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Biomedical subjects

R D Appel

Publications and source records attributed to R D Appel.

At least 37 records · Page 2Linked to original sources
PubMed1998

Multiple parameter cross-species protein identification using MultiIdent--a world-wide web accessible tool.

Recent increases in the number of genome sequencing projects means that the amount of protein sequence in databases is increasing at an astonishing pace. In proteome studies, this is facilitating the identification of proteins from molecularly well-defined organisms. However, in studies of proteins from the majority of organisms, proteins must be identified by comparing analytical data to sequences in databases from other species. This process is known as cross-species protein identification. Here we present a new program, MultiIdent, which uses multiple protein parameters such as amino acid composition, peptide masses, sequence tags, estimated protein pI and mass, to achieve cross-species protein identification. The program is structured so that protein amino acid composition, which is highly conserved across species boundaries, first generates a set of candidate proteins. These proteins are then queried with other protein parameters such as sequence tags and peptide masses. A final list of database entries which considers all analytical parameters is presented, ranked by an integrated score. We illustrate the power of the approach with the identification of a set of standard proteins, and the identification of proteins from dog heart separated by two-dimensional gel electrophoresis. The MultiIdent program is available on the world-wide web at: http://www.expasy.ch/sprot/multiident.h tml.

Amino Acid Sequence↗
PubMed1998

Trends in medical information retrieval on Internet.

Information on the World Wide Web is unstructured, distributed, multimedia and multilingual. Many tools have been developed to help users search for useful information: subject hierarchies, general search engines, browsers and search assistants. Although helpful, they present serious limitations, mainly in terms of precision, multilingual indexing and distribution. In this paper, we cover some on-line solutions to medical information discovery and present our own approach, the MARVIN (multi-agent retrieval vagabond on information network) project, which tackles medical information research with specialized cooperative retrieval agents. We also draw some outlines for future extensions.

Computer Systems↗
PubMed1998

The Health On the Net Code of Conduct for medical and health Websites.

Internet has become one of the most used communication media. This and the fact that no constraining information publishing policy exists have created an urgent need to control the quality of information circulating through this media. To this purpose, the Health On the Net Foundation has initiated the Code of Conduct (HONcode) for the health/medical domain. This initiative proposes guidelines to information providers, with the aim, on the one hand, of raising the quality of data available on the Net and, on the other hand, of helping to identify Internet sites that are maintained by qualified people and contain reliable data. The HONcode mainly includes the following ethical aspects: the author's credentials, the date of the last modification with respect to clinical documents, confidentiality of data, source data reference, funding and the advertising policy. This article presents the HONcode and its evolution since it was launched in 1996.

Advertising↗
PubMed1998

A multi-agent softbot to retrieve medical information on Internet.

World-Wide Web is a media where information is unstructured, distributed, multimedia and multilingual. Many tools have been developed to help users search for information: subject hierarchies, general search engines, browsers and search assistants. Although helpful, they show serious limitations, mainly in terms of precision, multilingual indexing and distribution. The M.A.R.V.I.N. project (Multi Agent Retrieval Vagabond on Information Networks) proposes solutions with a distribution of the indexing task in agents specialized in a given domain. M.A.R.V.I.N. has been successfully applied to the medical domain. The medical index and its associated search engine MedHunt (Medical Hunter) demonstrate the interest of such an approach with currently 50,000 indexed medical sites and more than 100,000 accesses each month.

Abstracting and Indexing↗
PubMed1998

The Health On the Net Code of Conduct for medical and health web sites.

The growth in the number of medical and health web sites and the varying quality of medical and health information currently available on the World-Wide Web has created the need for guidelines to help homogenise this quality. Health On the Net Foundation (HON) has initiated the Code of Conduct (HON-code) in response to concerns expressed to the Foundation, by members of the Net community. This article presents the HON-code's principles since its launch in 1996 and its status in 1997. This initiative offers information providers good practice guidelines and offers users an indication of commitment to quality by those providers.

Confidentiality↗
PubMed1997

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

Algorithms↗
PubMed1997

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms.

After two generations of software systems for the analysis of two-dimensional electrophoresis (2-DE) images, a third generation of such software packages has recently emerged that combines state-of-the-art graphical user interfaces with comprehensive spot data analysis capabilities. A key characteristic common to most of these software packages is that many of their tools are implementations of algorithms that resulted from research areas such as image processing, vision, artificial intelligence or machine learning. This article presents the main algorithms implemented in the Melanie II 2-D PAGE software package. The applications of these algorithms, embodied as the feature of the program, are explained in an accompanying article (R. D. Appel et al.; Electrophoresis 1997, 18, 2724-2734).

Algorithms↗
PubMed1997

Make2ddb: a simple package to set up a two-dimensional electrophoresis database for the World Wide Web.

Two-dimensional electrophoresis (2-DE) has become a highly reproducible protein separation technique that currently serves as the main basis for proteome research and in particular for protein identification. Also, the Internet provides large utilities for exchanging data, and we can observe increased interest among scientists to build remote 2-DE databases, since many members of the concerned community are now able to access the data. By preparing the data and programs that are required to create a federated 2-DE database, the Make2ddb package, described here, helps to build such a database on the user own World Wide Web site.

Computer Communication Networks↗
PubMed1997

Health On the Net automated database of health and medical information.

With the number of World Wide Web sites growing every day, the problem is not just to find information, but to locate the right piece of information. Current World Wide Web search engines have not resolved this problem as they most often return a long list of documents. The search result is then unusable because of the large number of answers from different domains and topics. Only complex queries may, in a given situation, produce a limited number of potentially relevant documents. To make searches more efficient and usable by common users, we now need intelligent and specialised search engines on the Net [1,2]. Health On the Net Foundation and the Molecular Imaging and Bioinformatics Laboratory at Geneva University Hospital have developed Multi-Agent Retrieval Vagabond on Information Networks (MARVIN), a robot that searches sites and documents specifically related to a given specialised field. One such robot has already been implemented and used for the medical and the 2D electrophoresis domains. Health On the Net Foundation has implemented the corresponding search engines, MedHunt (http://www.hon.ch/cgi-bin/find) for the medical field and 2DHunt (http://www.hon.ch/cgi-bin/2DHunt/find) for the 2D electrophoresis field.

Computer Communication Networks↗
PubMed1996

Rapid protein identification using N-terminal "sequence tag" and amino acid analysis.

Proteins can be identified by amino acid analysis and database matching, but it is often desirable to increase the confidence in identity through the use of other techniques. Here we describe a rapid protein identification method that uses Edman degradation to create a 3 or 4 amino acid N-terminal "sequence tag," following which proteins are subjected to amino acid analysis protein identification procedures. Edman degradation methods have been modified to take only 23 min per cycle, and rapid amino acid analysis techniques are used. The Edman degradation and amino acid analysis is done on a single PVDF membrane-bound protein sample. A computer database matching program is also presented which uses both amino acid composition and "sequence tag" data for protein identification. This method represents the most inexpensive, accurate, and rapid means of protein identification, which is ideal for the screening of proteomes separated by 2-D gel electrophoresis. The creation of N-terminal Edman degradation "sequence-tags" prior to peptide mass fingerprinting of samples should also be useful.

Amino Acid Sequence↗
PubMed1996

Federated two-dimensional electrophoresis database: a simple means of publishing two-dimensional electrophoresis data.

While a two-dimensional electrophoresis (2-DE) database is a relatively old concept, in recent years it generated renewed interest within the 2-DE community due to two main factors: (i) The high reproducibility of the current 2-DE method allows 2-DE images to be exchanged and compared between laboratories. (ii) The recent development of faster and more powerful techniques for protein identification such as microsequencing, matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) and amino acid composition makes the production of reference protein maps and 2-DE databases cost- and time-effective. Additionally, the Internet network's current increase in popularity, combined with the rapid growth of Internet-connected laboratories, provides a straightforward means of publishing and sharing 2-DE data. While a small number of laboratories have already successfully published their data over the net, the increasing number of 2-DE database servers that are currently being set up will sooner or later require some kind of standardization. Unfortunately, standardization can be a long and cumbersome process inevitably leading to undesirable compromises. A federated database offers a simple and efficient way to publish and share 2-DE data without the need for standardization. Taking advantage of Internet protocols such as World Wide Web, they allow each laboratory to maintain their own database and to interconnect it with other similar databases through the use of active cross-references. This paper first presents guidelines for building a federated 2-DE database that may easily be followed by most laboratories. It then briefly reviews the state-of-the-art in networked 2-DE databases, and finally describes the SWISS-2DPAGE database which fully implements the concept of a federated 2-DE database.

Computer Communication Networks↗
PubMed1996

Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database.

Numerous Escherichia coli proteins have already been characterized by two-dimensional gel electrophoresis (2-D PAGE), using carrier ampholytes in the first dimension (VanBogelen, R. A., Sankar, P., Clark, R. L., Bogan, J. A. and Neidhardt, F. C., Electrophoresis 1992, 13, 1014-1054). We present here a reference protein map of E. coli obtained with immobilized pH gradients (IPG) and available in a SWISS-2DPAGE format. Out of the protein spots identified in the E. coli gene protein database by Neidhardt's group, 153 have been identified in the E. coli gene protein database by Neihardt's group, 153 have been identified on the E. coli SWISS-2DPAGE database map by gel comparison and most of them were confirmed either by the analysis of amino acid composition (AAC) and/or N-terminal microsequencing. Additionally, five as yet unsequenced proteins were found. The E. coli SWISS-2DPAGE database is part of the ExPASy molecular biology server accessible through the Word Wide Web network.

Amino Acid Sequence↗
PubMed1996

The yeast SWISS-2DPAGE database.

The systematic sequencing of the yeast genome will soon be completed. A new challenge has been launched by the EUROFAN (European Functional Analysis) project whose goal is to elucidate the physiological and biochemical function of newly discovered open reading frames (ORF) from yeast. One of the approaches is to use protein-based technologies such as two-dimensional gel electrophoresis and protein identification in order to establish a yeast reference map. Modified protein patterns can be compared to the reference map which hopefully will help identify changes related, for example, to growth processes or developmental events. This paper describes the yeast SWISS-2DPAGE database in which charge separation was obtained using immobilized pH gradient (IPG). Proteins identified by gel comparison, amino acid composition analysis and/or microsequencing are recorded and described in an accessible uniform format. We have identified more than one hundred polypeptides, several of which were newly mapped. In addition, the yeast SWISS-2DPAGE database can be freely accessed through the World Wide Web (WWW) network on the ExPASy molecular biology server.

Databases, Factual↗
PubMed1996

Identification of proteins by their amino acid composition: an evaluation of the method.

Expression of different genomes can be studied by high-resolution two-dimensional electrophoresis (2-D PAGE). To help these studies, two-dimensional reference maps of different biological tissues and fluids have been built and can be found in the SWISS-2DPAGE database, accessible via the World Wide Web network on the ExPASy molecular biology server. Different techniques were used to identify the polypeptides. At the present time, the method considered to be the fastest and the most cost-effective is amino acid composition analysis (AAC). Proteins, transferred onto polyvinylidene (PVDF) membranes, were submitted to vapor-phase hydrolysis, derivatized with 9-fluorenylmethyl chloroformate (FMOC) and separated on an ODS-Hypersil column. Identification was obtained by using the program 'AACompIdent' available from ExPASy. In this work, different experimental parameters, such as contamination, reproducibility and accuracy, have been assessed. First, it has been found that a major source of contamination was human keratin. Next, amino acids have been classified into 'reliable' and 'nonreliable'. Accordingly, 'bias' and 'weights' were defined for each amino acid, which could be set in the 'AACompIdent' program. Finally, examples of identification, including the use of Edman degradation sequence tagging, are described.

Amino Acid Sequence↗
PubMed1996

In-house access to PACS images and related data through World Wide Web.

The development of a hospital wide PACS is in progress at the University Hospital of Geneva and several archive modules are operational since 1992. This PACS is intended for wide distribution of images to clinical wards. As the PACS project and the number of archived images grow rapidly in the hospital, it was necessary to provide an easy, more widely accessible and convenient access to the PACS database for the clinicians in the different wards and clinical units of the hospital. An innovative solution has been developed using tools such as Netscape navigator and NCSA World Wide Web server as an alternative to conventional database query and retrieval software. These tools present the advantages of providing a user interface which is the same, independent of the platform being used (e.g. Mac, Windows, UNIX), and an easy integration of different types of documents (e.g. text, images). A strict access control has been added to this interface. It allows user identification and access rights checking, as defined by the in-house hospital information system, before allowing the navigation through patient data records.

Computer Communication Networks↗