Table of Contents
Index
Glossary
Table of Contents
Index
Glossary

Scientific discourse relations

• Identify the scientific discourse relations that warrant the creation of an explicit link.

• Express the relevant discourse relations in links and present these links in the text of the modules involved, as well as in the navigation menu of each of the modules and in the Map of contents. The different labels that can be associated to scientific discourse relations are summarised in figure A.4.

I Relations based on the communicative function  

• Determine for each module if particular readers are unlikely to understand and/or accept all segments of the module. (Remark: if all readers will probably have problems understanding and accepting the module, the module is not self-contained and you have to add information.)

  In that case, include in the text of the module a link to a target that is aimed at increasing those readers' understanding and/or acceptance. In that link, express an elucidation relation, and/or an argumentation relation. Elucidation implies informative questions, whereas argumentation implies critical questions. The relata of such a relation can be, for example, particular statements made in the module, figures or formulae.

• The expression in links of relations based on the communicative function is aimed at answering the readers' questions. To identify those relations, use prototypical questions that readers may have about the relatum corresponding to the source of the link, which are to be answered by the relatum corresponding to the target of the link.

• When you make a relation based on the communicative function explicit, check if the same link should also express one or more content relations: how are the link and target supposed to increase the readers understanding and acceptance of the source?

I 1

Elucidation relations   (Is elucidated in, Elucidates)

• Determine which modules or segments of modules must be referred to in order to allow readers (that are less informed and/or more interested in the full details of the scientific discourse) to understand each part of the modules.
• Prototypical question: ``What is that and why is that the case? I don't understand this statement.'', as opposed to ``I don't accept this statement''.
• Connect by a link expressing an elucidation relation the segment of the module that some readers are likely to find unclear to the target that should elucidate it.
• If the relation is a general elucidation relation, rather than one of the specific types of elucidation given below, characterise the link expressing it with the labels `Is elucidated in' and `Elucidates'.

Notation: `S Is elucidated in Elucidates T' is denoted in the text of S as [link type: (is elucidated in); target: T], meaning ``(a segment of) the current module S is elucidated in or using the module T'', and in the text of T as [link type: (Elucidates); target: S], meaning that ``S contains a statement or other part that the current module T elucidates''.
Example: In the Situation module A08-m2a Stueckelberg oscillations are mentioned. Bernstein elucidates the phenomenon, i.e. he clarifies what are Stueckelberg oscillations and explains what causes them. The elucidation is made available by a link `A08-m2a Elucidans Elucidandum [Bernstein]'.

I 1.1

Clarification relations   (Is Clarified in, Clarifies)

• If it is unlikely that all readers will understand what some statement or other representation in the source means, i.e. if some readers will find it unclear, provide a link labelled as `Is clarified in' to a target that provides a clarification that is supposed to increase the readers understanding.
• A clarification relation is a specific kind of elucidation relation. Prototypical questions: ``What is that? How does that work?'', as opposed to ``How did that come about'', which requires an explanation.
• When making an clarification relation explicit, check in particular whether the link should also express an elaboration (or in particular carry the label `Is detailed in' or `More context in') or a similarity.

Notation: The link `S Is clarified in Clarifies T' is denoted in the text of S as [link type: (Is clarified in); target: T], meaning ``the (some piece of) module S is clarified in or using the module T'', and in the text of T [link type: (Clarifies); target: S] means that ``S contains an unclear statement or other representation that can be clarified by T''.
Example: In the Theoretical methods module A08-m3cii, the Airy description is used. The reader who does not know what that description amounts to is referred to Airy's article for further clarification:
`A08-m3cii is clarified in clarifies Rf_A0822'.

I 1.1.1

Definition relations (Is defined in, Defines) 

• If it is unlikely that all readers will understand what a particular notion or term in the source means, i.e. if some readers are probably unfamiliar with that term, provide a link labelled as `Is defined in' to a target that provides a definition.
• Prototypical questions: ``What does that term mean?'' or ``What is that object?''. A definition relation is a specific kind of clarification relation. You can define an existing term (lexically) by describing its meaning, define new term (stipulatively) by establishing its meaning, and you can provide a (so-called `real') definition of something (e.g. physical quantity, mathematical function), which is a description that allows the reader to identify its particular characteristics.

Notation: The link `S Is defined in Defines T' is denoted in the text of S as [link type: (Is defined in); target: T], meaning ``the definition of some particular term given in module S can be found in module T'', and in the text of T as [link type: (Defines); target: S], meaning ``that S contains something that requires a definition that is provided in T''.
Example: In the Theoretical methods module A08-m3cii the deflection function is used. The definition of a deflection function is given in the mesoscopic module MESO-m3c-defl:
`A08-m3cii Is defined in Defines MESO-m3c-defl'.

I 1.1.2

Specification relations (Specifications given in, Gives specifications of) 

• If it is unlikely that all readers will know what are the specific features of a particular object described in the source, provide a link labelled as `Specifications given in' to a target that provides a specification. In particular, connect the mention of an apparatus to its full technical specification by a link expressing a specification relation.
• Prototypical questions: ``What is the specification of that object?'' In particular, the reader may ask ``What are the technical specifications of that apparatus?'' or ``What are the particular features of that model?''. A specification relation is a particular type of clarification relation.

• When making a specification relation explicit, check in particular whether the link should also express a resolution relation, i.e. whether it should also be labelled as `Is detailed in'.

Notation: The link `S Specifications given in Gives specifications of T' is denoted in the text of S as [link type: (specifications given in); target: T], meaning ``the specification of some particular object described in module S can be found in module T'', and in the text of T as [link type: (gives specifications of); target: S], meaning that ``S contains the description of an object for which the full specification is given in the current module T''.
Example: The multiplier used in the detection system described in the Experimental methods module A07-m3a is a Bendix M306. For the full technical specification of that apparatus, a link is provided to the manufacturers:
`A07-m3a Specifications given in Gives specifications of (Bendix)'.

I 1.2

Explanation relations  (Is explained in, Explains)

• If the reader is unlikely to understand how the state of affairs given in the source came about, or what caused the phenomenon described in the source, provide a link labelled as `Is explained in' to a target that provides an explanation that is supposed to increase the readers understanding.
• Prototypical question: ``How did the state of affairs referred to in that statement come about?''. For example, the reader may ask: ``What caused this physico-chemical phenomenon, e.g. why is the harpoon reaction so efficient? Why is only the ground state present in this reaction? What caused these restrictions, e.g. why is the interpretation of the experimental results only qualitative?''.

  The question can be formulated as ``Why is that the case?'', if that is interpreted as an informative question. The main issue in explanation is ``I don't understand it'', as opposed to ``I don't accept it'', which implies argumentation. An explanation relation is a specific kind of elucidation relation. Remark that explanation does not provide an answer to the question what were the reasons for choosing a particular (experimental, theoretical, numerical, data analysis) method.

• When making an explanation relation explicit, also express the underlying causal relation.

Notation: `S Is explained in Explains T' is denoted in the text of S as [link type: (Is explained in); target: T], meaning ``(some piece of) the module S is explained in or using the module T'', and in the text of T as [link type: (Explains); target: S], meaning ``that S contains a statement or other representation of information, which has to be explained, that can be explained by a the current module T.
Example: In the Theoretical methods module A08-m3ci1 the relevant potential curves of sodium iodide are discussed. The basic shape of the curves is explained in the mesoscopic module on the atom-atom model MESO-m3c-mod. The explanation is made available by a link `A08-m3ci1 Is explained in Explains MESO-m3c-mod'.

I 2

Argumentation relations (Is argued in, Provides argumentation for) 

• Determine which modules or segments of modules must be referred to in order to allow readers (that are less informed and/or interested in the full details of the scientific discourse) to accept each part of the modules.
• Prototypical questions: ``How can that statement be justified?'' In other words, ``Why is that true? Why is that plausible? Why is that acceptable? What were the reasons to do that?''. The question can formulated as ``Why is that the case?'', if that is interpreted as a critical question. The main issue in argumentation is acceptance of the statement, as opposed to understanding it.
• Connect by a link expressing an argumentation relation the segment of the module that some readers are unlikely to accept without further argumentation to the target that should provide that argumentation.
• In the argumentation you can prove that the statement in the source is true, or justify it, if it cannot be proven rigorously. You can justify the choices that you have made in the research leading to the information represented in that statement in order to convince the reader that the information you have obtained is reliable and relevant.
• The argumentation can involve arguments supporting a standpoint given in the source module, and counterarguments refuting that standpoint. In that case, either show that these counterarguments are not strong enough to refute your standpoint, or indicate that the refuted standpoint was a hypothetical one and present and defend your modified standpoint.

Notation: The link `S Is argued in Provides argumentation for T' is denoted in the text of S as [link type: (is argued in); target: T], meaning ``T contains an argument relevant to the standpoint brought forward in here in S'', and in the text of T as [link type: (provides argumentation for); target: S], meaning that ``in S a standpoint has been put forward for which T provides arguments.
Example: Berry, and Hundhausen and Pauly have done calculations that confirm the expectations of the author of A05, which is presented as an argument in favour of the reliability of the procedure of the determination of the potential well depth and the resulting parameter
`A05-m5bi Is argued in Provides argumentation for R_A0510, R_A0514'.

 

II Content relations  

When you make a content relation explicit, check if the same link should also express one or more relations based on the communicative function: why are the link and target provided; to increase the readers understanding or their acceptance of the source?

  $\mbox{$\bullet$}$

II 1 Dependency relations in the problem-solving process (Depends on, Is used for)  

• Identify the problem-solving dependency relations (between information units) that warrant the creation of an explicit link: determine for each module if the information represented in it depends on the information associated to a previous step in the problem solving process, or if the information represented in it is used in a subsequent step in the problem solving process that is addressed in another module.

  To identify those relations, use prototypical questions that readers may have about the relatum corresponding to the source of the link, which are to be answered by the relatum corresponding to the target of the link. Prototypical question: ``What was the previous step in the problem-solving process that led to this information?''. In other words, ``Where does that information depend on? What has been used to obtain this information? ``

• Determine if the dependency relation is important enough to warrant the creation of a link, and if that is the case, make it explicit in a link. Present these links in the text of the modules involved, as well as in the navigation menu of each of the modules and in the Map of contents. At least include a link expressing the fact that
  • the Interpretation depends on the Treated results that are interpreted;
  • the Interpretation depends on the particular Theoretical methods used to interpret those results;
  • the Treated results depend on the Raw data that they are based on (if available);
  • the Treated results depend on the particular Methods used to generate the results;
  • the Raw data depend on the particular Methods used to generate the data;
  • the Findings depend on the Interpretation;
  • the Findings depend on the Central problem;
  • the information represented in Central problem is used in the Findings.
• If a dependency relation is not important enough to warrant the creation of a new link, but if a link has already been created to represent another type of relation between similar relata, express the dependency relation in that link as well. In particular express the dependency relation in any link that connects the Interpretation to the interpreted Treated results and to the particular Methods used in the process of interpretation, and in any link that connects the Treated results to the appropriate constituents of the Methods.

Notation: The link `S Depends on Is used for T', denoted in the text of S as [link type: (Depends); target: T], means that ``the information represented in S depends on the information in T'', in the sense that the reader of S is supposed to be sufficiently informed of T to understand S. In the text of T [link type: (Is used for); target: S] then means that ``the information given in T can be used to advance a problem-solving process to a subsequent stage, that is addressed in S''.
Example: The Treated results in A05-m4bi depend on the Experimental Methods used to generate them in module A05-m3a, and conversely the methods described in module A05-m3a can be used to get the Treated results: `A05-m4bi Depends on Is used in A05-m3c'.

II 1.1

Transfer relations   (Input from, Output to)

• Determine for each module if a particular manipulable item has been imported as input from another module, or if such an item is exported as output to another module, and if the relation is important enough to warrant the creation of a new link. Examples of such items are: formulae, figures, values of parameters.
• A transfer relation is a particlar type of dependency relation in the problem-solving process. Prototypical question: ``Where does that item come from?''.

Notation: The link `S Input from Output to T' is denoted in the text of S as [link type: (input from); target: T], meaning ``in the module S some item from module T is used as input'', and in the text of T [link type: (output to); target: S] means ``a piece of information from module T is exported as output to module S''.
Example: A theoretical value of the polarizability of K<sup>+</sup>, determined by Duren and Rittner, is used as input in A05-m5bi in the process of the interpretation in which some potential parameters are calculated: `A05-m5bi Input from Output to R_A053, R_A054'.

II 2

Elaboration relations  (Is elaborated in, Elaborates)

• If some readers are likely to require further information in order to fully understand and accept the information given in a module or a particular segment of a module, provide a link to a target with an elaboration of the source.
• Elaborating on a statement can involve filling in further details, or providing more context.
• If a link labelled as `Is elaborated in', or more specifically as `Is detailed in' or `More context in', does not carry a label associated to a relation based on the communicative function, that link by default expresses both an elucidation of the source and argumentation aimed at convincing the reader that the source is reliable and relevant in the situation at hand.
• Check if a link representing a particular elaboration relation should also express a synthesis relation: should a particular link labelled as `Is summarised in' or `More context in' also carry a label `Is generalised in' or `Is aggregated in'?

Notation: The link `S Is elaborated in Elaborates T' is denoted in the text of S as [link type: (is elaborated in); target: T], meaning ``the source S is `Elaborated upon' in the module T'', i.e. T provides more information on the subject than S, and in the text of T [link type: (elaborates); target: S] means that ``moving from T to S the information becomes more limited'', in the sense that S provides less information on the subject than T.
Example: The mesoscopic sketch of the situation provides both greater detail and a broader perspective than, i.e. an elaboration of, the microscopic Situation: `A05-m2a Is elaborated in Is limited in MESO-m2a'.

II 2.1

Resolution relations  (Is detailed in, Is summarised in)
If some readers are likely to require further details, i.e. a finer-grained account of the subject, provide a link carrying the label `Is detailed in' to a target with those details. A resolution relation is a specific kind of elaboration relation.

Notation: The link `S Is detailed in Is summarised in T' is denoted in the text of S as [link type: (detail); target: T], meaning ``the module S is `detailed' in the module T'', i.e. T provides more detailed information on the subject than S, and in the text of T [link type: (Is summarised in); target: S] means ``that S summarises that information in T, in the sense that S provides fewer details on the subject than T''.
Example: A module Experimental methods gives greater detail about a set-up than the abstract, which summarises the method that has been used: `A05-m1d Is detailed in Is summarised inA05-m3a'.

II 2.2

Context relations  (More context in, Is focused in)
If some readers are likely to require more context, i.e. more background on the subject, provide a link carrying the label `More context in' to a target with that background. A context relation is a specific kind of elaboration relation.

Notation: The link `S More context in Is focus in T' is denoted in the text of S as [link type: (More context in); target: T], meaning ``the module T provides more surroundings of (some segment of) the module S'', i.e. T provides more context than S, and in the text of T [link type: (Is focused in); target: S] means ``that S focuses on some aspect of the information in T''.
Example: Although the module Experimental methods gives greater detail about a set-up, the abstract gives a wider perspective of the situation in which the method is used. Going from the abstract to the methods module, the reader focuses on a more narrowly defined subject: `A05-m3a More context in Is focused in A05-m1d'.

II 3

Similarity   (Disagrees with, Is compared with, Agrees with)

• If you compare information provided in the module at hand, or a particular segment of it, to information given in another module, express the similarity of those relata in a link connecting the modules or segments of modules representing them. You can compare information represented in (a particular segment of) a module to information represented in another module of the same article or in a module that is part of another article.

• State in the text of the module in what respect the relata are similar.

• If a link representing a comparison does not carry a label associated to a relation based on the communicative function, that link by default expresses both an elucidation of the source and an argumentation relation aimed at convincing the reader that the source is reliable and relevant in the situation at hand. For example, you can compare different results obtained for similar systems in order to convince the reader of the reliability of those results, or compare the detector that you have used to the one used in some well-known research in order to clarify your set-up and in the same time to justify that it is reliable.
• Three labels can be associated to this relation: neutral comparison, agreement and disagreement.
  • Comparison
    Notation: The link `S Is compared with Is compared with T' is denoted in the text of S as [link type: (Is compared with); target: T], meaning ``the current module S is compared with module T'' (using the same system and a different method or vice versa).
    Example: The authors try to compare results of a Russian group, which has reported similar experiments, with the results presented in article A03-m4b. However, the energy ranges do not overlap, so that the results are not really comparable:
    `A03-m4b Is compared with Is compared with Rf_A0525'.
  • Agreement:
    Notation: The links S Agrees with Agrees with T is denoted in the text of S as [link type: (Agrees with); target: T], meaning ``the opinion expressed in module S agrees with the opinion expressed in module T''.
    Example: The value of the electron affinity that is obtained in the interpretation process agrees with the value suggested by Person:
    `A05-m5bi Agrees with Agrees with Rf<sub>A05</sub>2'.
  • Disagreement
    Notation:The link `S Disagrees with Disagrees with T' is denoted in the text of S as [link type: (Disagrees with); target: T], meaning ``the opinions expressed in module S disagrees with the opinion expressed in module T''.
    Example: The electron affinity A(Br₂) disagrees with the value obtained in A05 (which casts doubts on the applicability of the theory discussed in A05-m3c): `A05-m3c Disagrees with Disagrees with A03-m4'.
    

   

Figure A.4: The different types of labels associated to the scientific discourse relations.

II 4

Synthesis relations 

• There are two types of asymmetric synthesis relations between individual units and synthesised units: aggregation and generalisation
• Check if a link representing a synthesis relation should also express a hierarchical relation.

II 4.1

Aggregation relations  (Is aggregated in, Is segregated in)

• Identify the asymmetric relation between the information provided in modules focusing on aggregate concepts and the information represented in modules on its component concept. An aggregation relation can be expressed, for example, 1) between a microscopic module on a specific application of an entire set-up, and a mesoscopic module on a particular component of the apparatus, 2) between the complete set of theoretical methods and the component that is used for one particular step in the calculations, or the component that gives the particular approximation used to calculate a particular area.

• Identify aggregation relations in the context of hierarchical relations between constituent modules and compound modules.

• Check if a link labelled as an aggregation should also carry an elaboration label `Is summarised in' or `More context in', and vice versa if segregation entails details and a stronger focus.

Notation: The link `S Is aggregated in Is segregated in T' is denoted in the text of S as [link type: (is aggregated in); target: T], meaning ``the module T is an aggregate of (some segment of) the module S'', and in the text of T [link type: (Is segregated in); target: S] means ``that S is a component of the aggregate in T''.
Example: The Theoretical methods module A08-m3c (about the calculation of the differential cross section of the reaction using an atom-atom model) contains two components: A08-m3ci deals with the transition probability and subsequently A08-m3cii with the differential cross section, in which the transition probability is used. The link between the complex module and A08-m3ci carries the following label:
`A08-m3ci Is aggregated in Is segregated in A08-m3c'.

II 4.2

Generalisation relations  (Is generalised, Is specialised in)

• Identify the asymmetric relation between the information provided in modules focusing on specific concepts and the information represented in modules on the generalised concept. A generalisation relation can be expressed, for example, 1) between a microscopic module on the application of a set-up in specific measurements, and a mesoscopic module on the apparatus in general, 2) between the application of a specific combination of theoretical models and approximations to particular experimental results, and the general description and discussion of those theoretical methods, 3) between the specific application of numerical methods and the general account of them.

• Identify generalisation relations in the context of hierarchical relations between constituent modules and cluster modules, in which case the link is also implicitly labelled as `Article'.

  Check if a link labelled as a generalisation should also carry a range-based label `To wider range', or a resolution label `Is summarised in'.

Notation: The link `S Is generalised in Is specialised in T' is denoted in the text of S as [link type: (is generalised in); target: T], meaning ``the central concept of module T is a generalisation of a concept in the module S'', and in the text of T [link type: (Is specialised in); target: S] means ``that S represents a concept that is a special case of the general concept focused on in T''.
Example: The module Theoretical methods A08-m3ci about transition probability in general contains two constituent modules, A08-m3ci1 and A08m-3ci2, about two different, specific types of transition probability:
`A08-m3ci1 Is generalised is specialisation A08-m3ci'.

II 5. Causal relations  (To cause, To effect)

• If the cause for an effect stated in the module at hand is given elsewhere, refer to that cause by means of a link expressing a causal relation.
• Check in particular whether the link expressing a causal relation can also be labelled as an explanation.

Notation The link `S To cause To effect T' is denoted in the text of S as [link type: (To cause); target: T], meaning ``the cause of the state of affairs or phenomenon described in S is given in T'', and in the text of T [link type: (To effect); target: S] means ``that S gives an effect that is caused by something stated in T''.
Example: In the Theoretical methods module A08-m3ci2 it is stated that only the groundstates are taken into account. The cause why only those states are present in the system is given in A08-m3ci1:
`A08-m3ci2 To cause To effect A08-m3ci1'.