Abstract
Precise information retrieval
in semantic scientific digital
libraries
Hélène de Ribaupierre
Direction de thèse:
professeu...
PRECISE INFORMATION RETRIEVAL IN SEMANTIC SCIENTIFIC DIGITAL
LIBRARIES
Thèse présentée à la Faculté des sciences économiqu...
La Faculté des sciences économiques et sociales, sur préavis du jury, a autorisé
l’impression de la présente thèse, sans e...
Precise information retrieval in
semantic scientiﬁc digital libraries
THÈSE
présentée à la Faculté des sciences économique...
English Abstract
When scientists are looking for information in document collections, or on the
web, they generally have a...
Résumé en Français
Lorsqu’ils eﬀectuent des recherches de documents scientiﬁques ou techniques,
les scientiﬁques ont des o...
Acknowledgments
Sorry for the English speaking people, but even if my thesis is in English I prefer
writing my acknowledge...
vi
doctorant (conférences, mentorat, et j’en passe); Wanda pour m’avoir sustenté et
m’avoir permis de me défouler avec une...
Contents
1 Introduction 1
2 User model 7
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ...
viii Contents
4.4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
4.4.2 Implementation . . . . ...
Contents ix
C SciDeo ontology 205
D Methodology ontology 209
E Scientiﬁc object ontology 213
F Gender studies ontology 217...
List of Tables
2.1 "Why do you read scientiﬁc documents" (in percent, n=91) . . . . . 25
2.2 "Why do you read scientiﬁc do...
xii List of Tables
4.11 Cross-table between Workers A and scientist 1 for the ﬁve types of
discourse elements . . . . . . ...
List of Figures
2.1 A stage process version of Ellis’s behavioural framework (1993)
[Ellis et al. 1993] . . . . . . . . . ...
xiv List of Figures
3.8 SciAnnotDoc model ontology; orange classes are the SciDeo ontology 88
3.9 SciAnnotDoc ontology in ...
List of Figures xv
6.3 Irrelevance of the set of results by interface (some scores have been
inverted, so that all are in ...
Chapter 1
Introduction
This research thesis aims to develop models and tools for precise information re-
trieval and strat...
2 Chapter 1. Introduction
age their personal data (photos and video) than are available to manage or search
their professi...
3
meta-information not only at the document level but at a ﬁner level, such as the
section, paragraph, sentence, or word l...
4 Chapter 1. Introduction
notDoc) for scientiﬁc documents based on the user model, c) demonstrate that the
annotation mode...
5
2011. ACM.
Hélène de Ribaupierre and Gilles Falquet. Recherche d’information dans des
corpus scientiﬁques basée sur la s...
Chapter 2
User model
Contents
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2 State of the ...
8 Chapter 2. User model
2.4.2.7 Do you focus on speciﬁc fragments or parts of a doc-
ument, and which ones do you prioriti...
2.2. State of the art 9
inquiry, the nature of information needs, the objectives of searches performed by
users, and the n...
10 Chapter 2. User model
• Extracting: Selecting and identifying relevant material.
• Verifying: Checking that the informa...
2.2. State of the art 11
Figure 2.2: Information Search Process (ISP), Kuhlthau’s model, 1991
[Kuhlthau 1991, p.367]
Figur...
12 Chapter 2. User model
Wilson’s model Wilson began developing his model in 1981 (see ﬁgure 2.4)
[Wilson 1981]. The aim o...
2.2. State of the art 13
Figure 2.5: Wilson’s model of information-seeking behaviour (1981) [Wilson 1999,
p.252]
model, as...
14 Chapter 2. User model
Figure 2.6: Wilson’s model of information behaviour (1986) [Wilson 1999, p.257]
2.2. State of the art 15
The Ellis model has been used in other studies, such as the study by
[Meho & Tibbo 2003], in whic...
16 Chapter 2. User model
• Verifying: The scientists interviewed in this study were preoccupied with the
reliability and a...
2.2. State of the art 17
2.2.2 Scientiﬁc inquiry models, nature of the needs of information,
new forms of behaviour
Scient...
18 Chapter 2. User model
• To integrate ﬁndings into the current state of knowledge in an area
and the stages of research ...
2.2. State of the art 19
Figure 2.7: Garvey’s table for the nature of information needed at each stage by the
majority of ...
20 Chapter 2. User model
In a thorough and wide-ranging study on changes in scholars’ article-seeking
and reading patterns...
2.2. State of the art 21
In [Kembellec 2012], the authors also detected some diﬀerences between diﬀerent
ﬁelds of research...
22 Chapter 2. User model
(e.g., neuroticism, extraversion openness, agreeableness) may change this behaviour.
Considering ...
2.2. State of the art 23
using this system. DELIVER was a system deployed at the University of Illinois
at Urbana-Champaig...
24 Chapter 2. User model
2.3 Survey
Scientists have some speciﬁcity in their information-seeking behaviour, as demon-
stra...
2.3. Survey 25
articles stating that rain is wet), with answers measured on a Likert scale ranging
from strongly agree to ...
26 Chapter 2. User model
We found few diﬀerences between the domains of research regarding the rea-
sons why scientists re...
2.3. Survey 27
Figure 2.8: "Why do you read scientiﬁc documents by area of research by area of
research"; often answer
0"
...
28 Chapter 2. User model
Table 2.3: "Why do you read scientiﬁc documents by area of research" (in percent
n=91), year of b...
2.3. Survey 29
2.3.2.2 Do you read scientiﬁc papers to respond to a precise need
With regard to this issue, 83.5% of respo...
30 Chapter 2. User model
Table 2.5: "Where do you generally ﬁnd your answers by area of research" (in
percent, n=77) "soft...
2.3. Survey 31
Figure 2.10: "Where do you generally ﬁnd your answers by area of research"; often
answer
0"
20"
40"
60"
80"...
32 Chapter 2. User model
2.3.2.4 Do you often conduct a review of the literature
In response to the question, "Do you ofte...
2.3. Survey 33
2.3.2.5 Do you easily ﬁnd papers/books you are looking for without too
much noise (e.g., a paper that is ou...
34 Chapter 2. User model
Figure 2.12: "Would you like a retrieval system that would be able to ﬁnd articles
by their concl...
2.3. Survey 35
Figure2.13:Relationshipbetweentaskandwhatpartsareread
36 Chapter 2. User model
2.3.3 Survey Discussion and Conclusion
The reasons scientists read scientiﬁc documents appear to ...
2.4. Interview 37
2.4.1 Methodology
We conducted semi-directive interviews with scientists from diﬀerent areas of re-
sear...
38 Chapter 2. User model
readers looked at diﬀerent fragments depending on their ultimate task. We de-
ﬁned a list of task...
Precise information retrieval in semantic scientific digital libraries
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Precise information retrieval in semantic scientific digital libraries

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When scientists are looking for information in document collections, they generally have a precise objective in mind. They try to answer specific needs such as finding the definition of a concept, checking whether an idea has already been tested, or comparing the scientific conclusions of several documents. To build better information system model it is important to understand the needs of scientists in terms of information and their seeking information behaviour. The contributions of this thesis are to a) offer a user model; b) propose a generic annotation model (SciAnnotDoc) for scientific documents; c) demonstrate that the annotation model is realistic enough to be used by both manual and automatic methods of annotation; d) build a faceted search interface (FSAD) and e) evaluate the model with scientists and show that the FSAD interface is more effective than a keywords-search, notably in terms of user preference, recall and F1 measure.

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Precise information retrieval in semantic scientific digital libraries

  1. 1. Abstract
  2. 2. Precise information retrieval in semantic scientific digital libraries Hélène de Ribaupierre Direction de thèse: professeur Gilles Falquet FACULTÉ(DES(SCIENCES((ÉCONOMIQUES(ET(SOCIALES
  3. 3. PRECISE INFORMATION RETRIEVAL IN SEMANTIC SCIENTIFIC DIGITAL LIBRARIES Thèse présentée à la Faculté des sciences économiques et sociales de l’Université de Genève Par Hélène de Ribaupierre pour l’obtention du grade de Docteure ès sciences économiques et sociales mention : Système d’Information Membres du jury de thèse : Prof. Gilles FALQUET, directeur de thèse, Université de Genève Prof. Giovanna Di MARZO SERUGENDO, présidente du jury, Université de Genève Prof. Fabio CRESTANI, Università della Svizzera italiana USI, Lugano Prof. Henning MÜLLER, Université de Genève et Institut informatique de gestion, HES-SO, Valais Thèse N° 869 Genève, le 1er décembre 2014
  4. 4. La Faculté des sciences économiques et sociales, sur préavis du jury, a autorisé l’impression de la présente thèse, sans entendre, par là, n’émettre aucune opinion sur les propositions qui s’y trouvent énoncées et qui n’engagent que la responsabilité de leur auteur. Genève, le 1er décembre 2014 Le vice-recteur Denis HOCHSTRASSER Impression d’après le manuscrit de l’auteur
  5. 5. Precise information retrieval in semantic scientiﬁc digital libraries THÈSE présentée à la Faculté des sciences économiques et sociales de l’Université de Genève par Hélène de Ribaupierre Sous la direction de Prof. Gilles Falquet pour l’obtention du grade de Docteure ès sciences économiques et sociales mention systèmes d’information Membres du jury de thèse: M. Fabio CRESTANI, Professeur, Università della Svizerra Italiana Mme. Giovanna DI MARZO SERUGENDO, Professeure, présidente du jury M. Henning MULLER, Professeur, HES-SO Valais et Faculté de Medecine, Université de Genève Thèse n 869 Carouge, le 1er décembre 2014
  6. 6. English Abstract When scientists are looking for information in document collections, or on the web, they generally have a precise objective in mind. Instead of looking for docu- ments "about a topic T ", they rather try to answer speciﬁc needs such as ﬁnding the deﬁnition of a concept, ﬁnding results for a particular problem, checking whether an idea has already been tested, or comparing the scientiﬁc conclusions of several documents. The ﬁrst contribution of this thesis, is to understand better the needs of scientists in terms of information and their seeking information behaviour and to build a user model from these observations. The methodology used were interviews and a survey. One of the results was that scientists focus in chunks of texts (discourse elements) when they are seeking and reading scientiﬁc documents, and not at the entire document. The second contribution of this thesis is a generic annotation model for scientiﬁc documents using Semantic Web technologies (SciAnnotDoc model) based on the discourse elements that are most frequently used by scientists according to the user model: ﬁndings, hypothesis, deﬁnition, methodology and related work. The SciAn- notDoc model is based on four dimensions or facets: the metadata dimension, the conceptual dimension (terms and concepts), the discourse dimension and the rela- tionships dimension (relation between discourse elements). The diﬀerent dimensions are modelled into separate ontologies. The third contribution of this thesis is an automatic annotation process based on these ontologies. We annotated automatically 1’410 document in gender studies with the SciAnnotDoc model using syntactic patterns to discover the discourse elements at the sentence level. The fourth contribution of this thesis is the evaluation of the annotation model with "real users". We built a faceted-search based (FSAD) on the four dimension- s/facets of the SciAnnotDoc model. The evaluation by scientists showed that they seem to prefer and ﬁnd the results obtained using the FSAD more relevant and with a better recall than result provided by a keywords-search interface using a terms indexing. Keywords: Semantic publishing, Information retrieval, Ontology, Knowledge management
  7. 7. Résumé en Français Lorsqu’ils eﬀectuent des recherches de documents scientiﬁques ou techniques, les scientiﬁques ont des objectifs précis en tête. Avec l’augmentation des documents scientiﬁques disponibles aujourd’hui , répondre à ce besoin d’information est de plus en plus diﬃcile pour les scientiﬁques que cela soit en termes de temps ou de détection des documents pertinents dans cet océan de littérature. Il devient donc de plus en plus important d’avoir de bon moteurs de recherche qui répondent aux besoins des scientiﬁques. Pour ce faire, nous avons d’abord mené des interviews et une enquête auprès de scientiﬁques pour comprendre plus précisément comment ils recherchent leurs informations et travaillent avec les documents trouvés. Nous avons observé que les scientiﬁques recherchent leurs informations dans des éléments de discours précis qui peuvent varier suivant la tâche qu’ils ont à eﬀectuer, et non pas toujours dans le document en entier. A partir de ce modèle d’utilisateur, nous avons ensuite créé un modèle d’annotation (SciAnnotDoc) prenant en compte ces éléments de discours, de même que les diﬀérentes informations contenues dans le document scientiﬁque. Ce mod- èle est composé de quatre dimensions ou facettes: les méta-données, la dimension conceptuelle (les termes et les concepts), la dimension discursive et les relations de citations ou de références entre les diﬀérents éléments de discours d’un documents scientiﬁque. Le modèle a été implémenté en OWL et diﬀérentes ontologies ont été créées pour répondre aux diﬀérents besoins d’annotation des quatre dimensions. Dans une troisième phase, plusieurs méthodes d’annotation manuelle et automa- tique ont été évaluées. GATE a été choisi et utilisé pour annoter automatique- ment 1400 documents scientiﬁques en études genre. Des règles JAPE ont été créées basées sur la syntaxe grammaticale et des mots-clés pour détecter automatiquement les cinq éléments de discours (ﬁndings, déﬁnition, hypothèse, méthodes et travaux référencés). Finalement, ces annotations et l’eﬃcacité d’un tel système d’annotation ont été évaluées avec des scientiﬁques. Une interface en facette (FSAD) basée sur les quatre dimensions du modèle d’annotation a été créée pour cette évaluation est comparée à un système de recherche par mots-clés. Les observations semblent montrer que les scientiﬁques préfèrent le système (FSAD) basé sur SciAnnotDoc et trouvent que les résultats obtenus sont plus utilisables et ont un meilleur taux de rappel que ceux fournis par le système de recherche par mot-clés. Mots-clés: Publication sémantique, Recherche d’information, Ontologie, Représentation des connaissances
  8. 8. Acknowledgments Sorry for the English speaking people, but even if my thesis is in English I prefer writing my acknowledgements in French. Je remercie mon directeur de thèse et professeur Gilles Falquet, pour m’avoir donné la chance de me lancer dans une thèse en m’engageant sur un projet du Fond National1. Je le remercie pour ces merveilleuses heures passées à discuter de ma thèse, ou d’autres sujets autour d’un thé, sous un chêne ou encore sur un télésiège. Il m’a toujours encouragée à aller plus loin, même quand j’étais un peu découragée; à explorer d’autres pistes et à trouver mes propres chemins. Je le remercie aussi pour sa patience et ses conseils. Je remercie les membres de mon jury. Le professeur Fabio Crestani d’avoir accepté d’être membre de mon jury, et d’avoir lu et corrigé ma thèse; et de m’avoir donné de bonnes pistes de recherche future. Je remercie le professeur Henning Müller pour les mêmes raisons, de même que pour quelques conseils de skis, et de cueillette de champignons. Je remercie aussi ma présidente de jury la professeure Giovanna Di Marzo Seru- gendo pour avoir accepté de jouer ce rôle et pour ses conseils avisés. Je remercie Claudine Métral qui a eu la bonté de m’accueillir dans son bureau à l’ombre de ses plantes vertes pendant toutes ces années, et qui m’a donné de bons conseils, que ce soit sur ma thèse ou mon travail d’assistante, et avec qui j’ai eu de bons éclats de rire. Je remercie aussi Nizar Ghoula d’avoir bien voulu relire certains passages de ma thèse, et d’avoir été un collègue et ami sur qui j’ai pu m’appuyer pendant ces quelques années. Je remercie bien sûr le reste de l’équipe, mes collègues, les membres du CUI pour leurs point de vue et leur aide sur ma thèse. Marie-France mérite un remerciement particulier pour son soutien et sa patience avec certains de mes formulaires pas toujours bien remplis. Je remercie évidement ma mère pour tout, mais particulièrement pour sa relec- ture attentive de ma thèse, son aide et son soutien infaillible. Je remercie ma soeur pour ses conseils, ses relectures, ses corrections et son soutien; et bien sûr le reste de la famille pour son support tout au long de ce processus. Je remercie Roy pour la discussion assis sur les télésièges de Marble Mountain (Terre-Neuve) portant sur les diﬀérents techniques de traitements naturels du langage. Je remercie mes amis pour leur patience, même quand cela n’était pas tou- jours facile. Pour avoir supporté mes coups de gueule et mon humeur pas toujours rose. Je remercie plus particulièrement Raluca pour m’avoir donné le petit coup de pouce qu’il fallait quand je me décourageais; Lucile pour avoir lu mes complaintes (via What’s up ou email) et avoir partagé un grand nombre de mes expériences de 1 Ce travail a été eﬀectué grâce à deux subsides successifs du Fonds National (Ontology-Based Precise Multilingual Information Retrieval, n 122061; Precise information retrieval in semantic scientiﬁc digital libraries, n 138252)
  9. 9. vi doctorant (conférences, mentorat, et j’en passe); Wanda pour m’avoir sustenté et m’avoir permis de me défouler avec une raquette quand le besoin était trop grand; Lonneke pour m’avoir aidé à construire mon premier modèle d’annotation; Sandra pour une plume jaune qui a servit à écrire de longues pages de ma thèse et qui ne me quitte plus; ma mentor Franziska pour nos longues discussions et ses conseils avisés; Jelena, pour m’avoir dit de foncer et que la thèse serait mes plus belles années (j’en doute encore un peu); je remercie Ilinca pour ses sourires et me rappeler qu’une thèse c’est beau, mais il n’y a pas que cela. Je remercie encore pour leur patience, leur écoute et leur soutien tous mes proches et amis dont faire l’éloge ici serait trop longue. Finalement, je remercie tous mes amis, proches et collègues qui ont participé avec patience et bonne volonté aux diﬀérents interviews et évaluation du système: Alain, Anik, Caroline, Céline, Delphine, Dorina, Jean-Pierre, Kate, Lonneke, Lucile, Mélanie, Nizar, Sandra, Sandrine, Vanessa, Wanda, et les participants à l’enquête. Sans eux cette thèse n’aurait pas été possible. Je vous remercie tous en espérant n’avoir oublié personne.
  10. 10. Contents 1 Introduction 1 2 User model 7 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 2.2 State of the art . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2.1 Information-seeking behaviour models . . . . . . . . . . . . . 9 2.2.2 Scientiﬁc inquiry models, nature of the needs of information, new forms of behaviour . . . . . . . . . . . . . . . . . . . . . 17 2.3 Survey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.3.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.3.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 2.3.3 Survey Discussion and Conclusion . . . . . . . . . . . . . . . 36 2.4 Interview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 2.4.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 2.4.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 2.4.3 Interview, Discussion and Conclusion . . . . . . . . . . . . . . 46 2.5 Discussion and Conclusion . . . . . . . . . . . . . . . . . . . . . . . . 49 3 Annotation models for scientiﬁc documents 53 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 3.2 State of the art . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 3.2.1 Conceptual dimensions (1) . . . . . . . . . . . . . . . . . . . . 54 3.2.2 Meta-data dimension (2) . . . . . . . . . . . . . . . . . . . . . 55 3.2.3 Structural dimension (3) . . . . . . . . . . . . . . . . . . . . . 57 3.2.4 Rhetorical or discursive dimension (4) . . . . . . . . . . . . . 58 3.2.5 Relationships dimension (5) . . . . . . . . . . . . . . . . . . . 69 3.3 Our model: SciAnnotDoc . . . . . . . . . . . . . . . . . . . . . . . . 74 3.3.1 Components of the model . . . . . . . . . . . . . . . . . . . . 77 3.3.2 Formalisation of SciAnnotDoc . . . . . . . . . . . . . . . . . . 88 3.4 Discussion and Conclusion . . . . . . . . . . . . . . . . . . . . . . . . 100 4 Manual and automatic corpus annotation 101 4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 4.2 Manual annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102 4.3 Crowdsourcing annotation . . . . . . . . . . . . . . . . . . . . . . . . 106 4.3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 4.3.2 Scientists’ annotation study . . . . . . . . . . . . . . . . . . . 106 4.3.3 Amazon Mechanical Turk study . . . . . . . . . . . . . . . . . 109 4.3.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 4.4 Automatic annotation . . . . . . . . . . . . . . . . . . . . . . . . . . 114
  11. 11. viii Contents 4.4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114 4.4.2 Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . 116 4.4.3 Corpus statistics . . . . . . . . . . . . . . . . . . . . . . . . . 125 4.4.4 Annotation evaluation . . . . . . . . . . . . . . . . . . . . . . 128 4.4.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 4.5 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 5 Query model and Faceted search interface 131 5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 5.2 Query model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 5.2.1 Simple queries . . . . . . . . . . . . . . . . . . . . . . . . . . 135 5.2.2 Queries with multiple elements . . . . . . . . . . . . . . . . . 136 5.2.3 Examples of queries in SPARQL extracted from interviews . . 138 5.3 Faceted search on the SciAnnotDoc (FSAD) . . . . . . . . . . . . . . 140 5.3.1 Meta-data facet or dimension . . . . . . . . . . . . . . . . . . 142 5.3.2 Conceptual facet/dimension . . . . . . . . . . . . . . . . . . . 142 5.3.3 Discursive facet/dimension . . . . . . . . . . . . . . . . . . . 143 5.3.4 Relationships facet/dimension . . . . . . . . . . . . . . . . . . 144 5.3.5 Result’s visualisation . . . . . . . . . . . . . . . . . . . . . . . 145 5.4 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145 6 User evaluation 147 6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147 6.2 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 6.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 6.3.1 Questions answered after each task . . . . . . . . . . . . . . . 152 6.3.2 Questions asked after completion of the three tasks . . . . . . 157 6.3.3 Logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159 6.4 Discussion and Conclusion . . . . . . . . . . . . . . . . . . . . . . . . 165 7 Conclusion 169 7.1 User model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 7.2 Annotation models for scientiﬁc documents . . . . . . . . . . . . . . 169 7.3 Corpus annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172 7.4 Query model and FSAD . . . . . . . . . . . . . . . . . . . . . . . . . 173 7.5 User evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174 Bibliography 177 Glossary 195 A Survey Questions 199 B Semi-direct interview question 201
  12. 12. Contents ix C SciDeo ontology 205 D Methodology ontology 209 E Scientiﬁc object ontology 213 F Gender studies ontology 217 G Jape Rules 235 G.1 Macro common to all Jape rules . . . . . . . . . . . . . . . . . . . . . 235 G.2 Jape rules Findings . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236 G.3 Jape rules Deﬁnition . . . . . . . . . . . . . . . . . . . . . . . . . . . 245 G.4 Jape rules Methodology . . . . . . . . . . . . . . . . . . . . . . . . . 258 G.5 Jape rules Hypothesis . . . . . . . . . . . . . . . . . . . . . . . . . . 264
  13. 13. List of Tables 2.1 "Why do you read scientiﬁc documents" (in percent, n=91) . . . . . 25 2.2 "Why do you read scientiﬁc documents by area of research" (in per- cent n=91), "soft" science (SS), "hard" science (HS) and other (O) p = probability of signiﬁcance in a 2 test . . . . . . . . . . . . . . . 26 2.3 "Why do you read scientiﬁc documents by area of research" (in per- cent n=91), year of birth . . . . . . . . . . . . . . . . . . . . . . . . . 28 2.4 "Where do you generally ﬁnd your answers" (in percent, n=77) . . . 29 2.5 "Where do you generally ﬁnd your answers by area of research" (in percent, n=77) "soft" science ( SS), "hard" science (HS) and other (O) 30 2.6 "Where do you generally ﬁnd your answers" by year of birth (in percent, n=77) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.7 Do you often conduct a review of the literature (in percent, n = 77) . 32 2.8 "Do you often conduct a review of the literature?" by "Where do you generally ﬁnd answers" ?[Result] (in percent,n = 77) . . . . . . . . . 32 2.9 Sample Population . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 2.10 Speciﬁc purpose for searching for information . . . . . . . . . . . . . 40 2.11 How people search for information as a function of task . . . . . . . 42 3.1 The 23 relationships between citing and cited documents in CiTO [Shotton 2009a] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71 3.2 Example of the logical structure of an article in Feminist Studies . . 75 3.3 Example of the logical structure of an article in American Journal of Sociology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76 4.1 Coverage of the four manually annotated documents (Ref = references to other works) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 4.2 Fleiss’ Kappa measure, signiﬁcance [Wikipedia 2013] . . . . . . . . . 107 4.3 Fleiss’ kappa results for the three scientiﬁc annotators by discourse element type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 4.4 Fleiss’ kappa results for the two "expert" annotators in gender studies 108 4.5 Cross-table between scientist 1 and scientist 2 for the ﬁve types of discourse elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108 4.6 Precision/recall for scientist 2 (gold standard (GS)= scientist 1) . . . 108 4.7 Fleiss’ kappa results for the two groups of workers in Amazon Me- chanical Turk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 4.8 Cross-table between Workers A and Workers B for the ﬁve types of discourse elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 4.9 Fleiss’ kappa results for the ﬁve annotators (scientists and workers) on 158 sentences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 4.10 Fleiss’ kappa results for Workers A and scientist 1 (on 158 sentences 111
  14. 14. xii List of Tables 4.11 Cross-table between Workers A and scientist 1 for the ﬁve types of discourse elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 4.12 Fleiss’ kappa results for Workers B and scientist 1 (on 158 sentences 112 4.13 Cross-table between worker B and scientist 1 for the ﬁve types of discourse elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112 4.14 Precision/recall for the two annotators (GS=golden standard) . . . . 113 4.15 Number of articles by journals . . . . . . . . . . . . . . . . . . . . . . 119 4.16 Annotated corpus statistics . . . . . . . . . . . . . . . . . . . . . . . 125 4.17 Annotated corpus statistics by Discourse elements . . . . . . . . . . 125 4.18 Precision/recall values . . . . . . . . . . . . . . . . . . . . . . . . . . 128 6.1 Design experiment (Latin square rotation of tasks) . . . . . . . . . . 149 6.2 Sample Population (the number of the question related to the socio- demographic questionnaire . . . . . . . . . . . . . . . . . . . . . . . . 151 6.3 Relevance of the set of results . . . . . . . . . . . . . . . . . . . . . . 152 6.4 Relevance of the set of results in percent . . . . . . . . . . . . . . . . 153 6.5 Time to obtain information . . . . . . . . . . . . . . . . . . . . . . . 155 6.6 Number of requests . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 6.7 Satisfaction for each query . . . . . . . . . . . . . . . . . . . . . . . . 156 6.8 Satisfaction with the overall results . . . . . . . . . . . . . . . . . . . 156 6.9 Frustration with the set of results . . . . . . . . . . . . . . . . . . . . 156 6.10 Diﬃculty of the task . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 6.11 Average time (minutes) spent on a set of results and on an answer (the results for the FSAD participants are shown in bold) . . . . . . 160 6.12 Average time (minutes) spent on a set of results and on an answer (the results for the FSAD participants are shown in bold) . . . . . . 161 6.13 Average time (minutes) spent on a set of results and on an answer (the results for the FSAD participants are shown in bold) . . . . . . 162
  15. 15. List of Figures 2.1 A stage process version of Ellis’s behavioural framework (1993) [Ellis et al. 1993] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2 Information Search Process (ISP), Kuhlthau’s model, 1991 [Kuhlthau 1991, p.367] . . . . . . . . . . . . . . . . . . . . . . . . . 11 2.3 A comparison of Ellis’s model and Kuhlthau’s stage process model in [Wilson 1999, p.256] . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 2.4 Wilson’s model of information behaviour (1981) [Wilson 1999, p.251] 12 2.5 Wilson’s model of information-seeking behaviour (1981) [Wilson 1999, p.252] . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.6 Wilson’s model of information behaviour (1986) [Wilson 1999, p.257] 14 2.7 Garvey’s table for the nature of information needed at each stage by the majority of scientists involved in that stage of scientiﬁc work ([Garvey et al. 1974, p.120]) . . . . . . . . . . . . . . . . . . . . . . . 19 2.8 "Why do you read scientiﬁc documents by area of research by area of research"; often answer . . . . . . . . . . . . . . . . . . . . . . . . 27 2.9 "Why do you read scientiﬁc documents by area of research by years of birth"; often answer . . . . . . . . . . . . . . . . . . . . . . . . . . 27 2.11 "Where do you generally ﬁnd your answers by years of birth"; often answer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.10 "Where do you generally ﬁnd your answers by area of research"; often answer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.12 "Would you like a retrieval system that would be able to ﬁnd articles by their conclusions" . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 2.13 Relationship between task and what parts are read . . . . . . . . . . 35 2.14 Fragment read by person . . . . . . . . . . . . . . . . . . . . . . . . . 43 2.15 Fragments on which users focus as a function of task . . . . . . . . . 45 2.16 Fragment by tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 2.17 Fragment; comparison survey/interview . . . . . . . . . . . . . . . . 49 2.18 Relationship between tasks and parts read, as indicated by interview and survey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 3.1 Overview of the Harmsze model [Harmsze 2000, p.174] . . . . . . . . 59 3.2 Class structure of the scholarly discourse ontology (ScholOnto [Shum et al. 2007, p.9] . . . . . . . . . . . . . . . . . . . . . . . . . . 61 3.3 Scientiﬁc annotation models summarised . . . . . . . . . . . . . . . . 73 3.4 Method for the creation of the model . . . . . . . . . . . . . . . . . . 77 3.5 Conceptual model . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 3.6 An example of relationships between discourse elements: Correll, England and colleagues and human capital theory . . . . . . . . . . . 85 3.7 Lineage of idea or "ﬁl d’Ariane" . . . . . . . . . . . . . . . . . . . . . 86
  16. 16. xiv List of Figures 3.8 SciAnnotDoc model ontology; orange classes are the SciDeo ontology 88 3.9 SciAnnotDoc ontology in Protege . . . . . . . . . . . . . . . . . . . . 90 3.10 Methodology ontology: high-class level . . . . . . . . . . . . . . . . . 91 3.11 Methodology ontology: all classes and properties (to give an idea of the size and the structure of the ontology) . . . . . . . . . . . . . . . 92 3.12 Scientiﬁc object ontology: high-class level . . . . . . . . . . . . . . . 93 3.13 Scientiﬁc object ontology: A summary view (to give an idea of the size and the structure of the ontology) . . . . . . . . . . . . . . . . . 95 3.14 Gender studies ontology: high-class level . . . . . . . . . . . . . . . . 96 3.15 The GendStud ontology: A summary view (to give an idea of the size and the structure of the ontology) . . . . . . . . . . . . . . . . . . . . 97 3.16 Deﬁnition, Deﬁniendum, Deﬁniens concepts in the SciAnnotDoc . . . 98 3.17 Inference between discourse elements . . . . . . . . . . . . . . . . . . 99 4.1 Manual annotation of three paper documents . . . . . . . . . . . . . 104 4.2 Automated annotation process . . . . . . . . . . . . . . . . . . . . . 120 4.3 Gate Pipeline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 4.4 Annotation algorithm model . . . . . . . . . . . . . . . . . . . . . . . 122 4.5 Inference for the "Lineage of Idea" . . . . . . . . . . . . . . . . . . . 123 4.6 An example for the inference "Lineage of Idea" . . . . . . . . . . . . 124 4.7 Percentage discourse elements by journals (1= Gender and Soci- ety; 2= Feminist Studies; 3=Gender Issues; 4=Signs; 5=American Historical Review; 6= American Journal Of Sociology; 7=Feminist economist) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 4.8 Distribution of the concepts in the corpus . . . . . . . . . . . . . . . 127 4.9 Number of times the concepts "gender", "sex" or "discrimination" are evoked by year (normalised by the number of concepts by year) . 127 5.1 Query model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134 5.2 A instance of the query model (simple query) . . . . . . . . . . . . . 135 5.3 Transformation of a simple query in SPARQL with an AND between the discourse elements . . . . . . . . . . . . . . . . . . . . . . . . . . 135 5.4 Transformation of a simple query in SPARQL with an OR between the discourse elements . . . . . . . . . . . . . . . . . . . . . . . . . . 136 5.5 A instance of the query model (complex query) . . . . . . . . . . . . 136 5.6 Transformation of a complex query in SPARQL with an AND between the discourse elements . . . . . . . . . . . . . . . . . . . . . . . . . . 137 5.7 Representation of Q1 in SPARQL. . . . . . . . . . . . . . . . . . . . 138 5.8 The representation of Q2 in SPARQL . . . . . . . . . . . . . . . . . 139 5.9 Representation of Q3 in SPARQL. . . . . . . . . . . . . . . . . . . . 139 5.10 Adaptative-faceted search interface (with the four dimensions /facets) 141 6.1 Keyword search interface . . . . . . . . . . . . . . . . . . . . . . . . . 149 6.2 Relevance of the set of results by interface . . . . . . . . . . . . . . . 153
  17. 17. List of Figures xv 6.3 Irrelevance of the set of results by interface (some scores have been inverted, so that all are in the same direction (1= irrelevant or useless; 5 or 7=very useful or relevant) . . . . . . . . . . . . . . . . . . . . . 154 6.4 Total time (in minutes) spent on query by group and by task . . . . 163 6.5 Estimated precision and recall for the task 1 . . . . . . . . . . . . . . 164 6.6 Comparison of the number of results in a set of results and the irrel- evance of the set of result, task 2 . . . . . . . . . . . . . . . . . . . . 165 6.7 Number of queries and feeling of adequacy by interface for task 1 (adequacy; 1= very adequate; 2 = not at all adequate . . . . . . . . 166 6.8 Number of queries and feeling of adequacy by interface for task 2 (adequacy; 1= very adequate; 2 = not at all adequate) . . . . . . . . 167 6.9 Number of queries and feeling of adequacy by interface for task 3 (adequacy; 1= very adequate; 2 = not at all adequate) . . . . . . . . 167
  18. 18. Chapter 1 Introduction This research thesis aims to develop models and tools for precise information re- trieval and strategic reading in large scientiﬁc document collections. Recently, sys- tems supporting electronic scientiﬁc publications have introduced some improve- ments to the simple search of printed edition indices, but the revolution heralded by electronic publishing has not yet occurred. The construction of scientiﬁc knowledge is a long process that began hundreds of years ago. With the explosion of the number of publications (e.g., Medline has a growth rate of 0.5 million items per year [Nováček et al. 2010]), it has become very diﬃcult for scientists to ﬁnd information that is relevant to precise questions. As John of Salisbury stated, "Bernard of Chartres used to compare us to [puny] dwarfs perched on the shoulders of giants. He pointed out that we see more and farther than our predecessors, not because we have keener vision or greater height, but because we are lifted up and borne aloft on their gigantic stature."1 [Wikipedia 2014b]. Science is built on the knowledge that other scientists have brought and continue to bring to the equation. Today, the shoulders of giants have become diﬃcult to reach. One of the reasons for this is the diﬃculty in ﬁnding the right information. Indeed, the communication of scientiﬁc information is not as eﬃcient and eﬀective as it could be. In 1945, Bush [Bush 1945] argued that too many publications can be a problem because the information contained in these publications cannot reach other scien- tists. Bush expounded his argument using the example of Mendel’s laws of genetics, which were lost to the world for a generation because his publication did not reach the few people who were capable of understanding and extending this concept. The diﬃculty, according to Bush, is not the sheer number of publications but the fact that publications have been extended far beyond our present ability to make real use of these publications. He also argued that classiﬁcation by alphabetical or numerical order is not an ideal solution; instead, classiﬁcation should follow the same process as the human brain by the association of ideas, through "selection by association rather than indexing". Bush proposed the idea of the "Memex", in which individu- als could store all of their records, books and communications on microﬁlm. With the "Memex", individuals could create a trail of their readings or consultations by joining items, and scientists could use their trails to navigate the literature. This observation is still fully relevant. Today, scientists have better tools to man- 1 "Dicebat Bernardus Carnotensis nos esse quasi nanos, gigantium humeris insidentes, ut pos- simus plura eis et remotiora videre, non utique proprii visus acumine, aut eminentia corporis, sed quia in altum subvenimur et extollimur magnitudine gigantea."
  19. 19. 2 Chapter 1. Introduction age their personal data (photos and video) than are available to manage or search their professional data [Hannay 2010]. The publication model has not improved or evolved as rapidly as it could have. The process of searching for scientiﬁc documents has just begun to incorporate new technologies such as Semantic Web. Moreover, the format of publications has not evolved signiﬁcantly as the electronic format has become more popular. Currently, scientists in the domain of knowledge representation, information retrieval, the Semantic Web and semantic publishing continue to work on some of the models that Bush proposed. Of course, technology has improved since Bush’s "Memex", but the idea of being able to follow a trail of ideas, for example, has not yet been realised. It is possible to follow the trail that a publication leaves behind and to follow the references of an article, but it is not yet possible to follow the trail of a precise idea or the reproduction of a result. For instance, if scientists want to search for all publications related to the eﬀect that protein X could have on protein Y, they would have to ﬁnd not only all the publications related to these two proteins but also the correct passages in the documents, when this interaction is proven or not proven. In [Salton et al. 1993], Salton proposed an approach based on passage retrieval rather than considering a whole document. The author argues that it is not neces- sarily in the best interest of users to retrieve the entirety of a document, especially when the document is long, but it may be interesting to identify the most relevant passages. Traditional search engines can ﬁnd documents based on their metadata (e.g., title, author, year of publication) or by the words they contain (full-text search or keywords search). The ﬁrst search mode is eﬀective only when the user knows at least one metadata element, such as the title or author. However, scientists do not search only for documents whose metadata they know. Their need for information is often more complex, as are the questions they formulate in their cognitive processes. Existing scientiﬁc information retrieval systems cannot handle (at least) two types of cases representing diﬀerent information needs: 1. cases in which the information sought is composed of small pieces of informa- tion found in diﬀerent documents, such as "collect all the deﬁnitions of term X in a given domain or school of thought” or "ﬁnd all techniques to graphically represent knowledge bases in 3D"; 2. cases in which the expression of the information needed is complex and the information cannot be expressed by a list of keywords, such as "ﬁnd documents where author X disagrees with author Y about using methodology Z’". In both cases, typical document indexing schemes are ineﬃcient because 1) they represent each document as a whole and do not take their subparts into account and 2) they fail to represent knowledge about the semantic or rhetorical role of document elements. One way to circumvent these limitations is to semantically enrich documents by annotating their content with meta-information or to provide
  20. 20. 3 meta-information not only at the document level but at a ﬁner level, such as the section, paragraph, sentence, or word level. In addition, conventional information retrieval systems are based on the idea that each document has a certain degree of relevance to the user’s query, and only the most relevant documents must be selected. For scientists, the goal is often to ﬁnd all the documents that are associated with a very speciﬁc issue of interest. Moreover, even if scientists want to ﬁnd all such documents, they do not have time to read the retrieved documents in their entirety. Therefore, a search system must provide methods and tools for strategically reading these documents (i.e., for highlighting or selecting the passages that actually contribute to answering the user’s query). Various initiatives have been launched to improve the dissemination of knowledge and the way scientists discover new facts, claims, deﬁnitions, methodologies, and results. Two types of initiatives can be identiﬁed: e-science, which aims to construct a network of data to support new scientiﬁc discoveries, and [Hunter & Liu 2010, Bechhofer et al. 2013], Semantic Publishing [Shotton 2009b], which aims to improve new scientiﬁc discoveries by facilitating access to a diversity of publications. The present thesis belongs to the second category. The research presented herein investigated new paths that should reduce some of the diﬃculties scientists encounter in obtaining correct, relevant information. The ﬁrst step consisted of attempting to understand the needs of scientists when they initiate a process of information-seeking behaviour by questioning them with respect to the information need that triggers their search process. In this ﬁrst step, quan- titative and qualitative methods were used. The result of this ﬁrst step was a user model based on the review of literature, the survey and the interviews that helped to analyse scientists’ searching and reading behaviour for scientiﬁc documents. The second step was to create an annotation model of scientiﬁc documents that not only responds to the needs of scientists but is also realistic for use by an auto- matic annotation system. To paraphrase Bernard de Chartres, this thesis was built on the knowledge of scientists. In other words, the annotation model described herein is based on the user model as well as other annotation models proposed in the literature. The construction of this model was made in several iterations, with changes depending of the results observed throughout the survey and interviews. The third step was to test the annotation model by annotating a corpus. Sev- eral annotations methods were tested, including manual and automatic annotations. Manual annotations were performed using scientist and non-scientist annotators. The automatic annotation system was implemented using Natural Language Pro- cessing. The fourth step was to implement a faceted information retrieval system to query the scientiﬁc documents annotated using the annotation model and to evaluate it with scientists against another information retrieval system, speciﬁcally, one based on keywords. The contributions of this thesis are to a) oﬀer a user model built on the ba- sis of a survey and interviews with scientists in order to understand their speciﬁc information-seeking behaviour needs; b) propose a generic annotation model (SciAn-
  21. 21. 4 Chapter 1. Introduction notDoc) for scientiﬁc documents based on the user model, c) demonstrate that the annotation model is realistic enough to be used by both manual and automatic methods of annotation, d) build a faceted search interface (FSAD) based on the SciAnnotDoc and e) evaluate the model by obtaining the feedback of end users (sci- entists) and show that the FSAD interface is more eﬀective than a keywords-search, notably in terms of recall and F1 measure. The thesis is structured as follows. Chapter 2 discusses diﬀerent models of in- formation behaviour and information-seeking behaviour and presents studies that were conducted to understand scientists’ information behaviour and the nature of the needs of information. Chapter 3 discusses the scientiﬁc document annotation models reported in the literature and presents our model, the SciAnnotDoc model, a complete annotation model that is based on the aforementioned user model and is composed of diﬀerent ontologies that allow for the annotation of scientiﬁc doc- uments along a number of dimensions. Chapter 4 discusses automatic annotation frameworks and presents the methodology we used to annotate the corpus. Chapter 5 discusses query models and a faceted search interface and presents the interface we developed to query annotated scientiﬁc documents. Chapter 6 presents the results obtained from the evaluation of the system based on scientists’ feedback. Finally, conclusions and ideas for future studies are presented in Chapter 7. A glossary at the end of the chapters provides some deﬁnitions of the terms. Publications related to this thesis Some of the results presented in this thesis were published in diﬀerent conferences and workshops: Hélène de Ribaupierre and Gilles Falquet. User-centric design and evaluation of a semantic annotation model for scientiﬁc documents. In 13th International Conference on Knowledge Management and Knowledge Technologies, I-KNOW ’14, Graz, Austria, September 16-19, 2014, pages 1-6, 2014. Hélène de Ribaupierre and Gilles Falquet. Un modèle d’annotation sémantique centré sur les utilisateurs de documents scientiﬁques: cas d’utilisation dans les études genre. In IC-25èmes Journées francophones d’Ingénierie des Connaissances, pages 99-104, 2014. Hélène de Ribaupierre and Gilles Falquet. A user-centric model to semantically annotate and retrieve scientiﬁc documents. In Proceedings of the sixth international workshop on Exploiting semantic annotations in information retrieval, pages 21-24. ACM, 2013. Hélène de Ribaupierre. Precise information retrieval in semantic scientiﬁc dig- ital libraries. In CEUR doctoral symposium proceedings, EKAW2012. Galway, 2012. Hélène de Ribaupierre and Gilles Falquet. New trends for reading scientiﬁc doc- uments. In Proceedings of the 4th ACM workshop on Online books, complementary social media and crowdsourcing, BooksOnline ’11, pages 19-24, New York, NY, USA,
  22. 22. 5 2011. ACM. Hélène de Ribaupierre and Gilles Falquet. Recherche d’information dans des corpus scientiﬁques basée sur la structure du discours. In Ecole d’Automne en Recherche d’Information et Applications, pages 83-92, Saint-Germain-Au-Mont- D’or, 2010.
  23. 23. Chapter 2 User model Contents 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 2.2 State of the art . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.2.1 Information-seeking behaviour models . . . . . . . . . . . . . 9 2.2.2 Scientiﬁc inquiry models, nature of the needs of information, new forms of behaviour . . . . . . . . . . . . . . . . . . . . . 17 2.3 Survey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.3.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.3.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25 2.3.2.1 Reasons to read scientiﬁc documents . . . . . . . . . 25 2.3.2.2 Do you read scientiﬁc papers to respond to a precise need . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 2.3.2.3 Where do you generally ﬁnd the answers . . . . . . 29 2.3.2.4 Do you often conduct a review of the literature . . . 32 2.3.2.5 Do you easily ﬁnd papers/books you are looking for without too much noise (e.g., a paper that is out of the ﬁeld in which you are searching . . . . . . . . . 33 2.3.2.6 Do you use Google Scholar more often than a spe- cialised database (in your domain) . . . . . . . . . . 33 2.3.2.7 Would you like a retrieval system that would be able to ﬁnd articles by the content of their conclusions (i.e., all articles stating that rain is wet) . . . . . . . 33 2.3.3 Survey Discussion and Conclusion . . . . . . . . . . . . . . . 36 2.4 Interview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 2.4.1 Methodology . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 2.4.2 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 2.4.2.1 Reasons to search for and read a scientiﬁc document 38 2.4.2.2 How are you searching a scientiﬁc document . . . . 39 2.4.2.3 What are the databases or search engines you use to search for documents . . . . . . . . . . . . . . . . . 39 2.4.2.4 Do you search documents for a precise question . . 39 2.4.2.5 For each task, do you search for documents diﬀerently or with a diﬀerent search engine or database . . . . 41 2.4.2.6 Does the knowledge you have in a domain change the way you search for documents . . . . . . . . . . . . 43
  24. 24. 8 Chapter 2. User model 2.4.2.7 Do you focus on speciﬁc fragments or parts of a doc- ument, and which ones do you prioritise . . . . . . . 43 2.4.2.8 Do you focus on diﬀerent parts of a document de- pending on the task you must complete . . . . . . . 44 2.4.2.9 Do you read documents diﬀerently depending on the knowledge you have in the domain, and do you read speciﬁc sections . . . . . . . . . . . . . . . . . . . . 46 2.4.3 Interview, Discussion and Conclusion . . . . . . . . . . . . . . 46 2.5 Discussion and Conclusion . . . . . . . . . . . . . . . . . . . . 49 2.1 Introduction The number of scientiﬁc documents available today has made the information- seeking process more diﬃcult than ever. In 2011, the number of peer-reviewed journals in existence was estimated to be close to 26,7461. Thus, ﬁnding relevant information among this tremendous number of publications proves to be a diﬃ- cult task, especially for scientists who are searching for an answer to a very precise question, such as "Who has applied the theory of pertinence to translation?" Re- search in information science (as will be discussed in this section) shows that taking into account the diﬀerence between intra-individual variations2 and inter-individual variations3 can be important in the design of digital libraries and in the design of information retrieval systems (IRs). To build better scientiﬁc IRs, we must con- sider scientists’ need for information, the reason they are searching for information, the diﬃculties they encounter and the strategies they have created to avoid some of these diﬃculties. In [Wilson 1999], Wilson argues that if the designer under- stands the implications of user information-seeking behaviour, it should be possible to build better IRs. Studies about the information-seeking process have been con- ducted since 1960. A review of all such studies is well beyond the scope of this thesis. In this study, only the most well-known models will be described to provide the reader with a better understanding of the information-seeking behaviour pro- cess and the needs of users and to provide the reader with the ability to apply the lens of diﬀerent information-seeking behaviour models developed by scientists. A more complete review of these studies can be found in publications on the state of the art in [Case 2012, Ingwersen & Järvelin 2006, Wilson 1999]. The ﬁrst of these studies presents meta models for information-seeking behaviour, whereas the sec- ond presents studies on information problems that impact scientiﬁc and scholarly 1 site web: http://pages.cmns.sfu.ca/heather-morrison/appendix-c-how-many-active-scholarly- peer-reviewed-journals/. 2 "Intra-individual variations: changes which occur within individual scientists as their scientiﬁc work progresses." [Garvey et al. 1974, p.115] 3 "Inter-individual variations: diﬀerences between individual scientists (traditionally referred to as ‘individual diﬀerences’)." [Garvey et al. 1974, p.115]
  25. 25. 2.2. State of the art 9 inquiry, the nature of information needs, the objectives of searches performed by users, and the new behaviour introduced by electronic documents or the Web. 2.2 State of the art 2.2.1 Information-seeking behaviour models Ellis’s model: Ellis’s model is based on the ﬁrst investigation conducted by Ellis et al. on empirical studies covering a population of social scientists [Ellis 1989]. A second study was conducted in [Ellis et al. 1993], in which the authors com- pared scientists in the physical sciences to those in the social sciences. In [Ellis & Haugan 1997], the authors compared engineers and research scientists in an oil company. The methodology used to interview the scientists was semi-directive interviews. In the ﬁrst study [Ellis 1989], the authors modelled six features (start- ing, chaining, browsing, diﬀerentiating, monitoring and extracting). In the 1993 study [Ellis et al. 1993], the authors added two more features (verifying and end- ing). The extended (last) model (see ﬁgure 2.1) described eight features of the information-seeking patterns of scientists: Figure 2.1: A stage process version of Ellis’s behavioural framework (1993) [Ellis et al. 1993] • Starting: Identifying references that could serve as a starting point of the research cycle; asking colleagues and consulting literature reviews, online cat- alogues, indexes and abstracts. • Chaining: Following footnotes and citations in known material, the direction of which can be forward or backward. • Browsing: Looking for information in areas of potential interest. • Diﬀerentiating: Using known diﬀerences in information sources, such as au- thors’ names and journal hierarchies, to ﬁlter information. • Monitoring: Keeping knowledge about users’ area of research up to date by regularly following particular sources.
  26. 26. 10 Chapter 2. User model • Extracting: Selecting and identifying relevant material. • Verifying: Checking that the information is correct. • Ending: Activities that complete the information-seeking process. Ellis suggests that the interaction and the order of the eight features can vary. This model can be useful in providing a set of categories that allows for the analysis of information seeking at the individual level. In [Ellis & Haugan 1997], the authors conclude that even if sources of information diﬀer between diﬀerent ﬁelds of research, the behavioural characteristics remain similar. The authors consider the behavioural model to be quite robust in relation to the information-seeking patterns of physical scientists, engineers and social scientists. Kuhlthau model: Based on diﬀerent longitudinal4 empirical studies, Kuhlthau [Kuhlthau 1991] proposed a model composed of six stages (see ﬁgure 2.2). The ﬁrst study concerned high-school students who had to write an essay. The model developed by Kuhlthau suggests that people search and use information diﬀerently depending on the stages of the search process, which are deﬁned as follows: • Initiation: Users become aware of the need for information when they face a problem. • Selection: Users identify and select the general topic for seeking information. • Exploration: Users seek and investigate information on the general topic of interest. • Formulation: Users ﬁx and structure the problem to be solved. • Collection: Users gather pertinent information for the topic of interest. • Presentation: Users complete their search and implement the results of their search. This model, in contrast to Ellis’s model, proposes features in an order that cannot be changed. This diﬀerence between the two models may derive from the diﬀerences in the populations studied and in the tasks performed to retrieve infor- mation. Kuhlthau’s model also acknowledges the subjective characteristics (feelings and thoughts) of the user at each step. In his article, Wilson [Wilson 1999] compares Ellis’s model (see ﬁgure 2.1) and Kuhlthau’s model (see ﬁgure 2.2) to determine the similarities between them (see ﬁgure 2.3) and to merge the models, although the hypotheses underlying the two models are slightly diﬀerent. 4 The study was conducted over several years.
  27. 27. 2.2. State of the art 11 Figure 2.2: Information Search Process (ISP), Kuhlthau’s model, 1991 [Kuhlthau 1991, p.367] Figure 2.3: A comparison of Ellis’s model and Kuhlthau’s stage process model in [Wilson 1999, p.256]
  28. 28. 12 Chapter 2. User model Wilson’s model Wilson began developing his model in 1981 (see ﬁgure 2.4) [Wilson 1981]. The aim of his model was not to describe information behaviour but to draw attention to the interrelationships among concepts used in the ﬁeld. He suggests that information behaviour results from users’ recognition of needs. This behaviour can take several forms: 1) through a formal system, such as an informa- tion system or other information sources, or 2) through information exchange. In both cases, failure or success can be tested. When users are successful (i.e., when they believe that the information retrieved can fully or partially satisfy their needs), the search process can end. However, if the information does not satisfy the user’s needs, the user performs the search process again. Figure 2.4: Wilson’s model of information behaviour (1981) [Wilson 1999, p.251] In the same paper, Wilson presents a second (see ﬁgure 2.5) model for information-seeking behaviour that takes into account basic needs: • Physiological states, such as the need for food, water, and shelter; • Aﬀective states (sometimes called psychological or emotional needs), such as the need for attainment or domination; • Cognitive states, such as the need to plan or to learn a skill. Wilson argues that these three types of needs are interrelated. When an in- dividual engages in information-seeking behaviour, these needs may be fulﬁlled or may remain unfulﬁlled. The other factors that may intervene are the role of the person and the environment within which the person is living (see Figure 2.5). This
  29. 29. 2.2. State of the art 13 Figure 2.5: Wilson’s model of information-seeking behaviour (1981) [Wilson 1999, p.252] model, as described by Wilson, is a macro-model that describes information-seeking behaviour and suggests how information arises and what may prevent or aid the actual search for information. Wilson’s 1996 model [Wilson 1999] (see ﬁgure 2.6) represents a major revision of Wilson’s second model of 1981 (see ﬁgure 2.5), although the basic framework persists. The barriers are represented as "intervening variables", which, in the previous model, could be preventive or supportive of information-seeking behaviour. Wilson incorporates some concepts that activate information-seeking behaviour: 1) risk/reward theory, which may help to explain which sources of information may be used more often than others, and 2) social learning theory, which incorporates the concept of self-eﬃcacy5 The incorporation of diﬀerent variables that may or may not help the user to initiate searching behaviour is a good start to account for the barriers that can arise in users’ information-seeking process, which should be considered in the construction and evaluation of IRs. These "intervening variables" can have implications for the decisions involved in the construction of IRs and the methods and variables measured for evaluation. 5 "Perceived self-eﬃcacy is deﬁned as people’s beliefs about their capabilities to produce designated levels of performance that exercise inﬂuence over events that aﬀect their lives." [Bandura 1994, p.71].
  30. 30. 14 Chapter 2. User model Figure 2.6: Wilson’s model of information behaviour (1986) [Wilson 1999, p.257]
  31. 31. 2.2. State of the art 15 The Ellis model has been used in other studies, such as the study by [Meho & Tibbo 2003], in which the authors addressed the change introduced by the Web in information-seeking behaviour. The authors interviewed by email social scientists who were working in the same ﬁeld but in diﬀerent areas of the world. The authors’ ﬁndings are based on the eight features of the Ellis model and two additional features they identiﬁed for diﬀerent purposes: • Starting: Scientists ﬁrst search through their own personal collection. They also search online catalogues, indexes and abstracts. Scientists primarily use literature searches as a way to determine what has been published on a given research topic or to ﬁnd background information on a certain topic. • Chaining: Chaining is used to identify new sources of information or to sat- isfy a potential information needs. Chaining is performed by following the references obtained through reading and personal content (literature already known and owned by scientists in their own database and ﬁles). The resulting chains of citations are primarily based on topical relevance, the importance of the authors’ research, novelty, the publisher’s reputation, the time it takes to locate the information / material, or citation frequency). The authors show that the most important features for the chains of citations are topical rele- vance, authors’ reputation, and availability. • Browsing: All of the interviewed scientists were engaged in this part of the process, and it was an important aspect for them. Authors divided this part of the process into two diﬀerent processes: 1) browsing journals by searching through new issues of journals and the table of contents of relevant books and 2) browsing online catalogues, indexes and abstracts. • Monitoring: In their results, the authors demonstrate the diﬀerent ways sci- entists maintain awareness of research developments in their topic of interest. One of the ways that scientists maintain this awareness is by consulting lists of distribution, journals (based on their own subscriptions), conferences and colleagues. • Accessing: The authors show that accessing information can be an issue; de- pending on the source, access can be diﬃcult to obtain. • Diﬀerentiating: The scientists interviewed in the [Meho & Tibbo 2003] study evaluate and judge sources according to their nature, quality, relative impor- tance and usefulness. They also use diﬀerent sources to overcome problems of bias. • Extracting: Scientists identify and select relevant material from selected sources. The authors of the study analysed two types of extraction activ- ities: those applied to direct sources (e.g., books and journal articles) and those applied to indirect sources (e.g., bibliographies, indexes and abstracts, and online catalogues).
  32. 32. 16 Chapter 2. User model • Verifying: The scientists interviewed in this study were preoccupied with the reliability and accuracy of their sources because of the nature of their research. In fact, the extent of this preoccupation can vary with the nature of the research topic and the nature of the relation that scientists may have with national and government organisations. • Networking: Scientists communicate and maintain a close relationship with a broad range of people, such as friends, colleagues, and intellectuals working on similar topics, members of national organisations, government oﬃcials, and booksellers. • Information managing: In the interviews, scientists expressed the need for systems that help them ﬁlter, archive and organise the information they have collected. Meho and Tibbo ﬁnd that the personal collection is the most important source of information for scholars. The authors also show that the activities in which scientists are involved are not necessarily or entirely sequential, as Ellis argued, but they can be generally divided into four categories: 1) searching, 2) accessing, 3) processing, 4) ending.
  33. 33. 2.2. State of the art 17 2.2.2 Scientiﬁc inquiry models, nature of the needs of information, new forms of behaviour Scientists have created strategies to read documents rapidly. In [Tenopir et al. 2009], the authors analysed the reading patterns of science faculty members from 1977 through 2006 and found that the amount of reading increased, but the time spent reading an article diminished from 48 minutes in 1977 to 31 minutes in 2005. How- ever, because scientists read more articles, they spent 120 hours annually reading in 1977 versus 144 hours annually in 2005. The authors found that the amount of read- ing varied with the ﬁeld of research; for example, medical faculty read 414 articles per year versus 331 read by faculty in the natural sciences and 233 read by faculty in the social sciences. In [Nicholas et al. 2007], the authors found that users who tended to visit a Web site just once tended to publish the fewest papers. The au- thors found that the average time spent online for each full text item was 20-30 sec, which suggests that participants were checking documents online but not reading them online. The authors also found that the longer an article was, the more likely participants were to read the abstract or the summary and the less likely they were to look at the full text. Participants also spent more time online (42 sec) reading short articles (4-10 pages) than reading large articles (32 sec). The authors showed that search behaviour can vary as a function of academic ﬁeld and the amount of experience users have in their research ﬁeld. The study shows that scientists have developed diﬀerent strategies to read faster and to avoid unnecessary reading. It also appears that scientists tend to avoid reading long articles. By analysing these types of strategies, we can assume that the more targeted information is, the more useful it will be to scientists. Indeed, scientists need techniques that will help them directly target the information they are seeking. Consequently, IR designers must understand the nature of the information needed. In the literature, we can ﬁnd several studies that describe the nature of the information needs of scientists. In [Garvey et al. 1974], the authors deﬁned the nature of information needed by scientists as follows: • To aid in the perception or deﬁnition of a problem • To formulate a scientiﬁc or technical solution • To place work in its proper context with similar work that has already been completed • To relate work to ongoing work in an area • To select a design/strategy for data collection • To select a data-gathering technique • To design equipment or apparatus • To choose a data analysis technique • To enable full interpretation of collected data
  34. 34. 18 Chapter 2. User model • To integrate ﬁndings into the current state of knowledge in an area and the stages of research in which scientists may be involved: 1. Preliminary planning (general) 2. Speciﬁc planning: Theoretical/conceptual 3. Preparation of written research proposal 4. Preliminary experimentation/ﬁeld trials or mockups 5. Calibration, pretesting, etc. 6. Design and development of equipment/apparatus 7. Formulation of experimentation/study design 8. Collection of data 9. Analysis of data 10. Interpretation of results 11. Preparation for report of work In [Garvey et al. 1974], the authors also discuss the interaction between the na- ture of the information needs of scientists and the stage of research scientists have reached. For example, we can observe (see ﬁgure 2.7) that in the preliminary plan- ning stage, the nature of the information needs of scientists involve the perception or deﬁnition of a problem, the formulation of a scientiﬁc or technical solution, the placement of their work in its proper context with similar work that has already been completed (this nature of information need is involved in almost all stages except for the design and development of the equipment or apparatus) and the relation of their work to ongoing work in an area.
  35. 35. 2.2. State of the art 19 Figure 2.7: Garvey’s table for the nature of information needed at each stage by the majority of scientists involved in that stage of scientiﬁc work ([Garvey et al. 1974, p.120])
  36. 36. 20 Chapter 2. User model In a thorough and wide-ranging study on changes in scholars’ article-seeking and reading patterns, [Tenopir et al. 2009] showed that scientists in "hard" sciences in the US (n=880) read scientiﬁc documents for the following purposes: research (48.5%), teaching (22.5%), writing articles, proposals, or reports (10.8%), current awareness, keeping up to date (8.0%), continuing education (3.0%), advising oth- ers (2.9%), and other reasons (4.2%). The authors also asked scientists how the last article they had read had aﬀected their ways of thinking: 54.5% were inspired with new ways of thinking/new ideas, 39.9% obtained improved results, 26.6% nar- rowed/broadened/changed their focus, 12.4% saved time or other resources, 11.6% resolved technical problems, 7.4% were able to complete their work more quickly, 6.0% resulted in collaboration/joint research, and 5.6% provided other responses. In [Palmer et al. 2007], the authors interviewed subjects and found that scien- tists review documents for diﬀerent purposes: to assess their own work and the work of others, to solve short-term instrumental problems, to consult and talk shop and to form complex intellectual relationships among the vast body of neuroscience ﬁndings. In contrast with Ellis’s results [Ellis & Haugan 1997], which show no diﬀerences between academic ﬁelds in information-seeking behaviour, other studies show that information-seeking behaviour can vary depending on the ﬁeld of research or can be aﬀected by the personality of the seeker. This diﬀerence may be due to the fact that the more recent studies focus on a diﬀerent level of analysis from Ellis’s study. Whereas the Ellis model analyses information-seeking behaviour at the meta-level, more recent studies analyse this behaviour at a lower meta-level, taking into account what type of information scientists seek and how they do so. In [Garvey et al. 1974], the authors found that depending on the ﬁeld of research, scientists’ experience in research, and scientists’ experience in their exact ﬁeld of research, scientists do not share the same information needs. In fact, these needs vary depending on the stage of research in which scientists are involved. In [Bates 1996], the authors assume that the information-seeking process should be even more complex for interdisciplinary studies than for "classical academic disci- plines". In [Whitmire 2002], the authors study the diﬀerence in information-seeking behaviour between diﬀerent academic disciplines. The authors classify academic ﬁelds of research into the three dimensions described by Biglan6. The authors sur- veyed a total of 5176 undergraduate students in four-year institutions and found that diﬀerences exist between the "hard" and "soft" disciplines, between life and non-life sciences, and between pure and applied science. Students in "soft" disci- plines and "life" and "pure" science used online catalogues to a greater extent, asked librarians for help, read reference sections more often, used indexes more often, de- veloped their bibliographies more extensively, checked for citations more often, and checked out books more often than students in the "hard", "applied" and "non-life" sciences did. 6 Biglan [Biglan 1973]: 1) discipline-level paradigm (hard science and soft science); 2) practical application of research (pure and applied science); and 3) degree of involvement with the living or organic object of study (life versus non-life)
  37. 37. 2.2. State of the art 21 In [Kembellec 2012], the authors also detected some diﬀerences between diﬀerent ﬁelds of research (196 PhD students and researchers in the human sciences, social sciences and hard sciences were surveyed). The authors found that 89% of searches were performed using a commercial information retrieval system, with an overall preference for Google Scholar. For the hard sciences, the authors found no diﬀerences between PhD students in the beginning stages of their programmes, PhD students at the end of their programmes, and researchers. For the social sciences and human sciences, searches were also performed using other systems, such as OPAC. The authors found diﬀerences between PhD students who were beginning to write their theses and those in the ﬁnal stages of writing their theses, with the number of PhD students using systems such as OPAC decreasing from (44%) to (33%). Among researchers, 44% used OPAC. In [Nicholas et al. 2007], the authors address the bouncing7 behaviour of users of ScienceDirect. The authors analysed the logs of 800 senior academics in the life sciences, mathematics and medicine. [Nicholas et al. 2007] found that bouncing behaviour varies diﬀerent between ﬁelds of research. The authors also found that the number of times an item is viewed during a session changes as a function of the ﬁeld of research. Medical scientists tend to show the strongest bouncing behaviour. The authors also found that graduate students exhibit more signiﬁcant bouncing behaviour than senior scientists do. Heinström [Heinström 2005] deﬁned three diﬀerent types of patterns for surﬁng the Web. She analysed the relations between information-seeking behaviour and personality traits and found that psychological features had a stronger inﬂuence on student information-seeking behaviour than students’ academic background or their stage of thesis writing. The author categorised the participants into three groups: • Fast-surﬁng students: Students who wanted information available quickly and easily with the least eﬀort. Depth of information was not a concern. Students judged the relevance of the documents by their look, the type of document and whether documents were easily available. • Broad-scanning student: Students with exhaustive and ﬂexible information- seeking behaviour over a wide range of sources. These students developed their search gradually rather than planning it. • Deep-diving student: These students went beneath the surface in seeking in- formation. Students of this type showed quality and conscientiousness in their searches and worked hard to obtain high-quality information. These students sought greater quality than quantity. This study shows that it is not necessarily the academic ﬁeld that creates the variation in information-seeking behaviour between persons; psychological features 7 "Bouncing describes a form of behaviour in which users view only a few web pages from the vast number available and generally do not return to the same website very often, if at all." [Nicholas et al. 2007, p.1086]
  38. 38. 22 Chapter 2. User model (e.g., neuroticism, extraversion openness, agreeableness) may change this behaviour. Considering more than the diﬀerences between academic ﬁelds could be important in the design phase of IRs, but it could also be important to consider psychological features during the evaluation phase, as we will discuss in the evaluation chapter. Scientists have created diﬀerent strategies to avoid unnecessary reading of ar- ticles in the literature and to seek more eﬃcient ways to obtain information. As demonstrated above, some of these strategies can vary depending on the academic ﬁeld in which scientists are engaged or the personality traits of scientists. However, the diﬃculties that scientists may encounter in attempting to gather the information they need may arise due to other factors. In [Palmer et al. 2007], the authors sought to determine the eﬀect of characteristics of a problem to be solved (weak and strong) on information-seeking behaviour in the ﬁeld of neuroscience. The authors discussed two concepts derived from Simon’s theory (1986): weak and strong problem solving. Weak problem solving occurs when a problem space is ill structured, users have low domain knowledge and users take unclear or unsystematic steps in their research. These problems make the information-seeking process more diﬃcult and more time consuming. In [Palmer et al. 2007], the authors indicate that data- and literature- mining techniques are relatively weak, compared to data-driven searches and are often correlated with an ill-deﬁned problem focus. Palmer et al. also found that users use weaker techniques to search for new collaborations or strategic alliances, explore new domains and techniques, and gather new ideas and techniques. Users use stronger approaches to address problems when they already have a theory in mind. In this case, users have a high level of knowledge in the domain and pro- ceed with clear and calculated steps. Palmer et al. showed that weak and strong approaches are both important for users seeking information. The authors suggest that weaker practices have a greater potential for promoting innovation and new dis- coveries. Taking into account the impact of weak or strong problem solving could introduce new perspectives to the design of IRs and the evaluation of such systems. In [Renear & Palmer 2009a], the authors argue that scientists have problems locating very problem-speciﬁc information (methods, protocols). They also argue that scientists do not simply read individual articles in sequence but handle many articles simultaneously to search, ﬁlter, compare, arrange, link, annotate and analyse fragments of content to gather information as eﬃciently as possible. The authors call this behaviour "Strategic reading". The authors also argue that with the emergence of online indexing and navigation systems such as PubMed, Scopus, Google Scholar, and Citeseer, practices of strategic reading have intensiﬁed. Scientists search and browse literature as if they are playing video games, by rapidly moving through resources, changing search strings, chaining references, and accumulating bits of information, such as ﬁndings, equations, protocols and data. Scientists make rapid judgements across these documents. In [Bishop 1999], the authors showed that scientiﬁc writing is "disaggregated and reaggregated" in the process of constructing new knowledge in science and engineer- ing. In [Schatz et al. 2002, Bishop 1999], the authors used the DELIVER (DEsktop LInk to virtual Engineering Resources) system to analyse the behaviour of scientists
  39. 39. 2.2. State of the art 23 using this system. DELIVER was a system deployed at the University of Illinois at Urbana-Champaign within the scope of the Digital Libraries Initiatives project (1994-1998). The system indexed 66,000 articles from ﬁve professional societies in physics, engineering and computer science. DELIVER used the document struc- ture to index parts of documents, such as tables, ﬁgures and article titles; tags were generated in SGML. The authors found that scientists use diﬀerent parts of the doc- ument structure, such as abstracts, ﬁgures, equations, and bibliographic citations, in their own work for several purposes: • Identify a document of interest • Address the relevance of an article before retrieving or reading it • Create customised document surrogates after retrieval, for example, by com- bining bibliographic and other data • Provide speciﬁc pieces of information • Convey knowledge that is not easily rendered by words through ﬁgures and tables The authors also found that the participants read the title and abstract of a document ﬁrst and then skimmed section headings. More recently, Bishop et al. examined lists, summary statements, deﬁnitions and illustrations after key sections and observed that scientists read the conclusion and skimmed the references. This study showed that users may use a search engine to retrieve speciﬁc components of a document. However, the study was restricted to researchers in science and engineering. In sum, in these studies, the authors tended to ﬁnd that scientists search and read scientiﬁc documents diﬀerently depending on their ﬁeld of research, their psy- chological traits, and the diﬃculty of their tasks. The authors also found that scientists avoid having to read documents unnecessarily and that scientists attempt to concentrate their reading in certain parts of documents. However, despite the large number of studies about how scientists search for information of interest, there is a need for further studies on this subject. In this thesis, we sought to delve deeper into the reasons scientists read scientiﬁc documents and the parts of documents on which they focus.
  40. 40. 24 Chapter 2. User model 2.3 Survey Scientists have some speciﬁcity in their information-seeking behaviour, as demon- strated above. They have speciﬁc needs, and they construct certain strategies to search for information. However, although the literature regarding the information- seeking behaviour of scientists is abundant, a more complete approach is necessary to address certain questions and to build a better information retrieval system for scien- tiﬁc literature. We designed an on-line survey at a very early stage of this research8. The survey was constructed based on three hypotheses. The ﬁrst hypothesis is that scientists seek and read scientiﬁc documents for diﬀerent reasons. This hypothesis is based on the results of [Garvey et al. 1974, Palmer et al. 2007, Tenopir et al. 2009]. The second hypothesis is that scientists focus on diﬀerent parts of a document rather than the whole document. These parts are the hypothesis, deﬁnition, methodology, results, opinion/critique and conclusion. The third hypothesis is that depending on the ﬁeld of research, scientists do not seek information from the same parts of docu- ments. For example, a researcher in the social sciences may read the same document as a researcher in medicine but may focus on diﬀerent parts of the document. 2.3.1 Methodology The survey (see appendix A) features 15 sets of questions in English (see appendix A). The ﬁrst part is socio-demographic (age and sex) and concerns the domain of research (arts, social science, economic science, law, engineering, science, psychology and science of education, translation, theology, medicine and other). The next six questions are about the purpose of reading a document (to stay informed, to ﬁnd all/some other studies in your research domain, to analyse how studies are conducted in your ﬁeld, to compare studies, to ﬁnd references for writing your own papers, to ﬁnd ideas for your own research); the possible answers to these questions are yes, no or uncertain. The next set of six questions asks where users generally ﬁnd the answers to their questions (hypothesis, deﬁnition, methodology, results, opinion/critique, conclusion); the possible answers to these questions are distributed on a Likert scale from always to never. The next question is "Do you often do a review of literature?", with the answers to the question limited to yes, no or uncertain. The next question is about the ease of ﬁnding the document for which the scientist is searching; the possible answers correspond to a Likert scale ranging from strongly agree (it is easy to ﬁnd the document) to strongly disagree. The next question is about the use of a specialised database or search engine, such as PubMed or Citeseer, or the use of Google Scholar. This question asks which scientists use more often, Google Scholar or other specialised databases. Again, answers are measured on a Likert scale ranging from strongly agree to strongly disagree. The last question asks whether scientists want a retrieval system that would be able to ﬁnd articles based on the content of their conclusions (i.e., all 8 Some of the results presented in this section were published in [Ribaupierre & Falquet 2011, Ribaupierre 2012]
  41. 41. 2.3. Survey 25 articles stating that rain is wet), with answers measured on a Likert scale ranging from strongly agree to strongly disagree. The survey was sent by e-mail to 1,600 persons at the University of Geneva and other universities; only 91 responses were received (5.6% of answer), with 77 providing full answers. 2.3.2 Results We analysed our data using SPSS. The sample was composed of 34 females and 57 males (with an average age of 39 years old). The population was not well distributed among diﬀerent research areas: science (28), engineering (19), law (12), psychology and science of education (11), medicine (7), other (6), social science (5), economic science (1) and art (1). Therefore, for some of the hypotheses we posed, the analysis is diﬃcult, and results could be biased because of the small number of persons in some groups. Using the Biglan [Biglan 1973] classiﬁcation, the research areas were grouped into three categories: "hard" sciences (medicine, engineering and science), "soft" sciences (psychology, social science, economic science and art) and other. 2.3.2.1 Reasons to read scientiﬁc documents Participants in this survey agreed with all the reasons that were proposed for reading an article (see table 2.1). Table 2.1: "Why do you read scientiﬁc documents" (in percent, n=91) Why do you read scientiﬁc documents yes no uncertain To ﬁnd other studies in your research domain 94.5 2.2 3.3 To ﬁnd references for writing your own papers 90.1 5.5 4.4 To stay informed 83.5 7.7 8.8 To compare studies 81.3 8.8 9.9 To analyse how studies are conducted in your ﬁeld 72.5 9.9 17.6 To ﬁnd ideas for your own research 71.4 13.2 15.4
  42. 42. 26 Chapter 2. User model We found few diﬀerences between the domains of research regarding the rea- sons why scientists read scientiﬁc documents (see table 2.2). We can observe that respondents in "hard" sciences seem to be more interested in reading to analyse how studies are conducted than are respondents in "soft" sciences or others. The respondents in "soft" sciences seem to read to ﬁnd references for their own writing more than the respondents in "hard" sciences and "other" do. The respondents in "hard" sciences seem to read more to ﬁnd new idea for their own research than do the respondents in "soft" sciences or other (see ﬁgure 2.8). Table 2.2: "Why do you read scientiﬁc documents by area of research" (in percent n=91), "soft" science (SS), "hard" science (HS) and other (O) p = probability of signiﬁcance in a 2 test Why do you read sci- entiﬁc documents by area of research yes No Uncertain p SS HS O SS HS O SS HS O To stay informed 87.1 81.5 83.3 9.7 5.6 16.7 3.2 10.0 0.0 .424 To analyse how stud- ies are conducted in your ﬁeld 64.5 79.6 50.0 12.9 7.4 16.7 22.6 13.0 33.3 .418 To ﬁnd all/some other studies in your research domain 93.5 96.3 83.3 3.2 0.0 16.7 3.2 3.7 0.0 .117 To compare studies 80.6 83.3 66.7 9.7 7.4 16.7 9.7 9.3 16.7 .901 To ﬁnd references for writing your own pa- pers 96.8 87.0 83.3 3.2 5.6 16.7 0.0 7.4 0.0 .327 To ﬁnd ideas for your own research 67.7 75.9 50 19.4 7.4 33.3 12.9 16.7 16.7 .298 Year of birth did not have a signiﬁcant eﬀect, but it appears that a diﬀerence ex- ists between older scientists and younger scientists with respect to staying informed (see Table 2.3). It appears that older scientists are more likely to read scientiﬁc doc- uments with the aim of staying informed than younger scientists are. No signiﬁcant correlation was observed between age and research domain (r = .101, N = 91, p.340). It also appears that older and the youngest scientist are more likely to read scien- tiﬁc documents with the aim of funding references for writing their own papers (see ﬁgure 2.9).
  43. 43. 2.3. Survey 27 Figure 2.8: "Why do you read scientiﬁc documents by area of research by area of research"; often answer 0" 20" 40" 60" 80" 100" To"stay" informed"" To"analyse" how"studies" are"conducted" in"your"ﬁeld"" To"ﬁnd"all/ some"other" studies"in"your" research" domain"" To"compare" studies"" To"ﬁnd" references"for" wri=ng"your" own"papers"" To"ﬁnd"ideas" for"your"own" research"" So@"science" Hard"science" Other" Figure 2.9: "Why do you read scientiﬁc documents by area of research by years of birth"; often answer 0" 20" 40" 60" 80" 100" To"stay"informed""To"analyse"how" studies"are" conducted"in" your"ﬁeld"" To"ﬁnd"all/some" other"studies"in" your"research" domain"" To"compare" studies"" To"ﬁnd" references"for" wri=ng"your"own" papers"" To"ﬁnd"ideas"for" your"own" research"" 1940@1969"" 1970@1979"" 1980@...""
  44. 44. 28 Chapter 2. User model Table 2.3: "Why do you read scientiﬁc documents by area of research" (in percent n=91), year of birth Why do you read scientiﬁc documents by year of birth Yes No Uncertain p Year of birth 40-69 70-79 80-... 40-69 70-79 80-... 40-69 70-79 80-... To stay in- formed 96.7 74.0 79.4 3.3 11.1 8.8 0 14.8 11.8 .179 To analyse how studies are conducted in your ﬁeld 70.0 74.1 73.5 16.7 11.1 2.9 13.3 14.8 23. 5 .374 To ﬁnd all/- some other studies in your research domain 93.3 92.6 91.1 3.3 3.7 0. 3.3 3.7 2.9 .867 To compare studies 83.3 77.8 82.4 10.0 11.1 5.9 6.7 11.1 11.8 .897 To ﬁnd refer- ences for writ- ing your own papers 93.3 85.2 91.2 6.7 11.1 0 0 3.7 8.8 .167 To ﬁnd ideas for your own research 73.3 66.7 73.5 20.0 14.8 5.9 6.7 18.5 20.6 .302
  45. 45. 2.3. Survey 29 2.3.2.2 Do you read scientiﬁc papers to respond to a precise need With regard to this issue, 83.5% of respondents read scientiﬁc documents for a speciﬁc purpose, whereas 16.5% do not. 2.3.2.3 Where do you generally ﬁnd the answers Responses (see table 2.4) were grouped into three categories: "always" and "very frequently" responses were grouped into the category Often; "occasionally" and "rarely" responses were grouped into the category Sometimes; and "very rarely" and "never" responses were grouped into the category Never. Table 2.4: "Where do you generally ﬁnd your answers" (in percent, n=77) always sometimes never In results 75.0 23.7 1.3 In methodology 59.7 36.4 3.9 In conclusion 56.6 35.5 7.9 In deﬁnition 50.6 44.2 5.2 In opinion/critic 42.1 46.1 11.8 In hypothesis 40.3 46.8 13 We tested whether the domains of research diﬀered with respect to the parts of documents on which scientists focus (see table 2.5). All domains indicated interest in the results section. Respondents in the ﬁeld of "hard" sciences appeared to be more interested in the methodology section than those in "soft" sciences and other. Respondents in other and "soft" sciences appeared to be more interested in the conclusion section than those in "hard" sciences. No real diﬀerences were observed between the domains for the deﬁnition section. Respondents in "soft" sciences appeared to be more interested in the opinion/critique section. No diﬀerences were observed between the domains with respect to the hypothesis section (see ﬁgure 2.10). The only signiﬁcant diﬀerences observed were for the opinion/critique section, where p = 0.41, and the methodology section, where the diﬀerence was marginally signiﬁcant with p = 0.63. We tested also whether the age of the respondents diﬀered with respect to the parts of the documents (see table 2.6 and ﬁgure 2.11). We observed that young scientists are focusing more for the methodology with a signiﬁcant diﬀerence (p = 0.047). We also found a small diﬀerence for the hypothesis, where older scientists seems to be more interested, the diﬀerence is not signiﬁcant (p = 0.090).
  46. 46. 30 Chapter 2. User model Table 2.5: "Where do you generally ﬁnd your answers by area of research" (in percent, n=77) "soft" science ( SS), "hard" science (HS) and other (O) Often Sometimes Never p SS HS O SS HS O SS HS O Opinion/critic 64.3 30.2 20.0 25.0 55.8 80.0 10.7 14.0 0.0 .028 Hypothesis 46.4 38.6 20.0 35.7 52.3 60.0 19.9 9.1 20.0 .521 Deﬁnition 53.6 50.0 40.0 35.7 47.7 60.0 10.7 2.3 0.0 .455 Methodology 46.4 70.5 40.0 42.9 29.5 60.0 10.7 0.0 0.0 .063 Result 71.4 74.4 100 25.0 25.6 0.0 3.6 0.0 0.0 .485 Conclusion 64.3 48.8 80.0 25.0 44.2 20.0 10.7 7.0 0.0 .396 Table 2.6: "Where do you generally ﬁnd your answers" by year of birth (in percent, n=77) Often Sometimes Never p Year of Birth 40-69 70-79 80-... 40-69 70-79 80-... 40-69 70-79 80-... Opinion/critic 47.8 39.1 40.0 43.4 47.8 46.6 8.6 13.0 13.3 .652 Hypothesis 60.9 26.1 35.5 26.1 60.9 51.7 13.0 13.0 12.7 .090 Deﬁnition 43.5 52.2 54.8 43.5 43.5 45.1 13 4.3 3.2 .546 Methodology 39.1 78.3 61.3 52.2 65.2 35.5 8.7 0 3.2 .047 Result 78.3 69.9 57.9 17.4 8.7 5.3 4.3 0 1.3 .461 Conclusion 60.9 56.5 53.3 30.4 39.1 36.7 8.6 4.3 10.0 .995 Figure 2.11: "Where do you generally ﬁnd your answers by years of birth"; often answer 0" 20" 40" 60" 80" 100" Opinion/cri0c"" Hypothesis"" Deﬁni0on"" Methodology"" Result"" Conclusion"" "1940A1969"" "1970A1979"" 1980A...""
  47. 47. 2.3. Survey 31 Figure 2.10: "Where do you generally ﬁnd your answers by area of research"; often answer 0" 20" 40" 60" 80" 100" Opinion/cri0c"" Hypothesis"" Deﬁni0on"" Methodology"" Result"" Conclusion"" SoA"science" Hard"science" Other"
  48. 48. 32 Chapter 2. User model 2.3.2.4 Do you often conduct a review of the literature In response to the question, "Do you often conduct a review of the literature", 61.5% answered yes and 38.5% answered no. Table 2.7 shows that respondents in "soft" sciences review the literature less often than do those in "hard" sciences, with the diﬀerence being marginally signiﬁcant (p = .691). Regarding the section in which respondents are most interested (see table 2.8), the only signiﬁcant diﬀerence observed was for the results section (p = .019). Table 2.7: Do you often conduct a review of the literature (in percent, n = 77) "soft" science "hard" science other Yes 32.1 62.5 5.4 No 37.1 54.3 8.6 Table 2.8: "Do you often conduct a review of the literature?" by "Where do you generally ﬁnd answers" ?[Result] (in percent,n = 77) Do you ﬁnd generally your answer in the result part? Often Sometime Never Do you often conduct a review of the literature? Yes 84.0 14.0 2.0 No 75.9 23.7 1.3 Total 75.0 18.0 1.3
  49. 49. 2.3. Survey 33 2.3.2.5 Do you easily ﬁnd papers/books you are looking for without too much noise (e.g., a paper that is out of the ﬁeld in which you are searching Regarding the question "Do you easily ﬁnd papers/books you are looking for without too much noise", 60.4% agreed, 16.5% strongly agreed, 15.4% neither agreed nor disagreed, 6.6% disagreed and 1.1% strongly disagreed. No signiﬁcant diﬀerence was observed between the domains of research or between years of birth. 2.3.2.6 Do you use Google Scholar more often than a specialised database (in your domain) Regarding the question "Do you use Google Scholar more often than a specialised database", 19.8% strongly agreed, 20.9% agreed, 16.5% neither agreed nor disagreed, 29.7% disagreed and 13.7% strongly disagreed. No signiﬁcant diﬀerence was ob- served between the domains of research or between years of birth. 2.3.2.7 Would you like a retrieval system that would be able to ﬁnd ar- ticles by the content of their conclusions (i.e., all articles stating that rain is wet) Regarding the ﬁnal question, "Would you like a retrieval system that would be able to ﬁnd articles by the content of their conclusions", 26.4% strongly agreed, 30.8% agreed, 26.4% neither agreed nor disagreed, 8.8% disagreed and 7.7% strongly disagreed. No signiﬁcant diﬀerence was observed concerning the domains of research, but a signiﬁcant diﬀerence (see ﬁgure 2.12) was observed with respect to the year of birth (p = .033). The percentage of young persons indicating interest in this type of system was greater than the percentage of older persons indicating the same. No signiﬁcant diﬀerence was observed concerning the diﬃculty scientists encounter in ﬁnding their documents. We can observe in the cross-table (see Figure 2.13) between "What is the rea- son(s) you are reading scientiﬁc documents" and the parts of documents scientists read that there are signiﬁcant positive relationships between "to stay informed" and "results"; "to ﬁnd references for writing your own papers" and "conclusion"; "to analyse how studies are conducted in your ﬁeld" and "deﬁnition" and "method- ology"; and "to ﬁnd ideas for your own research" and "deﬁnition" and "hypothesis.”
  50. 50. 34 Chapter 2. User model Figure 2.12: "Would you like a retrieval system that would be able to ﬁnd articles by their conclusions"
  51. 51. 2.3. Survey 35 Figure2.13:Relationshipbetweentaskandwhatpartsareread
  52. 52. 36 Chapter 2. User model 2.3.3 Survey Discussion and Conclusion The reasons scientists read scientiﬁc documents appear to be the same as those indicated in [Garvey et al. 1974]. It appear that scientists in "hard" sciences more often read to ﬁnd how a study was conducted in their ﬁeld and to ﬁnd new ideas. In contrast, scientists in "soft" sciences appear to read to ﬁnd references to cite in their own papers. Few diﬀerences between the social sciences and physics in the study of [Garvey et al. 1974] were fund regarding the nature of the information needed. In addition, older scientists appear to read more to stay informed and older and youngest scientists seems to read to ﬁnd references for their own papers than the middle age categories do. It can be observed that scientists are more likely to ﬁnd their answers in certain types of sentences or paragraphs than in others. Among the proposed parts of documents, scientists focus primarily on the "results" section of scientiﬁc documents. Certain signiﬁcant diﬀerences can be observed: scientists in the "soft" sciences more often ﬁnd their answers in the "opinion/critique" section, which is due to the fact that such content ("opinion/critique") is observed more frequently in the "soft" sciences than in the "hard" sciences. In contrast, scientists in the "hard" sciences appear to read the "methodology" section more often than do scientists in the "soft" sciences. Older scientists read the "hypothesis" section more often than younger scientists do, but this diﬀerence is not signiﬁcant. In contrast, younger scientists appear to read the "methodology" section more often than older scientists do. Scientists who review the literature more often appear to ﬁnd their answers in the "results" section more often than other scientists do. Because this study did not answer all of the questions we proposed, especially questions that require more precise information regarding how scientists seek or read information, we conducted interviews to better understand these processes. 2.4 Interview The questionnaire was based on several hypotheses9: • Scientists search through scientiﬁc documents to ﬁnd an answer to a speciﬁc question • Scientists search through speciﬁc chunks of scientiﬁc documents • Scientists search through speciﬁc chunks of scientiﬁc documents depending of the task they have to fulﬁl • Scientists read scientiﬁc documents for a speciﬁc purpose • Scientists read speciﬁc fragments to answer to speciﬁc questions • Scientists read diﬀerent types of fragments depending on the tasks they intend to complete 9 Some of the results presented in this section were published in [Ribaupierre 2012, Ribaupierre & Falquet 2013]
  53. 53. 2.4. Interview 37 2.4.1 Methodology We conducted semi-directive interviews with scientists from diﬀerent areas of re- search and with diﬀerent levels of research expertise. The interviews were conducted in English or in French. The sample consisted of 10 participants (see table 2.9). A large part of the interview was devoted to determining the sections on which the scientists focused. Table 2.9: Sample Population Subject Year of birth Gender Field of research Highest educa- tion degree, if PhD year Nb of arti- cle writ- ten as ﬁrst au- thor Total nb of arti- cle pub- lished Nb of article read by month P1 1983 M Computer science Master 6 6 10 P2 1978 F Computer science 2009 15 20 10 P3 1976 F Linguistic/ Computer science 2008 17 29 25 P4 1961 M Computer science/ health Master 10 20 15 P5 1976 F Information System Master 1 10 3 P6 1946 F Psychology 1975 68 141 6 P7 1957 M Physics/Science History 1987 15 60 50 P8 1985 F Traduction & communication Master 2 3 20 P9 1983 F Social Science, Gender studies Master 1 1 15 P10 1974 F Medecine 2000 20 28 25 We constructed a questionnaire composed of 23 questions (see Appendix B), which formed the basis of the interview. The interview lasted one to two hours. The ﬁrst 13 questions were about socio-demographic data and the researchers’ level of expertise. The second part focused on search patterns, what type of IR system the researchers used, what type of information the researchers searched for, and what types of questions the researchers asked themselves before querying an IR system. The third part concerned the reading behaviour of the researchers, such as the speciﬁc part of a document (fragment) on which the researchers focused when they did not read the entire article. Speciﬁc questions were asked to investigate whether
  54. 54. 38 Chapter 2. User model readers looked at diﬀerent fragments depending on their ultimate task. We de- ﬁned a list of tasks that scientists can achieve while reading a document. This list was discussed between people within the research group and validated during the interviews. 2.4.2 Results 2.4.2.1 Reasons to search for and read a scientiﬁc document We established a list of reasons why scientists seek and read scientiﬁc documents. During the interviews, we discussed this list with the interviewees, and they were able to add new reasons during the interviews. The reasons that the interviewees agreed most strongly with were (in descending order): • to enhance their knowledge • to write papers • to ﬁnd a new idea/inspiration • to discover another point of view • look at a new idea • to stay informed • because they were advised by someone • to compare documents • to write a state-of-the-art review • to ﬁnd a speciﬁc deﬁnition • curiosity • to provide a new point of view • to compare methodologies • to provide expertise/review • to summarise their knowledge • to be able to take a position in a document • because it was referenced by another document • to resolve a problem • to build a model • to determine whether an idea was new or whether someone else had already worked on it.

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