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PubMedDate not supplied

Integrating content-based retrieval in a medical image reference database.

Image reference databases (IRDBs) are a recurrent research topic in medical imaging. Most IRDBs are designed to help experienced physicians in diagnostic tasks and require that users have prior extensive knowledge of the field for their use to be fruitful. Therefore, the educational potential of such image collections cannot be exploited thoroughly. In this paper we propose an image-indexing method to extend the functionalities of an existing medical IRDB and allow for its use in educational applications, as well as in computer-assisted diagnosis. Our method, based on the Kahrunen-Leève transform, has been used to develop a content-based search engine for tomographic image databases on which we are presently experimenting and which we aim to integrate into a working radiological IRDB installed at the University of Florence. Results achieved in our preliminary tests are also reported.

Brain↗

PubMed2006

Comparative evaluation of local and international reference databases for forearm densitometry: different impacts on diagnostic decisions.

Reference databases play a key role in the management of osteoporosis. The aim of this preliminary study was to compare the diagnostic consequences of using either an international or a local reference database in peripheral densitometry. For this purpose, standard curves for bone mineral density (measured by dual-energy X-ray absorptiometry at the distal and proximal forearm) were generated for healthy Hungarian men and women. In total, 303 healthy volunteers of both sexes (age range: 20-94 yr) were recruited from four osteoporosis centers. Subjects with medical conditions or taking medication affecting the bone metabolism were excluded. Bone densitometry was performed with pDEXA (Norland-Stratec, Fort Atkinson, WI) devices in each center after cross-calibration of the machines. The precision error of the forearm measurement was also determined (<1% in vitro, and 1.2-2.5% in vivo). In females, the peak forearm density was detected in the 30-39-yr group. The density decreased by 8% per 5 yr in early postmenopausal females, and by 10% per 10 yr in late postmenopausal females. In males, the highest bone mineral density was found in the 30-39-yr group for the distal forearm, but 1 decade later for the proximal site. Subsequently, a 5% decrease in density occurred per 10 yr, except in the 8th decade, in which a 20% decrease was demonstrated. One thousand four hundred thirty-four patients with suspected osteoporosis were classified according to the forearm density T-scores using both the new Hungarian reference database and the international database provided by the manufacturer. Comparison of the results measured at the distal forearm with the two different databases led to similar outcomes. However, at the proximal site, one fifth of the female patients were reclassified from the low-density group to the normal group using the domestic normative database. An opposite difference was observed for the males: use of the Hungarian reference data resulted in 40% more men being categorized in the low-density group than when the international normal database was applied. Our results suggest that not only geographic differences, but also the reference database used, can influence the prevalence of the diagnosis of osteoporosis. Further data are currently being collected to increase the statistical power of the study.

Absorptiometry, Photon↗

PubMed2003

Establishment and evaluation of bone mineral density reference databases appropriate for diagnosis and evaluation of osteoporosis in Chinese women.

This study was designed to establish Bone Mineral Density (BMD) Reference Databases for multiple skeletal sites appropriate for the diagnosis and evaluation of osteoporosis (OP) in Chinese women. We recruited 2702 healthy Chinese women, 5-96 years of age, for BMD assessment. BMD values at multiple skeletal sites including anteroposterior (AP) and lateral (Lat) lumbar spine, hip, and forearm were measured by dual-energy X-ray absorptiometry (DXA) using a QDR 4500A device; results were analyzed according to age group using eight regression models. BMD Reference Databases (CWD) were established according to the best regression equation and compared with Hologic reference databases for "Oriental Women" (OWD). Results indicated that the cubic regression model was superior to the quadratic, linear, logarithmic, and exponential regression models, etc. for our purpose, with a determinate coefficient ( R(2)) of 0.363-0.650 ( P = 0.000). We included 1636 female patients, aged 35-86 years, in our tests. In comparison with Hologic Reference Databases, the mean detection rate of OP in the newly established BMD Reference Databases for Chinese Women (CWD) was 16.0% +/- 2.68% lower (range, 13.7%-20.5%) at the AP spine, 16.8% +/- 11.0% lower (range, 3.5%-32.8%) at the Lat spine (except for L4), 18.7% +/- 4.6% lower (range, 12.6%-24.2%) at the hip, and 14.3% +/- 6.9% higher (range, 4.7%-24.3%) at the forearm. The difference in detection rates for OP was significant between the two reference databases ( P = 0.000), which was consistent with the differences in peak BMD values and the biological variability between them. Based upon our data, we confirmed that the Hologic BMD Reference Databases for Oriental Women (OWD) were not suitable for the diagnosis of OP in Chinese women; the BMD Reference Databases for Chinese Women (CWD) established in this study would provide reliable diagnostic standards for detection of OP in the women of South China.

Adolescent↗

PubMed2006

Thallium-201 myocardial SPECT in left bundle branch block: diagnosis of myocardial ischemia with a disease-specific reference database.

BACKGROUND: The aim of this study was to assess the value of a myocardial perfusion single photon emission computed tomography (SPECT) reference file for patients with left bundle branch block (LBBB). METHODS AND RESULTS: Tl-201 stress-redistribution myocardial perfusion SPECT studies of patients with complete, permanent LBBB were reviewed retrospectively. To develop a reference database, 18 patients with a low likelihood of coronary artery disease (CAD) were selected. Left ventricular regional average and standard deviation (SD) values of the reference file images were calculated. The diagnostic performance was tested on perfusion images of 49 patients with LBBB, undergoing both scintigraphic and coronary angiographic evaluation, and was compared with a commercial quantitative analysis system using a general reference database. The LBBB reference file performed significantly better in detecting epicardial CAD than did the general reference database (receiver operating characteristic area under the curve 0.835 +/- 0.06 vs 0.580 +/- 0.08, p < .01). Disease localization also was improved significantly in the territory of the left anterior descending and of the right coronary arteries. CONCLUSIONS: The use of a reference file of patients with LBBB and a low likelihood of CAD aids the detection and the localization of myocardial ischemia on Tl-201 myocardial SPECT images of this patient group.

Bundle-Branch Block↗

PubMed2006

Human protein reference database--2006 update.

Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein-protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (http://www.genprot.org), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data.

Databases, Protein↗

PubMed2003

[Quantitative bone ultrasound: impact of the application of two different reference databases to a population of 5.195 postmenopausal women].

BACKGROUND AND OBJECTIVE: The application of different reference databases to calculate the T-score values of the bone mineral density (BMD) using dual-energy X-ray absorptiometry techniques may result in variations in the number of subjects diagnosed with osteoporosis. There are no similar dataregarding quantitative bone ultrasound. To compare the results of the application of two different reference databases: the manufacturer's normal range and the Spanish normative data. PATIENTS AND METHOD: Evaluation of the heel ultrasound with a Sahara sonometer in 5,195 women >= 65 year-old who were attended for any reason in primary care centers. RESULTS: Bone ultrasound estimated BMD T-score mean values were 1.27 and 1.29 when applying the manufacturer's normal range and the Spanish normative data, respectively (p = 0.001). Percentages of women with a T-score below 2.50 standard deviations were 12.7% and 12.8% respectively. CONCLUSIONS: The application of these two reference databases shows very similar results which, although statistically different, are clinically irrelevant.

Age Factors↗

PubMed2005

Bioinformatics analyses of circular dichroism protein reference databases.

MOTIVATION: Circular dichroism (CD) spectroscopy has become established as a key method for determining the secondary structure contents of proteins which has had a significant impact on molecular biology. Many excellent mathematical protocols have been developed for this purpose and their quality is above question. However, reference database sets of proteins, with CD spectra matched to secondary structure components derived from X-ray structures, provide the key resource for this task. These databases were created many years ago, before most CD spectrophotometers became standardized and before it was commonplace to validate X-ray structures prior to publication. The analyses presented here were undertaken to investigate the overall quality of these reference databases in light of their extensive usage in determining protein secondary structure content from CD spectra. RESULTS: The analyses show that there are a number of significant problems associated with the CD reference database sets in current use. There are disparities between CD spectra for the same protein collected by different groups. These include differences in magnitudes, peak positions or both. However, many current reference sets are now amalgamations of spectra from these groups, introducing inconsistencies that can lead to inaccuracies in the determination of secondary structure components from the CD spectra. A number of the X-ray structures used fall short on the validation criteria now employed as standard for structure determination. Many have substantial percentages of residues in the disallowed regions of the Ramachandran plot. Hence their calculated secondary structure components, used as a foundation for the reference databases, are likely to be in error. Additionally, the coverage of secondary structure space in the reference datasets is poorly correlated to the secondary structure components found in the Protein Data Bank. A conclusion is that a new reference CD database with cross-correlated, machine-independent CD spectra and validated X-ray structures that cover more secondary structure components, including diverse protein folds, is now needed. However, that reasonably accurate values for the secondary structure content of proteins can be determined from spectra is a testament to CD spectroscopy being a very powerful technique.

Circular Dichroism↗

PubMed2006

[Orthorad--the online reference database of skeletal plain film radiography].

PURPOSE: It is evident that there is a growing need for Internet-based reference databases for reasons of practicability and due to the increasing use of reporting on digital workstations. The main advantages of online databases are expected with respect to plain film radiography and cross-sectional imaging. A reference database of skeletal plain film radiography was to be created using the Orthorad program. MATERIALS AND METHODS: The most important standard settings and special images of young and healthy adults in plain film radiography were collected over one year. All samples were approved for the Orthorad database by a board qualified radiologist. Based on the workflows of radiographers and radiologists, the records were organized by body part ( http://www.idr.med.uni-erlangen.de/orthorad/orthorad.htm ). This logical data structure will ensure that the tool serves as a source of information in two ways: On the one hand, the radiographer can access information on positioning, tube voltage and cassette format. On the other hand, the radiologist receives important knowledge regarding X-ray anatomy, reference data regarding the human skeleton, and information about the correct reporting for an image. RESULTS AND CONCLUSION: Orthorad is used as an online reference database for traumatologic plain film radiography to support radiographers and radiologists in their daily working routines. To date, user feedback has been positive.

Adult↗

PubMed2025

Persistent gaps and errors in reference databases impede ecologically meaningful taxonomy assignments in 18S rRNA studies: a case study of terrestrial and marine nematodes.

In metabarcoding studies, Linnaean taxonomy assignments of Operational Taxonomic Units (OTUs) or Amplicon Sequence Variants (ASVs) underpin many downstream bioinformatics analyses and ecological interpretations of environmental DNA (eDNA) datasets. However, public molecular databases (i.e., SILVA, EUKARYOME, BOLD) for most microbial metazoan phyla (nematodes, tardigrades, kinorhynchs, etc.) are sparsely populated, negatively impacting our ability to assign ecologically meaningful taxonomy to these understudied groups. Additionally, the choice of bioinformatics parameters and computational algorithms can further impact the accuracy of eDNA taxonomy assignments. Here, we use two in-silico datasets to show that taxonomy assignments using the 18S rRNA gene can be dramatically improved by curating Linnaean taxonomy strings associated with each reference sequence and closing phylogenetic gaps by improving taxon sampling. Using free-living nematodes as a case study, we applied two commonly used taxonomy assignment algorithms (BLAST+ and the QIIME2 Naïve Bayes classifier) across six iterations of the SILVA 138 reference database to evaluate the precision and accuracy of taxonomy assignments. The BLAST+ top hit with a 90% sequence similarity cutoff often returned the highest percentage of correctly assigned taxonomy at the genus level, and the QIIME2 Naïve Bayes classifier performed similarly well when paired with a reference database containing corrected taxonomy strings. Our results highlight the urgent need for phylogenetically-informed expansions of public reference databases (encompassing both genomes and common gene markers), focused on poorly sampled lineages which are now robustly recovered via eDNA metabarcoding approaches. Additional taxonomy curation efforts should be applied to popular reference databases such as SILVA, and taxon sampling could be rapidly improved by more frequent incorporation of newly published GenBank sequences linked to genus and/or species level identifications.

18S rRNA metabarcoding↗

PubMed2002

To establish the normal bone mineral density reference database for the Singapore male.

INTRODUCTION: The objective of this study was to establish the normal bone mineral density (BMD) reference curve for the Asian Singapore male. MATERIALS AND METHODS: Three hundred and eighty-three male subjects were enrolled; comprising of 309 Chinese, 44 Malays and 30 Indians resident in Singapore. Bone mineral density was measured at the lumbar spine and left hip using a Hologic QDR 4500 Elite dual-energy X-ray absorptiometry (DXA) scanner. RESULTS: The mean peak BMD for the average lumbar spine and the neck of femur was 1.006 g/cm2 and 0.97 g/cm2, respectively. The mean peak BMD was taken at the 20 to 24 years age group at both the hip and spine based on data distribution for the various age groups. The BMD corresponding to -2.5 standard deviations from the peak adult value was 0.719 g/cm2 for the average lumbar spine and 0.655 g/cm2 for the neck of femur. CONCLUSION: This Asian male BMD reference database, which is 10% and 5% lower than corresponding values from the Caucasian reference database, allows for more accurate diagnosis of osteoporosis in Asian males.

Absorptiometry, Photon↗

PubMed2026

Up-to-date, and taxonomy-curated mcrA reference databases for methanogen community profiling.

The methyl-coenzyme M reductase subunit alpha gene (mcrA) is an important phylogenetic marker for high throughput ecological profiling of methanogenic archaea, central to industrial biological methane production and greenhouse gas emissions. Yet, dedicated reference databases predate current relevant NCBI sequence accumulation and archaeal taxonomic revision. We present three updated mcrA reference databases: (i) one derived from NCBI-catalogued methanogen genomes (1572 sequences); (ii) a database built by expansion of a previously published reference dataset, leveraging the NCBI nucleotide collection (27,942 sequences); (iii) a curated-taxonomy version of the latter. The updated amplicon databases provide a ∼ 3.5-fold sequence richness expansion, extend genus-level richness from 31 to 83 taxa, more than 4-fold species-level richness, and incorporate novel lineages compared with the previous reference dataset (e.g. Thermoplasmatota-encompassed). All databases were formatted to support analysis with relevant contemporary software pipelines and packages. Overall, the generated databases facilitate a highly improved characterization of methanogen diversity and ecology.

Archaea↗

PubMed2000

The Spanish National Reference Database for Ionizing Radiations (BANDRRI)

The Spanish National Reference Database for Ionizing Radiations (BANDRRI) is being implemented by a reasearch team in the frame of a joint project between CIEMAT (Unidad de Metrologia de Radiaciones Ionizantes and Direccion de Informatica) and the Universidad Nacional de Educacion a Distancia (UNED, Departamento de Mecanica y Departamento de Fisica de Materiales). This paper presents the main objectives of BANDRRI, its dynamic and relational data base structure, interactive Web accessibility and its main radionuclide-related contents at this moment.

Journal Article↗

PubMed1998

Medical reference databases used by Army primary care physicians in field environments.

A cross-sectional survey of U.S. Army primary care physicians was done to answer two questions: (1) which medical reference materials are Army primary care physicians currently using when deployed to a field environment? and (2) what would they like to have for medical reference in a field environment? Of 740 surveys delivered to their intended recipients, 445 (60%) were returned. Currently, 96% of primary care physicians use books, 37% use journals, and 11% use computer software in their medical reference database. Of those now using books, 72% were satisfied with them, compared with 61% of those using journals and 45% of those using software. The most common book used was the Merck Manual. The most important characteristics desired in a field medical database were broad coverage, ease of use, and light weight. The majority of respondents believe that a good medial reference database is important but that current medical databases limit the quality of the medicine they practice in the field.

Attitude of Health Personnel↗

PubMed2002

SubtiList: the reference database for the Bacillus subtilis genome.

SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome project, SubtiList provides a curated dataset of DNA and protein sequences, combined with the relevant annotations and functional assignments. Information about gene functions and products is continuously updated by linking relevant bibliographic references. Recently, sequence corrections arising from both systematic verifications and submissions by individual scientists were included in the reference genome sequence. SubtiList is based on a generic relational data schema and a World Wide Web interface developed for the handling of bacterial genomes, called GenoList. The World Wide Web interface was designed to allow users to easily browse through genome data and retrieve information according to common biological queries. SubtiList also provides more elaborate tools, such as pattern searching, which are tightly connected to the overall browsing system. SubtiList is accessible at http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at http://genolist.pasteur.fr/.

Bacillus subtilis↗

PubMed1998

Comparison and cross-calibration of DXA systems: ODX-240 and Sophos L-XRA versus Hologic QDR-4500, for spinal bone mineral measurement. Translation of a reference database.

Replacement of dual-energy X-ray densitometry equipment may be necessary in time as a result of upgrading systems or new equipment. The lack of standardization in bone mineral density (BMD) measurements is known. Standardization efforts have been made for several years by the European Union under its organization COMAC-BME (Comité d'Actions Concertés-BioMedical Engineering) and by the International Committee for Standards in Bone Measurement. Cross-calibration is generally considered to be the result of linear regression between the measurements obtained with two densitometers. A major disadvantage of the regression method is the noncompatibility of the two formulae of calibration (Y versus X and X versus Y). In this study we considered cross-calibration in terms of a structural model that produced circular equations when, for example, three systems were cross-calibrated. Cross-calibration in this study was calculated from the measurement of the lumbar BMD of a population of 204 patients, with Hologic QDR-4500, ODX-240 and Sophos L-XRA systems. In vitro accuracy and short-term reproducibility of the three systems were studied. Using the structural calibration equation we transformed a reference database for L2-4 BMD obtained from a population of 983 French females, aged 11-47 years, on an ODX-240 to a reference database for a Hologic QDR-4500. A new young adult reference was obtained and consequently a new evaluation of the T-score for the Hologic QDR-4500.

Absorptiometry, Photon↗

PubMedDate not supplied

Integration of a multimedia teaching and reference database in a PACS environment.

In one radiology department, a computerized authoring and editing environment was developed and integrated with the picture archiving and communication systems (PACS) for creation of image-based electronic teaching files to replace a collection of printed film images. This multimedia database and authoring environment allows physicians to create reference databases for teaching and research directly from clinical cases being reviewed on PACS diagnostic workstations. The database engine allows users to generate stand-alone CD-ROMs (compact disks, read-only memory) and World Wide Web-based teaching files. The system is fully compliant with the Digital Imaging and Communications in Medicine (DICOM) standard and supports a large number of standard multimedia image file formats. The focus of the development was on convenience and ease of use of a generic system adaptable to all users. The software was integrated on the PACS workstations to allow users to add new cases to the database at any time and anywhere in the department. A pilot system was implemented in clinical operation, with a central server and several client units.

CD-ROM↗

PubMed2001

Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.

The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.

Databases, Factual↗

PubMed2025

PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2.

SUMMARY: PICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference genomes. We have constructed an updated database for PICRUSt2 that has substantially increased the number of bacterial (19,493 to 26,868) and archaeal (406 to 1,002) genomes as well as the number of functional annotations present. The previous PICRUSt2 database relied on many timely and computationally intensive manual processes that made it difficult to update. We constructed a new streamlined process to allow regular upgrades to the PICRUSt2 database on an ongoing basis, and used this process to create a new database, PICRUSt2-SC (Sugar-Coated). Additionally, we have shown that this updated database contains genomes that more closely match study sequences from a range of different environments. The genomes contained in the database therefore better represent these environments and this leads to an improvement in the predicted functional annotations obtained from PICRUSt2. AVAILABILITY AND IMPLEMENTATION: PICRUSt2 source code is freely available at https://github.com/picrust/picrust2 and at https://anaconda.org/bioconda/picrust2. The latest version of PICRUSt2 at the time of writing is also archived: https://doi.org/10.5281/zenodo.15119781. The PICRUSt2-SC database comes pre-installed with PICRUSt2 from version 2.6.0 onwards. Step-by-step instructions for making the updated database are at https://github.com/picrust/picrust2/wiki/Updating-the-PICRUSt2-database. All code used for the analyses and figures in this manuscript is at https://github.com/R-Wright-1/PICRUSt2-SC_application_note and https://doi.org/10.5281/zenodo.15119770.

Software↗