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In this glossary, we summarise our definitions. We also clarify how we use some terms that may give rise to misunderstanding.
Article: A scientific article is a document in which scientific information is presented, in particular a refereed original account of an original piece of research dealing with a particular topic, addressed to (relative) peers, published in a scientific journal.
Comment: In a broader sense of the word, a scientific article is a document in which information obtained from research is presented. We concentrate on scientific articles in the narrow sense of the word, which have the following distinguishing characteristics: the core of the information represents original research, the article is aimed at a target audience of fellow experts or at least other scientists, the article has been subjected to some form of peer review and the article has been published in a scientific journal of some form. This definition is given in section 2.1.3
Article, linear: An article is called linear if it consists of a single unit in which the information is presented in a single narrative, i.e. in the form of a traditional essay.
Comment: The linearity of an article is a property determined by the author. See also `sequential consulting'.
Article, modular: A modular article is an article with a modular structure, i.e. an article which consists of modules and links between modules that constitute a coherent unit for the purpose of communication.
Comment: A modular article represents a network of information within the total network of information in which the information presented in the article is embedded. The general definitions given in section 3.3, guidelines for writing a modular article in appendix A and examples in appendix C.
Characterisation space: A characterisation space is a space spanned by the dimensions of the typology, in which an entity is characterised by its location.
Comment: Our characterisation spaces are based on Gärdenfors's idea of conceptual spaces. See section 3.2.
Communication: By communication we mean the transfer of information from a human sender to a human receiver, for the purpose of increasing the receiver's knowledge, enabling him to carry out tasks, or influencing his attitudes and behaviour.
Comment: We consider a human-oriented, rather than a machine-oriented, notion of communication. See section 2.1.1.
Communication criteria: Communication criteria are the criteria which the presentation of scientific information, and in particular the structure of scientific articles, has to satisfy in order to be adequate in the light of the interactants profile.
Comment: The discussion of the characteristics of the process scientific communication via articles and the requirements of the interactants in that process lead to to the formulation of communication criteria for electronic articles in section 2.4.
Communicative function: Apart from its (propositional) content, a text has a communicative function.
We concentrate on the communicative functions 'informing' and justifying'. We have used the communicative function in the analyis of articles (see section 4.1.2). We also use the communicative function of the text (or other representation forms) in one module with respect to that in another module, i.e. the relation based on the communicative function, in the characterisation of the link between these modules. See section 4.3.3.
Conceptual function: The conceptual function of information is its function in the problem-solving process of the research.
A module distinguished by the conceptual function of the information is thus characterised by its function in the problem-solution patterns reflected in the article. We have called it the `conceptual function' to emphasise the fact that it works at the conceptual level, rather than the grammatical level for example (where we consider a concept as a largely learned open mental representation of some aspect of some universe of discourse. See [Thagard, 1992] for an overview of different interpretations of the notion of concept.)
Discourse: By discourse we mean a formal, orderly and usually extended expression of thought on a subject.
Comment: (Definition from WWWebster Dictionary) The discourse in a scientific article is the `story' that the authors are telling, reporting their work and justifying its reliability and relevance.
Document: A document is a representation of a `portion' of information (in some language, in some medium) that can be stored and retrieved separately.
Comment: Articles and books are examples of documents, as are modules. Thus a document may consist of 'subdocuments'. Traditionally documents are written on paper. However, in our broad definition a document may for example consist of an electronically stored non-verbal representation of information.
Documentbase: A documentbase is a structured collection regularly structured documents which can be accessed by more than one person and/or used for more than one purpose.
Comment: An example of a documentbase is a journal. This definition is phrased like the definition of a database given in [Frost, 1986]: a structured collection of regularly formatted data which can be accessed by more than one person and/or used for more than one purpose. That collection is arranged for ease and speed of retrieval, mostly by a computer. A knowledge base is then a collection of simple facts and general rules (i.e. complex facts) representing some universe of discourse.
Effectiveness: Having an intended or expected effect.
Comment: Communication is effective if the information needs of each interactant are satisfied, for example. We do not use the terms effectiveness and efficiency as synonymous, but as complementary.
Efficiency: The ratio of the effective output to the total input in a system.
Comment: Communication is efficient if no effort is wasted in the process, for example in the transmission of unneeded information.
Information, scientific: Scientific information is a conceptual representation of aspects of a universe (in particular `the real world'), based on scientific research.
Comment: We use a mental interpretation of the term information which allows for information to exist without succesful communication. It has to be represented in terms of a language and then encoded in a signal for communication. In the term `information', we do not restrict ourselves to with simple facts: information can be complex, consisting of smaller 'chunks' of information and various relations between them, which is sometimes called knowledge. Data are simple, factual information. See section 2.1.1
Interactants profile: A model in which the presumed characteristics are given of the prototypical interactants in the process of scientific communication via articles, as well as their requirements for effective and efficient communication.
Comment: A profile of the interactants in communication via scientific articles is sketched in section 2.2.2 and specified for the domain of experimental molecular dynamics in section 5.1.2.
Journal, scientific: A scientific journal is a documentbase in which certified documents of a particular type on a specified subject in science aimed at a specific target audience are published.
Comment: A journal thus is defined by its functions of certification and registration of articles, of (allowing for) archiving and of making the audience aware of it. In our broad definition of the word journal, we do not specify the medium or that is has to be a periodical. See section 2.1.3.
Library: A library is an information managing institution with tasks including acquisition and storage of published information with the purpose of making it available to and accessible for the target public.
Comment: The functions of libraries are changing. See [Scovill, 1995].
Link: A link is a uniquely characterised, explicit, directed connection between (parts of) modules that represents one or more different kinds of relevant relations between (parts of) modules or (parts of) the information units underlying those modules.
Comment: See section 3.1.2 for the abstract definition. Types of relations that can be represented in links in articles on experimental sciences are given in section 4.3, and on experimental molecular dynamics in general in section A.3.
Meta-information: Meta-information is information about the article.
Comment: Likewise, metadata are simple data about the article. Examples of meta-information are: the names of the authors, the date of publication and the abstract. We define the module Meta-information representing the meta-information of a modular article in section 4.2.7.
Modular model: A modular model is a model for structuring the representation of information in a distributed storage environment, in a particular domain and genre. The modular model gives the definitions of the types of 1) modules and 2) links that can constitute a modular structure, and 3) the rules for the composition of a modular structure.
Comment: See section 3.3 for the abstract definition, and chapter 4 for a domain specific modular model for articles on experimental sciences. In section 6.2.1 we indicate how our model can be adapted to other domains.
Modular structure: A modular structure is a pattern of modules and explicit links between modules.
Comment: See section 3.1.1 for the abstract definition. The structure is determined by the definition of the modules, the definition of the links and the rules for putting these together. A domain and genre specific definition of the ingredients of the modular structure is given in chapter 4 for articles on experimental sciences and in section A.1 for experimental molecular dynamics in particular. See appendix C for concrete examples of articles with a modular structure.
Module: A module is a uniquely characterised self-contained representation of a conceptual information unit, which is aimed at communicating that information.
Comment: Depending on the language in which the information is represented, a segment of a module can consist of, for example, a phrase, a paragrah, a mathematical formula, a figure, or a movie.
See section 3.1.1 for the abstract definition. A domain and genre specific definition of modules is given in chapter 4 for articles on experimental sciences and in section A.1 for experimental molecular dynamics in particular. See appendix C for concrete examples. There are different kinds of modules: elementary modules and complex modules, including compound and cluster modules.
Module, cluster: A cluster module is a complex module in which the central concept is a generalisation of the specific concepts focused on in each (elementary or complex) constituent module.
Comment: A cluster module does not change in nature when a particular constituent is added or removed. See section 4.2.2, and appendix A for domain specific definitions of cluster modules.
Module, complex: A complex module consists of a coherent collection of (elementary or complex) constituent modules and the links between them.
Comment: A complex module can contain elementary modules, as well as smaller complex modules. The relation between the constituent modules is a necessary ingredient, such that a set of unrelated modules does not form a complex module. See section 3.1.3 for the abstract definition. We distinguish two special kinds of complex modules: compound modules and cluster modules.
Module, compound: A compound module is a complex module that is an aggregate of (elementary or complex) constituent modules.
Comment: A compound module has to consist of a necessary minimum (and maximum) of constituent modules. See section 3.1.3 for the abstract definition, and section 4.2.2 and appendix A for domain specific definitions of compound modules.
Module, elementary: An elementary module contains information that cannot be represented in more than one separate module
Comment: See section 3.1.3 for the abstract definition.
Peer review: Peer review is the process of judging the quality of the information in and the presentation of an article by experts on the subject the article deals with, where the judgement is explicitized in the form of a recommendation.
Comment: The demarcation between the duties of the editor and the referee depend on the strategy of the journal or the publisher. In some journals, the editor is solely responsible for the rejection of the article, or the acceptance, possibly after modification. In other journals, the editor's work is of a more administrative nature, and the article is always judged by at least two referees.
Peer review is part of the process of scientific communication via articles. It can also take place after publication of the article, in the form of comments or ratings in some form attached to the published article. See section 2.1.3.
Publication: 1. The act or process of publishing or making public information represented in some language, in some medium.
2. A published document, representing information in some language, in some medium.
Comment: The act of making public primary scientific information is part of the process of scientific communication via articles described in section 2.1.1. Publication can take place in two ways: by disseminating the work to be published directly to the target audience, or by archiving it and making it available to the audience.
A publisher is an information managing person or institution whose tasks include the acquisition of unpublished information, the organisation of refereeing and certification, and the actual publication. Thus, the term `publisher' covers a lot more than `company selling paper journals'.
Relata: A relatum (plural relata) is one end of a relation: relations are between relata.
Comment: In section 4.3, we explain how the relata correspond to the source and the target of the link expressing the relation, and which types of relata can be distinguished in different cases.
Review paper: A review paper is a non-trivial compilation of articles.
Comment: In a review paper the information of existing articles is not only presented but also improved upon, made more explicit, detailed, precise, complete. It may be a review of the author's your own work or an overview of the current state of affairs in a certain area of science, in which the different approaches and developments are compared. Review papers are often used as the `tutorials of the researcher', who cannot find information advanced enough in existing books
Sequential reading: An article is consulted sequentially when it is consulted in a predefined order.
Comment: Contrary to linearity, 'sequentiality' is not a property of the article but of the way to consult it. The natural way to consult linear articles is sequentially. Modular articles can also be consulted sequentially. The author of a modular article has to indicate a preferred route which the reader can follow.
Typology A typology is a multidimensional classification, in which the categories are distinguished from a conceptual rather than an empirical perspective.
Comment: We use a typology to identify and characterise the modules and the links in the modular structure In section 3.2 the general features of the required typologies are discussed
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