-consuming, but the important parameters of each test have been consistently documented. Each test has a globally unique identifier, a label, an output type, a resource type, the Darwin Core terms used, a description, a dimension (from the Framework on Data Quality from TG1), an example, references, implementations (if any), test-prerequisites and notes. For each test, generic code is being written that should be easy for institutions to implement – be they aggregators or data custodians. A valuable product of the work of TG2 has been a set of general principles. One example is “Darwin Core terms are either: literal verbatim (e.g., dwc:verbatimLocality) and cannot be assumed capable of validation, open-ended (e.g., dwc:behavior) and cannot be assumed capable of validation, or bounded by an agreed vocabulary or extents, and therefore capable of validation (e.g., dwc:countryCode)”. Another is “criteria for including tests is that they are informative, relatively simple to implement, mandatory for amendments and have power in that they will not likely result in 0% or 100% of all record hits.” A third: “Do not ascribe precision where it is unknown.” GBIF, the ALA and iDigBio have committed to implementing the tests once they have been finalized. We are confident that many museums and herbaria will also implement the tests over time. We anticipate that demonstration code and a test dataset that will validate the code will be available on project completion.

scholarly journals Do Attentional Lapses Account for the Worst Performance Rule?

2021 ◽  
Vol 10 (1) ◽  
pp. 2
Author(s):  
Christoph Löffler ◽  
Gidon T. Frischkorn ◽  
Jan Rummel ◽  
Dirk Hagemann ◽  
Anna-Lena Schubert
Keyword(s):  
Time Distribution ◽  
Hierarchical Modeling ◽  
Reaction Times ◽  
Empirical Support ◽  
Response Time Distribution ◽  
Self Report ◽  
Task Completion ◽  
Published Data ◽  
Data Set ◽  
Attentional Lapses

The worst performance rule (WPR) describes the phenomenon that individuals’ slowest responses in a task are often more predictive of their intelligence than their fastest or average responses. To explain this phenomenon, it was previously suggested that occasional lapses of attention during task completion might be associated with particularly slow reaction times. Because less intelligent individuals should experience lapses of attention more frequently, reaction time distribution should be more heavily skewed for them than for more intelligent people. Consequently, the correlation between intelligence and reaction times should increase from the lowest to the highest quantile of the response time distribution. This attentional lapses account has some intuitive appeal, but has not yet been tested empirically. Using a hierarchical modeling approach, we investigated whether the WPR pattern would disappear when including different behavioral, self-report, and neural measurements of attentional lapses as predictors. In a sample of N = 85, we found that attentional lapses accounted for the WPR, but effect sizes of single covariates were mostly small to very small. We replicated these results in a reanalysis of a much larger previously published data set. Our findings render empirical support to the attentional lapses account of the WPR.

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