The influence of community recommendations on metadata completeness

Many communities use standard, structured documentation that is machine-readable, i.e. metadata, to make discovery, access, use, and understanding of scientific datasets possible. Organizations and communities have also developed recommendations for metadata content that is required or suggested for their data developers and users. These recommendations are typically specific to metadata representations (dialects) used by the community. By considering the conceptual content of the recommendations, quantitative analysis and comparison of the completeness of multiple metadata dialects becomes possible. This is a study of completeness of EML and CSDGM metadata records from DataONE in terms of the LTER recommendation for Completeness. The goal of the study is to quantitatively measure completeness of metadata records and to determine if metadata developed by LTER is more complete with respect to the recommendation than other collections in EML and in CSDGM. We conclude that the LTER records are broadly more complete than the other EML collections, but similar in completeness to the CSDGM collections.     

Completeness and validity in a national clinical thyroid cancer database: DATHYRCA

BackgroundAlthough a prospective national clinical thyroid cancer database (DATHYRCA) has been active in Denmark since January 1, 1996, no assessment of data quality has been performed. The purpose of the study was to evaluate completeness and data validity in the Danish national clinical thyroid cancer database: DATHYRCA.Study design and settingNational prospective cohort. Denmark; population 5.5 million. Completeness of case ascertainment was estimated by the independent case ascertainment method using three governmental registries as a reference. The reabstracted record method was used to appraise the validity. For validity assessment 100 cases were randomly selected from the DATHYRCA database; medical records were used as a reference.ResultThe database held 1934 cases of thyroid carcinoma and completeness of case ascertainment was estimated to 90.9%. Completeness of registration was around or above 90% in most instances. Perfect agreement on the diagnosis of thyroid carcinoma was found, both inter- and intra-observer, and κ values of selected variables showed overall good to excellent agreement.ConclusionIn a setup with public health insurance, personal identity numbers and extended governmental databases, it is possible to establish national clinical cancer databases with a satisfactory completeness and validity. The DATHYRCA database is considered reliable in terms of describing thyroid carcinoma at a national level.     

Completeness of chronic disease registration in general practice.

The completeness of chronic disease registration in four general practices was assessed by referring to the Hospital Activity Analysis. Overall, just over half (56%) of the 695 patients who had been discharged from hospital with a diagnosis of diabetes, cancer, myocardial infarction, epilepsy, hypertension, or thyroid disease were identified on the practice disease registers. Patients with diabetes were most likely to be identified (72%), and those who had had a myocardial infarct least likely (43%). If the standard of registration is to be improved general practitioners must be convinced of its value. The Hospital Activity Analysis might be used widely to audit and improve practice registers.     

QUALITY OF THE TRIASSIC–JURASSIC BIVALVE FOSSIL RECORD IN NORTHWEST EUROPE

Abstract: The quality of the Triassic–Jurassic bivalve fossil record in northwest Europe has been measured using the Simple Completeness Metric (SCM). The SCM has been applied to the fossil record of total bivalve diversity and to the records of different ecological guilds. The Westbury and Lilstock Formations record high SCM values for most ecological groups. The ‘Pre‐Planorbis Beds’ of the lower Lias Group, however, witness a precipitous decline in the completeness of most guilds and emigration of taxa due to localized marine anoxia is a likely cause. Neither variation in lithofacies, shell mineralogy, sedimentary rock outcrop area, nor sequence architecture can convincingly explain the observed patterns of completeness. Our SCM data reveal that the Early Jurassic fossil record of infaunal suspension‐feeding bivalves is significantly poorer than that of epifaunal bivalves. Any differences in the apparent Rhaetian extinction rates between these two guilds should therefore be viewed with caution. Analyses of selectivity during the Late Triassic mass extinction based on studies of global databases appear robust in light of our SCM data. Nevertheless, future investigations of the Triassic–Jurassic benthic marine ecosystem undertaken at a finer‐resolution, may need to account for the poor quality of the Early Jurassic fossil records of certain ecological guilds, such as the infaunal suspension‐feeding taxa.     

Automated identification of acute hepatitis B using electronic medical record data to facilitate public health surveillance

Background

Automatic identification of notifiable diseases from electronic medical records can potentially improve the timeliness and completeness of public health surveillance. We describe the development and implementation of an algorithm for prospective surveillance of patients with acute hepatitis B using electronic medical record data.

Methods

Initial algorithms were created by adapting Centers for Disease Control and Prevention diagnostic criteria for acute hepatitis B into electronic terms. The algorithms were tested by applying them to ambulatory electronic medical record data spanning 1990 to May 2006. A physician reviewer classified each case identified as acute or chronic infection. Additional criteria were added to algorithms in serial fashion to improve accuracy. The best algorithm was validated by applying it to prospective electronic medical record data from June 2006 through April 2008. Completeness of case capture was assessed by comparison with state health department records.

Findings

A final algorithm including a positive hepatitis B specific test, elevated transaminases and bilirubin, absence of prior positive hepatitis B tests, and absence of an ICD9 code for chronic hepatitis B identified 112/113 patients with acute hepatitis B (sensitivity 97.4%, 95% confidence interval 94–100%; specificity 93.8%, 95% confidence interval 87–100%). Application of this algorithm to prospective electronic medical record data identified 8 cases without false positives. These included 4 patients that had not been reported to the health department. There were no known cases of acute hepatitis B missed by the algorithm.

Conclusions

An algorithm using codified electronic medical record data can reliably detect acute hepatitis B. The completeness of public health surveillance may be improved by automatically identifying notifiable diseases from electronic medical record data.     

The fossil record of ichthyosaurs,completeness metrics and sampling biases

Ichthyosaurs were highly successful marine reptiles with an abundant and well‐studied fossil record. However, their occurrences through geological time and space are sporadic, and it is important to understand whether times of apparent species richness and rarity are real or the result of sampling bias. Here, we explore the skeletal completeness of 351 dated and identified ichthyosaur specimens, belonging to all 102 species, the first time that such a study has been carried out on vertebrates from the marine realm. No correlations were found between time series of different skeletal metrics and ichthyosaur diversity. There is a significant geographical variation in completeness, with the well‐studied northern hemisphere producing fossils of much higher quality than the southern hemisphere. Medium‐sized ichthyosaurs are significantly more complete than small or large taxa: the incompleteness of small specimens was expected, but it was a surprise that larger specimens were also relatively incomplete. Completeness varies greatly between facies, with fine‐grained, siliciclastic sediments preserving the most complete specimens. These findings may explain why the ichthyosaur diversity record is low at times, corresponding to facies of poor preservation potential, such as in the Early Cretaceous. Unexpectedly, we find a strong negative correlation between skeletal completeness and sea level, meaning the most complete specimens occurred at times of global low sea level, and vice versa. Completeness metrics, however, do not replicate the sampling signal and have limited use as a global‐scale sampling proxy.     

Quantifying the completeness of the bat fossil record

Bats (Chiroptera) are one of the most successful extant mammalian orders, uniquely capable of powered flight and laryngeal echolocation. The timing and evidence for evolution of their novel adaptations have been difficult to ascertain from the fossil record due to chronological gaps and the fragmentary nature of most fossil bat material. Here, we quantify the quality of the bat fossil record using skeletal and character completeness metrics, which respectively document for each taxon what proportion of a complete skeleton is preserved, and the proportion of phylogenetic characters that can be scored. Completeness scores were collected for 441 valid fossil bat species in 167 genera from the Eocene to the Pleistocene. All metrics record similar temporal patterns: peak completeness in the Lutetian stage reflects the presence of Lagerstätten, while subsequent stages have very low completeness, except an Aquitanian high and a Pleistocene peak in skeletal completeness. Bat completeness is not correlated with intensity of sampling through geological time but has a weak negative correlation with publication date. There is no correlation between taxonomic richness and completeness, as the bat record predominately consists of diagnostic but isolated teeth. Consequently, bat skeletal completeness is the lowest of any previously assessed tetrapod group, but character completeness is similar to parareptiles and birds. Bats have significantly higher character completeness in the northern hemisphere, probably due to heightened historical interest and presence of Lagerstätten. Taxa derived from caves are more complete than those from fluviolacustrine and marine deposits, but do not preserve highly complete specimens.     

Accuracy of diagnostic content of hospital activity analysis in infectious diseases.

Hospital activity analysis (HAA) was used to identify 2151 patients in whom the diagnostic code fell within the infectious disease categories of the International Classification of Disease. The clinical notes of these patients were examined by a doctor and in 414 (19.2%) the diagnostic coding was incorrect. Diarrhoea and viral infections were miscoded most often. The possibility of inaccuracy must be considered when HAA aggregated data are used for planning purposes. Accuracy could be improved if clinicians routinely completed the diagnostic sections of the HAA form.     

A Revision of the Genus Androsace L. in China (Cont.)

A revision of the Chinese species of Androsace updates our knowledge of the genus by providing a brief historical survey, character analysis, discussion on generic relationships and geographical distribution, and a key to species currently recognized. For the sake of completeness, the key is supplemented by an enumeration, and a record of the known distribution of each species. Furthermore, some specimen citations and additional notes on species previously very incompletly known are also included. Seven new species and two infraspecific taxa are described.     

The mosasaur fossil record through the lens of fossil completeness

The quality of the fossil record affects our understanding of macroevolutionary patterns. Palaeodiversity is filtered through geological and human processes; efforts to correct for these biases are part of a debate concerning the role of sampling proxies and standardization in biodiversity models. We analyse the fossil record of mosasaurs in terms of fossil completeness as a measure of fossil quality, using three novel, correlating metrics of fossil completeness and 4083 specimens. A new qualitative measure of character completeness (QCM) correlates with the phylogenetic character completeness metric. Mean completeness by species decreases with specimen count; average completeness by substage varies significantly. Mean specimen completeness is higher for species‐named fossils than those identified to genus and family. We consider the effect of tooth‐only specimens. Importantly, we find that completeness of species does not correlate with completeness of specimens. Completeness varies by palaeogeography: North American specimens show higher completeness than those from Eurasia and Gondwana. These metrics can be used to identify exceptional preservation; specimen completeness varies significantly by both formation and lithology. The Belgian Ciply Formation displays the highest completeness; clay lithologies show higher completeness values. Neither species diversity nor sea level correlates significantly with fossil completeness. A generalized least squares (GLS) analysis using multiple variables agrees with this result, but reveals two variables with significant predictive value for modelling averaged diversity: sea level, and mosasaur and plesiosaur‐bearing formations (the latter is redundant with diversity). Mosasaur completeness is not driven by sea level, nor does completeness limit the mosasaur diversity signal.     

Accuracy and Completeness of Drug Information in Wikipedia: A Comparison with Standard Textbooks of Pharmacology

The online resource Wikipedia is increasingly used by students for knowledge acquisition and learning. However, the lack of a formal editorial review and the heterogeneous expertise of contributors often results in skepticism by educators whether Wikipedia should be recommended to students as an information source. In this study we systematically analyzed the accuracy and completeness of drug information in the German and English language versions of Wikipedia in comparison to standard textbooks of pharmacology. In addition, references, revision history and readability were evaluated. Analysis of readability was performed using the Amstad readability index and the Erste Wiener Sachtextformel. The data on indication, mechanism of action, pharmacokinetics, adverse effects and contraindications for 100 curricular drugs were retrieved from standard German textbooks of general pharmacology and compared with the corresponding articles in the German language version of Wikipedia. Quantitative analysis revealed that accuracy of drug information in Wikipedia was 99.7%±0.2% when compared to the textbook data. The overall completeness of drug information in Wikipedia was 83.8±1.5% (p<0.001). Completeness varied in-between categories, and was lowest in the category “pharmacokinetics” (68.0%±4.2%; p<0.001) and highest in the category “indication” (91.3%±2.0%) when compared to the textbook data overlap. Similar results were obtained for the English language version of Wikipedia. Of the drug information missing in Wikipedia, 62.5% was rated as didactically non-relevant in a qualitative re-evaluation study. Drug articles in Wikipedia had an average of 14.6±1.6 references and 262.8±37.4 edits performed by 142.7±17.6 editors. Both Wikipedia and textbooks samples had comparable, low readability. Our study suggests that Wikipedia is an accurate and comprehensive source of drug-related information for undergraduate medical education.     

Community Completeness: Linking Local and Dark Diversity within the Species Pool Concept

Biodiversity of ecological communities has been examined widely. However, comparisons of observed species richness are limited because they fail to reveal what part of the differences are caused by natural variation in species pool size and what part is due to dark diversity – the absence of suitable species from a species pool. In other words, conventional biodiversity inventories do not convey information about how complete local plant communities are. We therefore propose the community completeness concept – a new perspective on the species pool framework. In order to ascertain community completeness, we need to estimate the extent of dark diversity, for which several methods are under development. We recommend the Community Completeness Index based on a log-ratio (or logistic) expression: ln(observed richness/dark diversity). This metric offers statistical advantages over other methods (e.g. the proportion of observed richness from the species pool). We discuss how community completeness can be related to long-term and successional community stability, landscape properties and disturbance patterns as well as to a variety of biotic interactions within and among trophic levels. The community completeness concept is related to but distinctive from the alpha-beta-gamma diversity approach and the community saturation phenomenon. The Community Completeness Index is a valuable metric for comparing biodiversity of different ecosystems for nature conservation. It can be used to measure the success of ecological restoration and vulnerability to invasion by alien species. In summary, community completeness is an interface between observed local observed species richness and dark diversity, which can be useful both in theoretical and applied biodiversity research.     

Comparison of patient questionnaire,medical record,and audio tape in assessment of health promotion in general practice consultations.

OBJECTIVE--To determine what proportion of health promotion activities reported by the patient is recorded in the general practice notes and to compare these methods of assessing health promotion with audio tape analysis. DESIGN--Secondary analysis of data obtained in a controlled trial of differing appointment lengths. After each consultation the medical record was examined and the patient invited to completed a questionnaire. A subsample of consultations was audio taped. SETTING--Nottinghamshire. SUBJECTS--16 general practitioners from 10 practices. This report includes 3324 consultations with patients aged > or = 17, with data on measurement of blood pressure and advice about smoking and alcohol. RESULTS--Data from questionnaire and medical notes were available for 2281 consultations. Advice on smoking was recorded in the notes in 30.9% of cases in which a patient reported it (for alcohol and measurement of blood pressure, 44.4% and 82.7% of cases respectively). In 516 cases analysis of audio tape and review of records was performed. Advice on smoking was recorded in the patient''s notes in 28.6% of cases in which it was detected on audio tape (for alcohol, 31.1% of cases). In 335 consultations data from audio tape and questionnaire were available. Advice on smoking was reported by patients in 73.9% of cases in which it was detected on audio tape (for alcohol, 75.0% of cases). CONCLUSIONS--Review of the medical record is a reasonably accurate method of assessing measurement of blood pressure in the consultation but would lead to significant underestimation of advice about smoking and alcohol.     

Computer-based Hypertension Clinic Records: A Co-operative Study

A computer-based medical record system has been developed to help with research into hypertension and the management of patients with hypertension. Standard medical records are replaced by data collection forms and case notes printed by the computer. A computer-generated document for recording information at follow-up visits contains an up-to-date summary of the important clinical features with warnings of risk factors. A blood-pressure graph and a letter for the general practitioner are produced on request. The system has been used in three clinics for two years and is being tested in general practice. Information on 900 newly-referred patients has been recorded and at present data on 30 to 40 new patients and 160 follow-up visits are added each month.     

GPAC: benchmarking the sensitivity of genome informatics analysis to genome annotation completeness

In view of the recent explosion in genome sequence data, and the 200 or more complete genome sequences currently available, the importance of genome-scale bioinformatics analysis is increasing rapidly. However, computational genome informatics analyses often lack a statistical assessment of their sensitivity to the completeness of the functional annotation. Therefore, a pre-analysis method to automatically validate the sensitivity of computational genome analyses with regard to genome annotation completeness is useful for this purpose. In this report we developed the Gene Prediction Accuracy Classification (GPAC) test, which provides statistical evidence of sensitivity by repeating the same analysis for five different gene groups (classified according to annotation accuracy level), and for randomly sampled gene groups, with the same number of genes as each of the five classified groups. Variability in these results is then assessed, and if the results vary significantly with different data subsets, the analysis is considered "sensitive" to annotation completeness, and careful selection of data is advised prior to the actual in silico analysis. The GPAC test has been applied to the analyses of Sakai et al., 2001, and Ohno et al., 2001, and it revealed that the analysis of Ohno et al. was more sensitive to annotation completeness. It showed that GPAC could be employed to ascertain the sensitivity of an analysis. The GPAC bendhmarking software is freely available in the latest G-language Genome Analysis Environment package, at http://www.g-language.org/.     

Paleontological completeness of the record of lower tertiary mollusks,U.S. Gulf and Atlantic coastal plains: Implications for phylogenetic studies

Choice of method in phylogenetic analysis should involve some consideration of the quality or completeness of the available fossil record. If it is poor, cladistic methods are preferable; if it is good, stratophenetic methods may be valid. A concept of paleontological completeness, defined herein, is useful for judging the quality of a given fossil record. This paper considers eight possible measures of paleontological completeness, and evaluates their value as phylogenetically useful estimates of the quality of the fossil record. Of the eight measures, Sadler‐Schindel type analysis of stratigraphic completeness and analysis of geographic ranges appear to be the most useful and reliable. The remaining six are useful only as rough approximations of the quality of the record, or as supporting evidence for conclusions based on other methods. Use of these eight measures on the lower Tertiary molluscan record of the U.S. Gulf and Atlantic coastal plains indicates that this record is approximately 30–50% complete. This is probably not complete enough to trust purely stratophenetic approaches to phylogenetic analysis, but is too complete to ignore the record in favor of a purely atemporal, cladistic approach. The concept of paleontological completeness may be useful in estimating the quality of this and other fossil records for non‐phylogenetic purposes, such as studies of evolutionary rates and diversity and extinction patterns.     

Randomised controlled trial of computer-held medical records in hypertensive patients.

A total of 278 hypertensive patients in three clinics were randomly allocated to have their medical records held in a computer system (136) or on standard hospital notes (142). For the computer system the doctor completed a structured input form, and the information on symptoms, physical findings, and diagnoses was more complete than that in the standard notes. This resulted in certain symptoms and risk factors being recognised more often when the computer system was used. The hypertension clinics'' routines were not disrupted by the introduction of a computer-held system, and follow-up consultation times were not affected by the type of records kept, although the first consultation took eight minutes longer when computer documents were completed. The patients remained in the trial for one year and clinical management was assessed from blood pressure control, drop-out rates, and the frequency of performing investigations. These estimates of management showed no significant difference between the two groups, but the attempt to tailor the computer system to help management made the system acceptable to the doctors using it. The computer system continues to be used and is providing data for research into hypertension.     

LIVE BIRTH CERTIFICATES—Evaluation of Medical and Health Data in California

In a study of 1,609 single live births occurring in San Francisco County, the information on the birth certificate was compared with that on the hospital record to determine completeness and accuracy of the items reported on the certificate.Items such as color or race of mother, age of mother, birth weight and birth length of child were well recorded on the certificate and agreed with information found in the hospital record.Medical conditions were grossly underreported on the birth certificate. Conditions relating to the mother were more frequently recorded than those relating to the infant, but the birth certificates recorded less than one-fifth of all medical conditions of both mother and infant that were entered in the hospital records.Methods suggested for improving the quality of maternal and newborn morbidity information include revision of the medical section of the present certificates of live birth and fetal death and use of a precoded hospital record.     

Completeness of NOEs in protein structures: A statistical analysis of NMR data

The completeness of experimentally observed NOE restraints of a set of 97 NMR protein structures deposited in the PDB has been assessed. Completeness is defined as the ratio of the number of experimentally observed NOEs and the number of 'expected NOEs'. A practical definition of 'expected NOEs' based on inter-proton distances in the structures up to a given cut-off distance is proposed. The average completeness for the set of 97 structures is 68, 48, and 26% up to 3, 4, and 5 Å cut-off distances, respectively. For recent state-of-the-art structures these numbers are approximately 90, 75, and 45%. Almost 20% of the observed NOEs are between atoms that are further than 5 Å apart in the final structures. The completeness is independent of the relative surface accessibility and does not depend strongly on residue type, secondary structure or local precision, although the number of observed NOEs in these classes varies considerably. The completeness of NOE restraints is a useful quality criterion in the course of structure refinement. The completeness per residue is more informative than the number of NOEs per residue, which makes it a useful tool to assess the quality of the NMR data set in relation to the resulting structures.