The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.

Byzantine medical manuscripts: towards a new catalogue, with a specimen for an annotated checklist of manuscripts based on an index of Diels' Catalogue.

Greek manuscripts containing medical texts were inventoried at the beginning of the 20th century by a team of philologists under the direction of Hermann Diels. The resulting catalogue, however useful it was when new and still is today, needs to be updated not only because some manuscripts have been destroyed, certain collections and single items have changed location, new shelfmark systems have been sometimes adopted and cataloguing has made substantial progress, but also because in Diels' time the concept of ancient medicine was limited, the method used in compiling data was not standardized and, in a time of manual recording and handling of information, mistakes could not be avoided. The present article is an introduction to a new catalogue of Greek medical manuscripts. In the first part, it surveys the history of the heuristic and cataloguing of Greek medical manuscripts from the 16th century forward; in the second part, it highlights the problems in Diels' catalogue and describes the genesis and methods of the new catalogue, together with the plan for its completion; and in the third part, it provides a sample of such a new catalogue, with a list of the Greek medical manuscripts in the libraries of the United Kingdom and Ireland.

Las reglas angloamericanas de catalogación y la norma ISO 690 - 1 y 2 / Anglo-American Cataloguing Rules and ISO 690 to 1 and 2

Se define la catalogación como etapa del ciclo de procesamiento de la información, así como sus diferencias con el proceso de descripción bibliográfica. Se comparan las reglas angloamericanas de catalogación, segunda edición, con las normas ISO 690 - 1 y 2 para la descripción bibliográfica con respecto a: organismo creador, finalidad, alcance, estructura, tipos de asientos, niveles de descripción y sintaxis(AU)

Cataloguing, a phase within the cycle of information processing, as well as its differences with the process of bibliographic description, is defined. The Anglo-American Cataloguing Rules, in their second edition, are compared with the norms ISO 690 -1 and 2 of bibliographic description concerning: creative organization, purpose, reach, structure, type of records, levels of description and syntax(AU)

New directions in medical e-curricula and the use of digital repositories.

Medical educators involved in the growth of multimedia-enhanced e-curricula are increasingly aware of the need for digital repositories to catalogue, store and ensure access to learning objects that are integrated within their online material. The experience at the Faculty of Medicine at McGill University during initial development of a mainstream electronic curriculum reflects this growing recognition that repositories can facilitate the development of a more comprehensive as well as effective electronic curricula. Also, digital repositories can help to ensure efficient utilization of resources through the use, re-use, and reprocessing of multimedia learning, addressing the potential for collaboration among repositories and increasing available material exponentially. The authors review different approaches to the development of a digital repository application, as well as global and specific issues that should be examined in the initial requirements definition and development phase, to ensure current initiatives meet long-term requirements. Often, decisions regarding creation of e-curricula and associated digital repositories are left to interested faculty and their individual development teams. However, the development of an e-curricula and digital repository is not predominantly a technical exercise, but rather one that affects global pedagogical strategies and curricular content and involves a commitment of large-scale resources. Outcomes of these decisions can have long-term consequences and as such, should involve faculty at the highest levels including the dean.

PRECIS: protein reports engineered from concise information in SWISS-PROT.

MOTIVATION: There have been several endeavours to address the problem of annotating sequence data computationally, but the task is non-trivial and few tools have emerged that gather useful information on a given sequence, or set of sequences, in a simple and convenient manner. As more genome projects bear fruit, the mass of uncharacterized sequence data accumulating in public repositories grows ever larger. There is thus a pressing need for tools to support the process of automatic analysis and annotation of newly determined sequences. With this in mind, we have developed PRECIS, which automatically creates protein reports from sets of SWISS-PROT entries, collating results into structured reports, detailing known biological and medical information, literature and database cross-references, and relevant keywords.

Medical illustration: from caves to cyberspace.

The human body has been depicted in ancient cave-paintings, in primitively sculpted figures, and through all the ages in various forms of artistic expression. The earliest medical texts were descriptive but not illustrated. Later, as it became clear that knowledge of the human body and all its systems was essential to the practice of healing, texts were accompanied by illustrations which became an integral part of the teaching process. The illustrators included artists, whose interest was primarily artistic, but who were sometimes employed by surgeons or physicians to illustrate their texts. Occasionally, the physicians or scientists accompanied their texts with their own illustrations, and in the last century, medical illustration, in its infinite variety of techniques, has been developed as a profession in its own right. As knowledge was extended, permitted by social and cultural change, as well as by technological advances, the types of illustrations have ranged from gross anatomy through dissections showing the various organ systems, histological preparations, and radiological images, right up to the computerized digital imagery that is available today, which allows both static and dynamic two- and three-dimensional representations to be transmitted electronically across the world in a matter of seconds. The techniques used to represent medical knowledge pictorially have been as varied as the illustrators themselves, involving drawing, engraving, printing, photography, cinematography and digital processing. Each new technique has built on previous experience to broaden medical knowledge and make it accessible to an ever-widening audience. This vast accumulation of pictorial material has posed considerable problems of storage, cataloguing, retrieval, display and dissemination of the information, as well as questions of ethics, validity, manipulation and reliability. This paper traces these developments, illustrating them with representative examples drawn from the inexhaustible store of documents accumulated over more than two millennia.

MCM generator: a Java-based tool for generating medical metadata.

In a previous paper we introduced the need to implement a mechanism to facilitate the discovery of relevant Web medical documents. We maintained that the use of META tags, specifically ones that define the medical subject and resource type of a document, help towards this goal. We have now developed a tool to facilitate the generation of these tags for the authors of medical documents. Written entirely in Java, this tool makes use of the SAPHIRE server, and helps the author identify the Medical Subject Heading terms that most appropriately describe the subject of the document. Furthermore, it allows the author to generate metadata tags for the 15 elements that the Dublin Core considers as core elements in the description of a document. This paper describes the use of this tool in the cataloguing of Web and non-Web medical documents, such as images, movie, and sound files.

Virtual shelves. II: A unified catalog for a heterogeneous collection.

We describe a unified catalog of traditional and digital resources in medical informatics, using standard cataloging principles (AACR2), schemes (LCC), and coding formats (USMARC). The unified catalog integrates the bibliographic records of physical items in the heterogeneous collection with the bibliographic records of network accessible digital items, using prescribed cataloging formats to new effect. The unified catalog is collections-based. We do not use the MARC 856 field to specify the network location of a digital item. The location of a digital item is determined by mapping its call number through a location guide to a network address. This mapping is strictly isomorphic to the way the shelf location of a physical item is determined within the bounds of a controlled collection.

Cataloging Internet resources.

The number of resources available on the Internet continues to expand exponentially, but finding appropriate resources is still a fragmented, hit-or-miss operation. Traditional library expertise in bibliographic description and access should be applied to the management of this emerging body of material. In the process, catalogers will be able to assess the adequacy of current tools (e.g., cataloging codes, machine-readable cataloging formats, integrated library systems) for providing access to Internet resources and will contribute credibly to design or redesign of access tools. This paper outlines the major issues that must be considered in cataloging electronic resources.

Descriptive cataloging for collections of medical art.

Conserving our profession's historical record would be aided by creating a guide for recording bibliographical information associated with medical art. A guide of this nature should conform to currently accepted national standards for bibliographical listings, reflect the cataloging needs of these specialized materials, and contain a sample data collection sheet. Such a guide would provide a starting point for new or undocumented collections to begin organizing and listing their holdings. This article presents a cataloging guide that is specific to the needs of collecting medical art and that conforms, in both language and structure, to established guidelines for descriptive cataloging.

Government documents and the online catalog.

Prior to planning for implementing the NOTIS system, the Vanderbilt Medical Center Library had not fully cataloged its government publications, and records for these materials were not in machine-readable format. A decision was made that patrons should need to look in only one place for all library materials, including the Health and Human Services Department publications received each year from the central library's Government Documents Unit. Beginning in 1985, these publications were added to the library's database, and the entire 7,200-piece collection is now in the online catalog. Working with these publications has taught the library much about the advantages and disadvantages of cataloging government documents in an online environment. It was found that OCLC cataloging copy is eventually available for most titles, although only about 10% of the records have MeSH headings. Staff time is the major expenditure; problems are caused by documents' irregular nature, frequent format changes, and difficult authority work. Since their addition to the online catalog, documents are used more and the library has better control.