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PubMed1999

Position-specific annotation of protein function based on multiple homologs.

I present in this work an algorithm for deriving protein functional annotations which are position-specific. The input is based on the results of a sequence similarity search of the query sequence against a sequence database. Strings of words are extracted from the descriptions of the proteins, and the correlation between proteins having the same descriptors and the amino acid conservation is used to compute a score that indicates which descriptor is likely to describe better the function of each particular residue. Analysis of the score curves and comparison of different functions allows an easy detection of parts of the sequence associated to different function. Different levels of functional specificity can be compared, allowing to choose the one that suits better the function of the protein. Immediate applications of this algorithm are, support for (automated) methods of protein functional annotation, and database coherence check.

Algorithms↗

PubMed2000

Standardized annotation of nuclear medicine images.

There are no generally accepted standards for annotating nuclear medicine images. This is a potential problem whenever hardcopies from other centers are being evaluated, reinterpreted or compared to actual images of the same patient. Proposals for image annotation are elaborated to support image evaluation by a third party. In this paper, examples are given of lung scintigraphy, thyroid scintigraphy, bone scintigraphy both in planar and SPECT techniques, renal function scintigraphy, myocardial perfusion scintigraphy, and PET. They are presented to stimulate discussion in the nuclear medicine community.

Forms and Records Control↗

PubMed2001

Improving delivery of preventive health care with the comprehensive annotated reminder tool (CART).

OBJECTIVES: We assessed the effect of the Comprehensive Annotated Reminder Tool (CART) on physician adherence to preventive services recommendations. STUDY DESIGN: Using a randomized pretest/posttest control group design, we assigned physicians to the CART group or the control group, followed up prospectively, and evaluated for appropriate adherence to guidelines. The 3 age-specific versions of the CART annotated history and physical examination form contained up to 49 preventive services recommendations. POPULATION: All resident physicians in a large family practice residency program were studied over the course of 1 academic year. OUTCOMES MEASURED: We performed blinded chart reviews to assess the appropriateness of preventive services ordered by the physicians before the introduction of the CART, during its use, and after its removal. A multiple-choice test completed before and after the use of the CART forms assessed knowledge. RESULTS: When the CART was used, the appropriateness of physician preventive behavior increased by 21% overall. The appropriateness of history, physical examination, and laboratory interventions increased by 33%. When the CART was removed, physician behavior returned to baseline (P < or = .0025 for 16 of 20 interventions). No significant differences were observed in the control group over time. Knowledge increased over the study period for all physicians (P < or = .005) but did not differ significantly between the treatment and control groups (P = .608). CONCLUSIONS: Use of the CART significantly improved physician performance in the appropriate delivery of preventive care.

Delivery of Health Care↗

PubMed2002

The CATH protein family database: a resource for structural and functional annotation of genomes.

Over the last decade, there have been huge increases in the numbers of protein sequences and structures determined. In parallel, many methods have been developed for recognising similarities between these proteins, arising from their common evolutionary background, and for clustering such relatives into protein families. Here we review some of the protein family resources available to the biologist and describe how these can be used to provide structural and functional annotations for newly determined sequences. In particular we describe recent developments to the CATH domain database of protein structural families which have facilitated genome annotation and which have also revealed important caveats that must be considered when transferring functional data between homologous proteins.

Databases, Protein↗

PubMed2001

Bioinformatics issues for automating the annotation of genomic sequences.

The rapid explosion in the amount of biological data being generated worldwide is surpassing efforts to manage analysis of the data. As part of an ongoing project to automate and manage bioinformatics analysis, the authors have designed and implemented a simple automated annotation system, which is described in this paper. The system is applied to existing GenBank/DDBJ/EMBL entries and compared with existing annotations to illustrate not only potential errors but also that they are generally not up-to-date, as a result of new versions of analysis tools and updates of genomic repositories. We highlight the important Bioinformatics issues of storage and management of information to ensure data and results are kept up-to-date in light of new information becoming available. Surprisingly, from just four database entries, a significant number of new features were found. We describe the results as well as identify important issues that need to be addressed in order to automate the re-analysis/re-annotation of genomic sequences within a reasonable timeframe.

Computational Biology↗

PubMed2002

Representation and processing of complex DNA spatial architecture and its annotated genomic content.

This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementary to other representations as textual, linguistics or syntactic ones. The DNA is well known as a three-dimensional structure. Whereas, the spatial information plays a great part during its evolution and its interaction with the other biological elements This work will motivate investigations in order to launch new bioinformatics studies for the analysis of the spatial architecture of the genome. Besides, in order to obtain a friendly interactive visualization, a powerful graphic modeling is proposed including DNA complex trajectory management and its annotated-based content structuring. The paper describes spatial architecture modeling, with consideration of both biological and computational constraints. This work is implemented through a powerful graphic software tool, named ADN-Viewer. Several examples of visualization are shown for various organisms and biological elements.

DNA↗

PubMed1999

The Feasibility of Using Proteome Expression Profile for Genome Annotation.

By investigating into the expression data from ECO2DBASE (Edition 6),the feasibility of using proteome expression profile for genome annotation was tested. Based on our newly developed CRC (cellular role cluster) method,79 proteins extracted from ECO2DBASE were clustered into 4 CRCs. Function related proteins tend to be clustered into same CRC. Total 9 aminoacyl-tRNA synthetases were clustered into CRC2, whereas 4 heat-shock proteins into CRC3. These results indicate with enough proteome expression data and the efficient algorithm, proteome expression profile can provide very important information for genome annotation, while this kind of information is sequence-independent.

Journal Article↗

PubMed2002

[Annotation of complete genomic sequence of 3p24-p25 478 kb of human DNA].

OBJECTIVE: To annotate the human genome 3p24-p25 478 kb complete sequence. METHODS: The protein-coding genes in the genomic sequence were identified by using ab initio gene finding, homology-based similarity database searching and all or partial mRNA aligning with genomic sequence, and the content feature of the genomic sequence were analyzed by using EMBOSS package. RESULTS: Two known genes SLC6A1 and SLC6A11 were identified; as well as the GC content of this genomic sequence was 47% and 3 putative CpG islands were predicted in the genomic sequence, located in 130,685-131,516 bp, 307,090-307,870 bp and 415,585-416,308 bp, respectively. CONCLUSIONS: The methods, as mentioned above, might be used for annotating the biological information in the genomic sequence, such as gene structure, GC content, CpG island.

Base Sequence↗

PubMed2003

Open-source toolkit for simple XML annotation.

Use of Extensible Markup Language (XML) is increasingly prevalent among medical informatics projects. Many of these projects involve, at some point, the interaction between a researcher and specialized XML documents for the purpose of annotating the XML data. We offer a simple toolkit to assist these researchers. Our solution is a simple, yet fully functional, annotation system that can easily be adapted to the needs of the researcher. All of the materials for this toolkit are freely available.

Algorithms↗

PubMed1992

Use of neurodevelopmental treatment as an intervention: annotated listing of studies 1980-1990.

This annotated bibliography presents a listing of research investigations on the effectiveness of neurodevelopmental treatment, an approach developed by the Bobaths in managing the neuromotor problems of infants, toddlers, children, and adults with neuromotor disorders. The annotated listing of 19 articles appearing in peer-reviewed journals between 1980 and 1990 is presented by category of experimental design (single-subject, quasi-experimental, and experimental). Each research article was reviewed for research question, conceptual framework, research design, findings, and limitations. The bibliography should be useful for educators, clinicians, and researchers in evaluating current research and in developing strategic plans for research. The implications for clinical practice and program development are discussed.

Activities of Daily Living↗

PubMed1992

An annotated algorithm approach to clinical guideline development.

The Urinary Incontinence in Adults Guideline Panel facilitated the ready elucidation of its guideline's management recommendations through the use of an annotated algorithm approach. The algorithms created as part of this guideline differ from previous algorithms in two ways: (1) they employ systematic annotation to link explicitly the algorithms' recommendations to the literature, and (2) they contain patient counseling and decision nodes to depict the major preference-dependent decision or branch points in the algorithm. We believe that these two innovations can help ensure the clinical validity of guidelines' algorithms while preserving appropriate clinical flexibility and respecting patient preferences.

Algorithms↗

PubMed2005

Immunogenetics Sequence Annotation: the Strategy of IMGT based on IMGT-ONTOLOGY.

IMGT, the international ImMunoGeneTics information system((R))(http://imgt.cines.fr) created in 1989, by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Université Montpellier II and CNRS, Montpellier, France, is a high quality integrated information system, secialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex of human and other vertebrates and related proteins of the immune system that belong to the IgSF and Mhc superfamilies. IMGT/LIGM-DB, the first and the largest IMGT database, manages more than 92,000 IG and TR nucleotide sequences from human and 150 other vertebrate species in May 2005. IMGT/LIGM-DB provides expertly annotated sequences and standardized knowledge based on IMGT-ONTOLOGY, the first ontology for immunogenetics and immunoinformatics. The strategy developed by IMGT, for the IG and TR nucleotide sequence annotation, involves two different approaches that depend on the nature of the sequences, genomic DNA (gDNA) or complementary DNA (cDNA).

Animals↗

PubMed2003

[MGAP-A microbe genome annotation platform].

A Microbe Genome Annotation Platform (MGAP) was developed and applied to the cynobacterium PCC7002 genome annotation. Various bioinformatics software tools from sequence analysis to gene identification and function prediction were implemented in MGAP. Protein sequence databases SWISSPROT and PDBseq, protein information resource InterPro and COG were also integrated in the platform. The web interface of MGAP has the functionality to display a circular map of gene distribution and GC contents throughout the genome. Detailed information such as the DNA and protein sequence, the location of genes on chromosomes can be viewed by clicking the corresponding object within the map. MGAP is based on a PC/Linux system affordable for small biological laboratories and has the advantage of using free software tools including MySQL, Apache and Perl.

Cyanobacteria↗

PubMed2006

Functional annotation and analysis of Korean patented biological sequences using bioinformatics.

A recent report of the Korean Intellectual Property Office (KIPO) showed that the number of biological sequence-based patents is rapidly increasing in Korea. We present biological features of Korean patented sequences though bioinformatic analysis. The analysis is divided into two steps. The first is an annotation step in which the patented sequences were annotated with the Reference Sequence (RefSeq) database. The second is an association step in which the patented sequences were linked to genes, diseases, pathway, and biological functions. We used Entrez Gene, Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Through the association analysis, we found that nearly 2.6% of human genes were associated with Korean patenting, compared to 20% of human genes in the U.S. patent. The association between the biological functions and the patented sequences indicated that genes whose products act as hormones on defense responses in the extra-cellular environments were the most highly targeted for patenting. The analysis data are available at http://www.patome.net.

Base Sequence↗

PubMed2005

Design of a system for combined analysis of microarray-based gene expression and FlyBase-derived annotation in Drosophila.

In recent years, researchers began to utilize both the experimental microarray data and the annotation data from FlyBase to identify Drosophila genes that might encode certain functions. So far, they have to manually combine data from both the microarray experiment and the FlyBase, which is a slow and tedious process. The goal of this research is to construct a flexible relational database system that integrates the microarray data with annotation information from FlyBase.

Animals↗

PubMed2005

Online annotation tool for dental radiology.

Dental imaging plays a significant role in the process of diagnoses of oral cancer. In this project, an online annotation tool for dental radiology is developed to support systematic annotation, which includes image findings, descriptive information on the lesion, patient characteristics and pathology data. This tool will be available for the dental schools in US who are interested in the creation of dental image archives for teaching and research.

Humans↗

PubMed2006

Finding GeneRIFs via gene ontology annotations.

A Gene Reference Into Function (GeneRIF) is a concise phrase describing a function of a gene in the Entrez Gene database. Applying techniques from the area of natural language processing known as automatic summarization, it is possible to link the Entrez Gene database, the Gene Ontology, and the biomedical literature. A system was implemented that automatically suggests a sentence from a PubMed/MEDLINE abstract as a candidate GeneRIF by exploiting a gene's GO annotations along with location features and cue words. Results suggest that the method can significantly increase the number of GeneRIF annotations in Entrez Gene, and that it produces qualitatively more useful GeneRIFs than other methods.

Algorithms↗

PubMed1990

Annotated bibliography on the reuse of hemodialyzers.

The following annotated bibliography on the reuse of hemodialyzers is offered as a service to nephrology nurses needing information on this subject. The articles with the exception of two, are those published in the medical literature from 1980-1989. For ease of access, the articles are divided into the following categories: general information/reading, dialyzer performance, disinfectant, physiologic response, and infection control. Additionally, very brief descriptions of the primary contents of the articles are included. Many of the articles also contain material in addition to that summarized in the annotation. The bibliography is a selection of the hundreds available. For a more thorough study of reuse, we recommend that the reader access the additional citations listed in the bibliographies of the individual articles included herein. No attempt was made to critique the quality of the studies being reported. Readers are encouraged to examine the articles first hand, incorporating the findings into their own clinical settings.

Bibliographies as Topic↗