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At least 703 records · Page 39Linked to original sources
PubMed1992

[Development and organization of a knowledge-based documentation system for ophthalmologic video documentation].

We introduce a system for documentation of ophthalmological video tapes. This system can be implemented without regarding the German data security law (Bundesdatenschutzgesetz), because the documentation of the patient identification and the video tape identification number is done manually and separated from the EDP-supported documentation of the video tape identification number and the contents of the tape. But the use of a controlled vocabulary framework for diagnosis and surgery can be considered as the main advantage of this system. This enables a complete and fast retrieval to all records containing the terms searched for. Our system provides additional space for non-standardized text-documentation, e.g. comments etc... The implemented search-editor allows a fast retrieval to all records by input of strings, which can be connected by boolean expressions.

Computer Security↗
PubMed2005

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

Cell Line, Tumor↗
PubMed1997

Recognition of promoter DNA by subdomain 4.2 of Escherichia coli sigma 70: a knowledge based model of -35 hexamer interaction with 4.2 helix-turn-helix motif.

In Escherichia coli, subdomains 2.4 and 4.2 of the primary transcription factor sigma 70 are the most highly conserved regions and are responsible for the recognition of -10 and -35 promoter elements respectively. Mutational studies provide evidence to this end and indicate that the side chains of subdomain 4.2 make specific contacts with the nucleotides at -35. Subdomain 4.2 is highly conserved among group-1 sigma factors and is strongly homologous to the classical helix-turn-helix (HTH) motif shared by bacteriophage lembda cl, Cro, the CAP protein and other homeodomain proteins, suggesting that sigma factor also belongs to the HTH class of proteins. In this study, a single point mutation of the conserved hydrophobic residue valine at position 576, in the 4.2 subdomain results in a mutant that is transcriptionally inefficient although conformationally similar to wild-type sigma. The mutant sigma, like wild-type, migrates as a 87 kDa protein on SDS gels and has 50% helicity. However, transcription at "extended -10 promoter' by RNA polymerase containing mutant sigma 70-V576G, synthesized appreciable amount of RNA product, when compared with that generated by sigma 70-W434G, a mutation in -10 DNA binding domain. A model of HTH motif for the conserved 20 residue region of 4.2 domain of E. coli sigma 70 as well as its mutant sigma 70-V576G and sigma 70-V576T were constructed based on five other homologous HTH motifs from DNA-protein complexes for which X-ray or NMR structure is available. A B-DNA structure was designed for -35 region using sequence dependent base pair parameters. The modeled HTH structure was docked into the major groove formed by the -35 hexamer DNA using the DNA-recognition rules and amino acid-nucleotide base contact information of homologous DNA-protein complexes. Analysis of the residue contact information of the model was tested and found to have good agreement with the experimental reports.

Amino Acid Sequence↗
PubMed1994

Selection of rural assistive technology using a HyperCard-based knowledge system.

Resources and expertise on selecting assistive technology appropriate for an agricultural work setting are scarce. To meet this need a prototype knowledge system for the selection and documentation of rural assistive technology (BNG DATA) was developed to aid professionals working with farmers, ranchers, and agricultural workers with physical disabilities. The knowledge system consists of a hypertext database of technology examples and a decision support system that helps users identify solution alternatives to meet consumers' needs. End-user acceptance of BNG DATA was determined through field trials and an evaluation questionnaire administered to staff of the U.S. Department of Agriculture's AgrAbility Project. Using a statistical experiment in conjunction with the questionnaire, it was concluded that BNG DATA significantly reduced the time required by end users to find acceptable solution alternatives for consumers and increased the end users' confidence in the solutions they obtained. This manuscript describes the development and testing of BNG DATA, focusing on the selection of appropriate technology.

Agriculture↗
PubMed1995

Use of knowledge bases and QSARs to estimate the relative ecological risk of agrichemicals: a problem formulation exercise.

Ecological risk assessments can be used to establish the likelihood that an adverse effect will result from exposure to one or more chemicals. When evaluating contaminated sites with many chemicals present, risk assessors must grapple with the problem of quickly identifying the chemicals that are most likely to be of concern, based on effect and exposure assessment information. Many times data gaps exist and the risk assessor is left with decisions on which models to use to estimate the parameter of concern. In the present paper, a procedure is presented for ranking agrichemicals, utilizing the ASTER (ASsessment Tools for the Evaluation of Risk) system. The procedure was employed to rank the relative ecological risk of forty-nine pesticides historically used in agricultural sites in the Walnut Creek watershed near Ames, lowa, USA. Empirical data from the ASTER system were used when available in the associated databases, and quantitative structure-activity relationships and expert systems were invoked when data were lacking. Separate rankings were conducted based on major species taxonomic groupings. Resulting toxic effects thresholds were compared to surface water concentrations.

Agrochemicals↗
PubMed2000

Ontology-based knowledge representation for bioinformatics.

Much of biology works by applying prior knowledge ('what is known') to an unknown entity, rather than the application of a set of axioms that will elicit knowledge. In addition, the complex biological data stored in bioinformatics databases often require the addition of knowledge to specify and constrain the values held in that database. One way of capturing knowledge within bioinformatics applications and databases is the use of ontologies. An ontology is the concrete form of a conceptualisation of a community's knowledge of a domain. This paper aims to introduce the reader to the use of ontologies within bioinformatics. A description of the type of knowledge held in an ontology will be given.The paper will be illustrated throughout with examples taken from bioinformatics and molecular biology, and a survey of current biological ontologies will be presented. From this it will be seen that the use to which the ontology is put largely determines the content of the ontology. Finally, the paper will describe the process of building an ontology, introducing the reader to the techniques and methods currently in use and the open research questions in ontology development.

Artificial Intelligence↗
PubMed2001

The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.

UNLABELLED: TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system (Wingender et al., Nucleic Acids Res., 28, 316-319, 2000). It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal transduction pathways like complexes, signaling molecules, and their states are stored together with information about their interaction in an object-oriented database. The database interface provides clickable maps and automatically generated pathway cascades as additional ways to explore the data. All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, SWISS-PROT, EMBL, PubMed and others). AVAILABILITY: The database is available over (http://transpath.gbf.de) for interactive perusal. As an exchange format for the data, eXtensible Markup Language (XML) flatfiles and a Document Type Definition (DTD) are provided.

Algorithms↗
PubMedDate not supplied

Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures.

An approach is described for modelling the three-dimensional structure of a protein from the tertiary structures of several homologous proteins that have been determined by X-ray analysis. A method is developed for the simultaneous superposition of several protein molecules and for the calculation of an 'average structure' or 'framework'. Investigation of the convergence properties of this method, in the case of both weighted and unweighted least squares, demonstrates that both give a unique answer and the latter is robust for an homologous family of proteins. Multi-dimensional scaling is used to subgroup of the proteins with respect to structural homology. The framework calculated on the basis of the family of homologous proteins, or of an appropriate subgroup, is used to align fragments of the known protein structures of high sequence homology with the unknown. This alignment provides a basis for model building the tertiary structure. Different techniques for using the framework to model the mainchain of various globins and an immunoglobulin domain in the structurally conserved regions are investigated.

Models, Molecular↗
PubMedDate not supplied

Knowledge based modelling of homologous proteins, Part II: Rules for the conformations of substituted sidechains.

This paper describes a rapid, automated procedure which can be used for model building sidechains using (i) spatial information from sidechains in topologically equivalent positions as far as such a correlation is observed, and then (ii) most probable conformations of the sidechains in the respective secondary structure type. Analysis of topologically equivalent residues in the structurally conserved regions of a family of proteins implies that the spatial positions of the atoms in the sidechains rather than conformations should be considered when model building. Rules for the modelling of all 20 side-chains from each other in alpha-helical, beta-sheet and loop regions--a total of 1200--are established. Cluster analysis is used on positional data from the sidechain atoms of structurally equivalent residues in an homologous family to guide modelling. The most probable conformation for the sidechain is used for modelling atoms where no useful guidance is obtainable from equivalent sidechains of the homologous proteins. In order to test the procedure we have modelled the sidechains of the residues in the structurally conserved regions of myoglobin from four other globins. The automated procedure described here has been incorporated into the program COMPOSER.

Models, Molecular↗
PubMed1998

Three-dimensional structures of the cysteine proteases cathepsins K and S deduced by knowledge-based modelling and active site characteristics.

Human cathepsins K and S are recently identified proteins with high primary sequence homology to members of papain superfamily, including cathepsins B, L, H and papain. Models of the tertiary structures of cathepsins K and S and their complexes with a specific substrate and inhibitor were constructed and compared with the recently determined X-ray structure of cathepsin K. A major problem in the determination of the three-dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. The framework of the tertiary structures of cathepsins K and S consisted of structurally conserved regions from the tertiary structure of the papain superfamily and the variable regions were constructed with fragments of other proteins from the protein data base. Based on docking studies the non-bonded interaction energies of ligands with the cathepsins were estimated. These energies correlate with experimentally determined substrate and inhibitory potency.

Binding Sites↗
PubMed2002

Knowledge-based selection of targets for structural genomics.

The problem of rational target selection for protein structure determination in structural genomics projects on microbes is addressed. A flexible computational procedure is described that directly incorporates the whole body of annotation available in the PEDANT genome database into the sequence clustering and selection process in order to identify proteins that are likely to possess currently unknown structural domains. Filtering out gene products based on predicted structural features, such as known three-dimensional structures and transmembrane regions, allows one to reduce the complexity of neighbor relationships between sequences and all but eliminates the need for further partitioning of single-linkage clusters into disjoint protein groups corresponding to homologous families. The results of a large-scale computation experiment in which exemplary target selection for 32 prokaryotic genomes was conducted are presented.

Algorithms↗
PubMed2002

Research issues for minority dementia patients and their caregivers: what are the gaps in our knowledge base?

This article highlights the current state of dementia research in ethnic minority populations. Studies are sparse, and an increased effort to recruit and retain minorities for dementia studies is required to properly treat and serve these families. An examination of research in the areas of minority caregiver issues (service needs, service use, affiliation with a support group) and patient evaluation is provided.

Adult↗