Bioinformatics and Genomics for PhysiciansBioinformatics and Genomics for Physicians
Doug
BrutlagLeder, P., Clayton, D. A., & Rubenstein, E. (Eds.). (1994). Introduction to Molecular Medicine. New York NY: Scientific American Inc. 333 Pages.
Maulik, S., & Patel, I. (1996). Molecular Biotechnology: Therapeutic Applications and Strategies. New York: John Wiley and Sons Inc.
Barnett, O., Shortliffe, E., Chueh, H., Piggins, J., Greenes, R., Cimino, J., Musen, M., Clayton, P., Humphreys, B., Kingsland, L. r. and et al. (1994). Patient care applications on Internet. Proc Annu Symp Comput Appl Med Care, , 1060.
Bergman, R. (1994). The world at their fingertips: rural providers turn to Internet. Hosp Health Netw, 68(14), 52.
Brinkley, J. F., Eno, K. and Sundsten, J. W. (1993). Knowledge-based client-server approach to structural information retrieval: the Digital Anatomist Browser. Comput Methods Programs Biomed, 40(2), 131-45.
Structural information can be defined as data and knowledge about biological objects ranging in size from molecules to the whole body. A framework is described for organizing structural information around a well-defined set of terminology and semantic relationships, and for disseminating multimedia structural information by means of a wide-area information server that is accessible over the internet. A Macintosh-based client of this server, called the Digital Anatomist Browser, has been used to teach neuroanatomy for the last 2 years. The client-server approach provides each student unlimited access to a rapidly growing knowledge base of structural biology that, while immediately useful for anatomy teaching, has the potential to be an organizing framework for other kinds of medical knowledge as well.
Buhle, E. L., Jr., Goldwein, J. W. and Benjamin, I. (1994). OncoLink: a multimedia oncology information resource on the Internet. Proc Annu Symp Comput Appl Med Care, , 103-7.
This paper describes OncoLink, the first multimedia World-Wide-Web (WWW) and gopher server focusing on cancer information for both the health care professional and the patient. OncoLink provides an internetworked hypertext and multimedia resource linking people, computers and information together in an easy to use fashion. Our objective in developing OncoLink is to provide comprehensive and timely information about many aspects of oncology for both patients and healthcare providers. Specifically, OncoLink's purposes are: (1) the rapid dissemination of information relevant to treatment of cancer and concomitant problems; (2) education of health care personnel (at all levels) in the field; (3) education of patients and families of patients who have cancer; (4) posting of clinical trials and eligibility criteria; (5) the rapid collection and dissemination of quality, peer-reviewed information pertinent to oncology in general and specific subspecialties; (6) provide a well-organized, frequently updated hypertext system to access other quality cancer information resources on the Internet. OncoLink attempts to provide one-stop shopping for the patient, healthcare provider, researcher or Internet browser searching for cancer-related information. Since its inception on March 7, 1994, OncoLink has averaged more than 36,000 accesses per month from around the world. While also accessible by text-based gopher servers, preliminary observations infer increased use of multimedia and hypertext documents over traditional text-only resources. From the large following of users, it is clear that electronic dissemination of high quality, peer-reviewed cancer information is very popular. We conclude OncoLink is both useful and has wide interest in the international community.(ABSTRACT TRUNCATED AT 250 WORDS)
Chiang, D. (1994). Reaching NLM through the Internet. Med Ref Serv Q, 13(1), 83-92.
Currently, many of the electronic services are still new, and there may be a need for further fine-tuning and changes. Having separate electronic addresses for each service rather than having one centralized address will make it easier for NLM to identify and isolate questions or problems. The Appendix summarizes the commands and addresses mentioned in this article.
Corn, M. and Johnson, F. E. (1994). Connecting the health sciences community to the Internet: the NLM/NSF grant program. Bull Med Libr Assoc, 82(4), 392-5.
In 1992, as part of its high-performance computing and communications initiative, the National Library of Medicine decided to provide health sciences institutions with Internet connection grants similar to those offered to universities by the National Science Foundation. Although library involvement is not required, librarian and library uses have been the most common category in the applications received.
D'Alessandro, M. P., Galvin, J. R., Erkonen, W. E., Lacey, D. L., Curry, D. S., Holtum, E. A. and Santer, D. M. (1994). The virtual hospital: creating and organizing a ubiquitous health sciences organization on the Internet. Proc Annu Symp Comput Appl Med Care, , 1061.
Durkin, C. (1994). Accessing Internet--tips for hospital librarians. Natl Netw, 19(2), 10-1.
Frisse, M. E., Kelly, E. A. and Metcalfe, E. S. (1994). An Internet primer: resources and responsibilities. Acad Med, 69(1), 20-4.
The ease with which individuals can access the Internet and with which institutions can make information available on the Internet explains the exponential growth of this national resource. Once one accomplishes the difficult task of installing network services and establishing an ongoing mechanism for their support, it is relatively simple to use software systems such as those described in this article to gainfully traverse the Internet for a wide range of professional activities. But, as we have discussed, every step of the process, from simple naming conventions to organizations and ongoing maintenance of network-based information services, should proceed only after careful consideration of a network growing hourly in complexity. Despite the power of the technology available on one's desktop, one can often be frustrated by the small decisions: what is my colleague's email address? How can I most effectively find relevant information on home health care software? How should I organize a gopher server? When is WAIS preferable to Gopher or W3? Who will help me learn more? The process comes full circle back to academic medical institutions. The usefulness of the Internet hinges upon the policies these institutions create to aid the organization and dissemination of medical information, and in the means they use to make their constituents aware of the pitfalls and potentials of various technologies.(ABSTRACT TRUNCATED AT 250 WORDS)
Fuller, S. S. (1995). Internet connectivity for hospitals and hospital libraries: strategies. Bull Med Libr Assoc, 83(1), 32-6.
Access to Internet resources and communications has rapidly become a necessity in many hospitals nationally. The results of a Pacific Northwest pilot Intenet connections project provides important evidence of the value of librarians in establishing such connections in their institutions The pilot project has resulted in a wealth of information regarding approaches to promoting the utility of the Internet to health professionals in hospitals. Roles that librarians are playing in support of such connections include facilitator, negotiator, provider, publisher, integrator, and educator.
Gnassi, J. A., Bormel, J. I., Blewett, D. R., Kim, R. J. and Barnett, G. O. (1994). A medical information resource server: one stop shopping on the Internet. Proc Annu Symp Comput Appl Med Care, , 1025.
Guay, T. (1994). An introduction to Internet for medical professionals. Physician Assist, 18(6), 69-74.
This article is a wonderful description of what I think is the most remarkable communication and information system ever devised. INTERNET is literally a world of data, dialogue, and discourse on any topic imaginable, right at your fingertips. I invite all PAs to begin to explore the world of interpersonal computing via INTERNET. I am putting together a list of PAs with E-Mail accounts to provide a forum for sharing information and linking PAs with common interests.
Hollander, S. M. and Lanier, D. (1995). Orientation to the Internet for primary care health professionals. Bull Med Libr Assoc, 83(1), 96-8.
Kleeberg, P. (1993). Medical uses of the Internet. J Med Syst, 17(6), 363-6.
Lacroix, E. M., Backus, J. E. and Lyon, B. J. (1994). Service providers and users discover the Internet. Bull Med Libr Assoc, 82(4), 412-8.
Although the Internet has evolved over more than twenty years, resources useful to health information professionals have become available on the Internet only recently. A survey conducted by the Regional Medical Libraries of the National Network of Libraries of Medicine in the fall of 1993 indicates that libraries at academic institutions are much more likely to have access to the Internet (72%) than are libraries in hospital environments (24%). Health information professionals who take on the challenge and exploit the Internet's resources find rewards for themselves and their clients. The basic electronic mail capability of the Internet allows colleagues to collaborate, communicate, and participate in daily continuing education. Internet terminal and file-transfer capabilities provide improved access to traditional resources and first-time access to new electronic resources. Through the Internet, online catalogs are available worldwide, and document delivery is faster, cheaper, and more reliable than ever before. Institutions can make organizational, full-text, online, and publication information available through Internet tools such as direct file-transfer protocol (FTP), menu-based Gopher, and hypertext-based Mosaic. The National Library of Medicine (NLM) is among organizations finding new ways to provide service through the Internet. NLM now uses electronic mail to communicate with users, FTP service to distribute publications, and tools such as Gopher and Mosaic to distribute publications and graphics and connect users to online services. The Internet allows service providers and health sciences information professionals to work in a rich, new medium whose potential is just beginning to be explored. At the same time, its characteristics--including lack of formal organization, standards, quality control, and permanence--pose a challenge.
McColligan, E. E., Samuell, R. L. r., Jones, W. T., Moon, W. A., Pretnar, S. Z. and Johns, M. L. (1994). Providing access to healthcare information resources using Internet Gopher technology as a part of a state-wide medical information network. Proc Annu Symp Comput Appl Med Care, , 990.
An Internet healthcare information resources Gopher server is described as a part of a state-wide medical information network. The development of the server and its design and operation are presented. The potential impact of this technology on the healthcare delivery process and issues associated with the use of public domain information resources are discussed.
Mikita, E. G. and Drusedum, L. A. (1993). Introducing health sciences librarians to the Internet. Med Ref Serv Q, 12(3), 1-12.
The Internet is no longer just for the adventurous explorers or the technical experts--it has found its way into the mainstream of librarianship. New users are coming onto "the net" in droves. A wealth of information is currently available dealing with the mechanics of the Internet and there are general guides to the available resources. More work needs to be done, however, in developing subject specific materials. This paper will report on the strategy that Scott Memorial Library, Thomas Jefferson University, has employed to develop staff skills and awareness and to take advantage of the resources and opportunities that the network provides for the health sciences community.
Moynihan, J. J. (1995). Healthcare opportunities on the Internet. Healthc Financ Manage, 49(1), 98.
Rambo, N. (1994). An operational view of the role of health librarians in informatics. Health Libr Rev, 11(3), 161-6.
The National Library of Medicine is currently funding the Pilot Connections project to promote and support use of the INTERNET in community health care settings. With previous networking applications of this kind largely confined to academic and research environments, the health librarian has emerged as the agent with the unique knowledge and skills to participate in and manage organizational change. An experiment in applied informatics, the Pilot Connections project shows how health librarians should be aware of the expanding opportunities that exist for them to help their organizations cope more effectively with the external trends and forces currently affecting the role and value of information.
Rauch, S., Holt, M. C., Horner, M. and Rambo, N. (1994). Community hospitals and the Internet: lessons from pilot connections. Bull Med Libr Assoc, 82(4), 401-6.
Community hospitals in rural and isolated areas have had little access to the Internet. In 1992, the National Library of Medicine funded a pilot project to be conducted by the University of Washington and seven community hospitals in the northwestern United States. The goals of the project were to connect the hospitals to the Internet and study the uses made of this resource. A number of administrative, technical, financial, and organizational problems were dealt with in the attempt to establish the Internet connections and introduce this resource to these health care settings. This paper examines these issues and presents conclusions drawn from the experiences of the project team.
Schneider, D. (1993). INTERNET: linking nurses, scholars, libraries. Reflections, 19(1), 9.
Weinstein, L. (1994). LIFENET/INTERNET and the health science librarian. Spec Libr, 85(1), 16-23.
The Medical Library Center of New York, a cooperative library agency for the health sciences, developed a program to offer an electronic communications system (LIFENET) with access to the Internet for its members. Information on documentation and training as well as statistics on the subsequent use of the system and of the Internet are discussed in the article. Specific examples of how health science librarians are using the system include bibliographic verification, reference, research on integrated library systems, production of duplicate journal lists, and professional activities such as electronic mail and discussion groups (listservs).
Wood, E. H. (1994). MEDLINE: the options for health professionals. J Am Med Inform Assoc, 1(5), 372-80.
The bibliographic database MEDLINE, produced by the National Library of Medicine (NLM), is a computerized index to the world's biomedical literature. The database can be searched back to 1966 and contains 6.8 million records. The various means of access are divided, for the purposes of this article, into three categories: logging onto a remote host computer by telephone and modem or by the Internet; subscribing to part or all of the database on compact disc (CD-ROM); and leasing the data on a transport medium such as magnetic tape or CDs for loading on a local host computer. Decisions about which method is preferable in a given situation depend on cost, availability of hardware and software, local expertise, and the size of the intended user population. Trends include increased access to the Internet by health professionals, increased network speed, links from MEDLINE records to full-text databases or online journals, and integration of MEDLINE into wider health information systems.
Appel, R. D., Sanchez, J. C., Bairoch, A., Golaz, O., Miu, M., Vargas, J. R. and Hochstrasser, D. F. (1993). SWISS-2DPAGE: a database of two-dimensional gel electrophoresis images. Electrophoresis, 14(11), 1232-8.
This publication presents the SWISS-2DPAGE database which gathers data on proteins identified on various two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) maps. Each SWISS-2DPAGE entry contains data on one protein, including mapping procedures, physiological and pathological data and bibliographical references, as well as several 2-D PAGE images showing the protein location. Links are also provided to other databases such as SWISS-PROT, EMBL, PROSITE and OMIM. The database has been set up on a server which may be accessed from any computer connected to the internet and it also makes it possible to display the theoretical location of proteins, the positions of which are not yet known on the 2-D PAGE.
Brandt, K. A. (1993). The GDB Human Genome Data Base: a source of integrated genetic mapping and disease data. Bull Med Libr Assoc, 81(3), 285-92.
The GDB Human Genome Data Base refers collectively to GDB and OMIM, Online Mendelian Inheritance in Man. GDB and OMIM are linked databases that provide an international repository for information generated by the Human Genome Initiative. GDB contains human gene mapping data, while OMIM offers the text of Dr. Victor A. McKusick's catalog of genetic disease and phenotype descriptions. These databases, updated and edited continuously, integrate bibliographic and full-text information with several types of mapping data. They are accessible through a flexible interface and are available through SprintNet and the Internet to the scientific community without cost. This paper provides an overview of the context, development, structure, content, and use of these databases.
Canhos, V. P., Manfio, G. P. and Blaine, L. D. (1993). Software tools and databases for bacterial systematics and their dissemination via global networks. Antonie Van Leeuwenhoek, 64(3-4), 205-29.
The dynamic expansion of the taxonomic knowledge base is fundamental to further developments in biotechnology and sustainable conservation strategies. The vast array of software tools for numerical taxonomy and probabilistic identification, in conjunction with automated systems for data generation are allowing the construction of large computerised strain databases. New techniques available for the generation of chemical and molecular data, associated with new software tools for data analysis, are leading to a quantum leap in bacterial systematics. The easy exchange of data through an interactive and highly distributed global computer network, such as the Internet, is facilitating the dissemination of taxonomic data. Relevant information for comparative sequence analysis, ribotyping, protein and DNA electrophoretic pattern analysis is available on-line through computerised networks. Several software packages are available for the analysis of molecular data. Nomenclatural and taxonomic 'Authority Files' are available from different sources together with strain specific information. The increasing availability of public domain software, is leading to the establishment and integration of public domain databases all over the world, and promoting co-operative research projects on a scale never seen before.
Chiang, D. (1994). Reaching NLM through the Internet. Med Ref Serv Q, 13(1), 83-92.
Currently, many of the electronic services are still new, and there may be a need for further fine-tuning and changes. Having separate electronic addresses for each service rather than having one centralized address will make it easier for NLM to identify and isolate questions or problems. The Appendix summarizes the commands and addresses mentioned in this article.
Cuticchia, A. J., Fasman, K. H., Kingsbury, D. T., Robbins, R. J. and Pearson, P. L. (1993). The GDB human genome data base anno 1993. Nucleic Acids Res, 21(13), 3003-6.
Version 5.0 of the Genome Data Base (GDB) was released in March 1993. This document describes some of the significant changes to the types of data which are stored within the GDB. In addition to handling a wider scope of data, the GDB 5.0 application software now supports the X-Windows protocol. Although the GDB software still remains the most widely utilized method for accessing the data, alternate methods of access are now available, including direct SQL (Structured Query Language) queries, FTP (Internet File Transfer Protocol), WAIS (Wide Area Information Server), and other tools produced by third-party developers.
Heumann, K., George, D. and Mewes, H. W. (1994). A new concept of sequence data distribution on wide area networks. Comput Appl Biosci, 10(5), 519-26.
Accepted concepts in distributed applications design have been applied in the development of a network-based system for the synchronization of remote sequence database access sites by an incremental update mechanism. Computer hardware requirements, network bandwidth, and stability considerations make centralized access to essential computerized resources undesirable. A network model has been developed to distribute access over a collection of remotely situated computer centers. The formally independent database-access nodes join to form a heterogeneous, long distance, co-operating network that can compensate for the deficiencies of unstable network links thereby ensuring uninterrupted access to the resource. In order to guarantee consistency among these nodes, several distributed transaction protocols have been investigated; based on these results, a prototype system has been implemented. A layered software architecture makes the distributed transaction protocol transparent to the individual database system and the underlying network. Individual components of this network communicate by means of Remote Procedure Calls (RPCs). A prototype software system operates to synchronize up to data copies of the PIR-International Protein Sequence Database (Barker et al., 1993) at a number of different sites using the public Internet as the transport vehicle.
Nowak, R. (1993). Draft genome map debuts on Internet [news]. Science, 262(5142), 1967.
O'Donnell, C. (1994). Obtaining software via INTERNET. Methods Mol Biol, 24, 345-54.
Peitsch, M. C., Wells, T. N., Stampf, D. R. and Sussman, J. L. (1995). The Swiss-3DImage collection and PDB-Browser on the World-Wide Web. Trends Biochem Sci, 20(2), 82-4.
Woodsmall, R. M. and Benson, D. A. (1993). Information resources at the National Center for Biotechnology Information. Bull Med Libr Assoc, 81(3), 282-4.
The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, was established in 1988 to perform basic research in the field of computational molecular biology as well as build and distribute molecular biology databases. The basic research has led to new algorithms and analysis tools for interpreting genomic data and has been instrumental in the discovery of human disease genes for neurofibromatosis and Kallmann syndrome. The principal database responsibility is the National Institutes of Health (NIH) genetic sequence database, GenBank. NCBI, in collaboration with international partners, builds, distributes, and provides online and CD-ROM access to over 112,000 DNA sequences. Another major program is the integration of multiple sequences databases and related bibliographic information and the development of network-based retrieval systems for Internet access.