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H2PTM (1989) Burridge

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An electronic book for molecular biology
An electronic book for molecular biology
Jane M. Burridge
IBM Eurocoordination
Tour Pascal, La Défense 7 Sud Cedex 40
F-92075 Paris La Défense
actes du colloque H2PTM 1989 Paris
publié dans H²PTM89 : Communication interactive, Paris, France, 1990
Livre électronique; Système d'information; Lien; Hypermédia; Biologie moléculaire; Classification

As scholars, researchers and authors we are rarely satisfied with the fixed, sequential and two-dimensional nature of the printed information source. We like to annotate, underline, highlight, cut-and-paste; we often attach other pieces of information, such as photographs; we pencil in reference to related textes or other sources. Other sources of information available to us, databases for instance, would also benefit greatly from the provision of such facilities. The provision of on-line access and search facilities of increasing sophistication helps, of course, but currently available systems fail far short of the complete information system one might imagine for the future.

One can envisage a system in which a potentially limitless store of all types of information can be navigated with ease; in which drawings of three-dimensional objects can be manupulated; sequences of events animated; relevant sounds heard. A system in which the individual may not only follow links and associations defined by the compilers, but also define links of their own to personal information resources or to areas of information relevant to their particular fiels of interest In other words, an information source which may be personalised.

As early as 1945, Vannevar Bush, the scientific adviser to President Roosevelt, envisaged system in which individuals would store all their books, records and communications and then form paths through this information to allow rapid access to specific items. The vision of this “memex” device served as inspiration for the development of “hypertex”—a term coined late Sixties—and “hypermedia” systems.

A hypertext system allows an author or group of authors to annotate texts, create notes to point readers to other places in the body of the referenced text, or to bibliographic data; link related items of information together, and create paths and networks through a body of related material. Readers can browse through linked, cross-referenced and annotated texts in an orderly but not necessarily sequential manner. A hypermedia system provides these facilities, extended to include graphics, images, sound and animation.

Such a body of inter-related pieces of information resembles the way in thish the human mind holds and associates information more closely than does the flat or linear structure imposed by the need to use the written or printed word. Early hypermedia systems were restricted in that links were pre-programmed. Interactive links in newer systems give users a freedom limited only by their imagination.

Collaboration between IBM and Oxford University Press in the UK has led to the publication of the Oxford English Dictionary on CD-ROM, with software which allos the user to search through the dictionary in ways impossible—or at least highly impractical—with the printed version. The collaboration is continuing with a molecular biology project to explore the publication, on CD-ROM, of numerical date, texts, graphics and images which need to be browsed, searched and manipulated interactively. Such a reference work could, in principle, accomodate data of many types. It is especially appropriate for molecular data, since the large sets are generated by machine and are also processed by machine. In addition of course, molecular structures are complex three-dimensional shapes, whose structures and properties are best presented as pictures on a screen rather than on paper, especially when pictures can be manipulated in three dimensions.

The CD-ROM publication holds numerical data defining 400 or so large protein molecules together with several hundred high resolution colour pictures depicting these molecules, several texts describing key properties, regularities, and peculiarities of molecules, and some programs. A flexible multi-windowing environment allows textual material to be formatted to windows on the screen, browsed, searched, and hypertext-like links followed; images to be displayed, re-sized, panned, scrolled and re-scaled; numerical data to be browsed, or in more structured form, explored and searched; and molecular graphics of various types to be generated in real time from the numerical data.

Through the use of icons representing hierarchical arrangements of pieces of information and groups of such pieces, a reader can select information from this database according to a variety of classification schemes: for example a pictorial represtation of a virus structure might be arrived at by navigating through the picture library; by navigating through classification according to molecular function (and choosing viruses); by the name of the virus; and so on using as many classifications as authors and editors see fit to provide.

Hypertext / hypermedia tools fulfila dual role, being both means of authoring, and aids to accessing, information. The role of editor, technical editor, and publisher need to be redefined; aids must be developed not just for producing new publications in electronic form, but also for capturing existing publications.

However these questions have not been addressed in the present project, which concentrates on the “reader” rather than the “author”.

Such a system will be a vital tool for both research and teaching in the molecular sciences; equally clearly this project represents just one application of a general principle. Some part of a system must be specific, of course, to the molecular sciences, but much of it—including the windowing, and the handling of image and graphics—will be general enough to allow other systems to be built. Each of the applications added by tailoring these basic components will represent a small step along the road towards the total information systems of the future.