=Paper=
{{Paper
|id=Vol-1364/paper1
|storemode=property
|title=Studying the History of Pre-Modern Zoology with Linked Data and Vocabularies
|pdfUrl=https://ceur-ws.org/Vol-1364/paper1.pdf
|volume=Vol-1364
|dblpUrl=https://dblp.org/rec/conf/esws/TounsiFZVC15
}}
==Studying the History of Pre-Modern Zoology with Linked Data and Vocabularies==
https://ceur-ws.org/Vol-1364/paper1.pdf
Studying the History of Pre-Modern Zoology
with Linked Data and Vocabularies
Molka Tounsi1 , Catherine Faron Zucker1 , Arnaud Zucker1 ,
Serena Villata2 , and Elena Cabrio2
1
Univ. Nice Sophia Antipolis, France
tounsi.molka@etu.unice.fr, faron@unice.fr, zucker@unice.fr
2
Inria Sophia Antipolis Méditerranée, France
serena.villata@inria.fr, elena.cabrio@inria.fr
Abstract. In this paper we first present the international multidisci-
plinary research network Zoomathia, which aims the study of the trans-
mission of zoological knowledge from Antiquity to Middle Ages through
varied resources, and considers especially textual information, includ-
ing compilation literature such as encyclopaedias. We then present a
preliminary work in the context of Zoomathia consisting in (i) extract-
ing pertinent knowledge from mediaeval texts using Natural Language
Processing (NLP) methods, (ii) semantically enriching semi-structured
zoological data and publishing it as an RDF dataset and its vocabulary,
linked to other relevant Linked Data sources, and (iii) reasoning on this
linked RDF data to help epistemologists, historians and philologists in
their analysis of these ancient texts.
Keywords: History of Zoology, Semantic Analysis of Mediaeval compi-
lations, Linked Data and Vocabularies
1 Introduction
Scholars concerned with cultural issues in Antiquity or Middle Ages have to
deal with a huge documentation. The literary material is a significant part of
this material, but the commonly used technology supporting these researches is
to date far from satisfactory. In spite of pioneering undertakings in digitization
since the 70’s, historians and philologists still have access to few tools to operate
on texts, mostly limited to lexical searches. Therefore they stand in need for
more intelligent tools, in order to overcome this word-dependency, to access the
semantics of texts and to achieve more elaborated investigations.
The Semantic Web has an increasing role to play in this process of provid-
ing new methodological implements in cultural studies. During the last decade,
several works addressed the semantic annotation and search in Cultural Her-
itage collections and Digital Library systems. They focus on producing Cultural
Heritage RDF datasets [1, 4], aligning these data and their vocabularies on the
Linked Data cloud [2, 7], and exploring and searching among heterogenous se-
mantic data stores [5, 8, 3, 6].
7
The international research network Zoomathia3 has been set up to address
this challenge in the area of History of Science. It aims to develop intercon-
nected researches on History of Zoology in pre-modern times and to raise col-
laborative work involving philologists, historians, naturalists and researchers in
Knowledge Engineering and Semantic Web. In this context, we conducted a
preliminary work, presented in this paper, on the fourth book of the late me-
diaeval encyclopaedia Hortus Sanitatis (15th century), which compiles ancient
texts on fishes. Each chapter of this book is dedicated to one fish, with possible
references to other fishes. In this work we aim at (i) automating information
extraction from these texts, such as zoonyms, zoological sub-discipline (ethol-
ogy, anatomy, medicinal properties, etc.); (ii) building an RDF dataset and its
vocabulary representing the extracted knowledge, and link them to the Linked
Data; and finally, at (iii) reasoning on this linked data to produce new expert
knowledge. We build upon the results of two previous French research projects
on structuring mediaeval encyclopaedias in XML according to the TEI model
and manualy annotating author sources (SourceEncyMe project4 ) and zoonyms
(Ichtya project5 ).
The paper is organized as follows: Section 2 presents the general aim of
Zoomathia. Section 3 presents our work on knowledge extraction from the medi-
aeval encyclopaedia Hortus Sanitatis, while Section 4 describes the publication
of a linked RDF dataset and its vocabularies. Section 4.3 presents preliminary
work on the exploitation of these data to support the study of the history of
pre-modern zoology, and Section 5 concludes the paper.
2 The Zoomathia Research Network
Zoomathia primarily focuses on the transmission of zoological knowledge from
Antiquity to Middle Ages. Manual search and computing on ancient and me-
diaeval texts enable to address the quantitative dimension of data but fail to
answer the epistemological demands, which concern the scientific relevancy and
the diachronic features of the documentation. A large range of investigations on
specific topics is inaccessible through simple lexical queries and requires a rich,
scientific and semantic annotation. When investigating, for example, on etho-
logical issues (such as animal breeding, intraspecific communication or technical
skills) or on pharmaceutical properties of animal products, we have to face a
scattered documentation and a changing terminology hampering a direct access
to and a synthetic grasp of the topics studied. An automatized and semantic-
based process will help to link and cluster together the related data, compare
evidences in a diachronic approach and to figure out the major trends of the
cultural representations of animal life and behaviour.
3
http://www.cepam.cnrs.fr/zoomathia/
4
http://atelier-vincent-de-beauvais.irht.cnrs.fr/
encyclopedisme-medieval/programme-sourcencyme-corpus-et-sources-des-en
cyclopedies-medievales
5
http://www.unicaen.fr/recherche/mrsh/document_numerique/projets/ichtya
8
In this network, we aim at both (i) identifying a corpus of zoology-related
historical data, in order to progressively encompass the whole known documen-
tation, and (ii) producing a common thesaurus operating on heterogeneous re-
sources (iconographic, archaeological and literary). This thesaurus should enable
to represent different kinds of knowledge: zoonyms; historical period; geograph-
ical area; literary genre; economical context; zoological sub-discipline (ethology,
anatomy, physiology, psychology, animal breeding, etc.). The aim is to synthesize
the available cultural data on zoological matters and to crosscheck them with a
synchronic perspective. This would enable to reach the crucial concern, i.e. to
precisely assess the transmission of zoological knowledge along the period and
the evolution of the human-animal relations. Finally, this thesaurus should be
published on the Linked Data and linked to modern reference sources (biological
and ecological) to appraise the relevance of the historical documentation.
3 Knowledge Extraction from Historians and Texts
3.1 Interviews of Historians
We conducted several interviews with three Historians participating in Zoomathia
to explicit a list of major knowledge elements which would be useful in the study
of the transmission of ancient zoological knowledge in mediaeval texts. Among
them, let us cite the presence (or absence) of zoonyms in the corpus texts, variant
names or name alternatives given to an animal (polyonymy), the relative volume
of textual records devoted to a given zoonym, references to a zoonym and fre-
quency of occurrences related to it out of their dedicated chapter, geographical
location of the described animals, numerical data in the text (size, longevity,
fertility, etc.) and other animal properties related to zoological sub-disciplines
(ethology, anatomy, physiology, psychology, animal breeding, etc.).
3.2 Extraction of Zoonyms and Animal Properties from Texts
We processed two versions of book 4 of Hortus Sanitatis, the original Latin
text and its translation in French. We used the XML structured version of these
texts, identifying the 106 chapters of the book, divided in paragraphs, themselves
including citations. We used TreeTagger to parse Latin and French texts and
determine the lemmas and part of speech (PoS) of each word in the text. We
searched for the resources available to support the knowledge extraction process.
A lexicon of fish names in French and in Latin has been provided by the Ichtya
project and we — Knowledge Engineers and Historians — collaboratively built a
thesaurus of zoological sub-disciplines and concepts involved in the descriptions
relative to these sub-disciplines. Then we defined two sets of syntactic rules for
French and Latin to recognize zoonyms from the lexicon of fish names among
the lemmas identified in the texts. For instance one of the rules to recognize that
a Latin text deals with longevity is the occurence of the verb vivere followed by
a numeric value followed by the noun annis (ablative plural of annus).
9
We conducted a similar processing of the same two texts to extract zoological
sub-disciplines and animal properties. We defined two sets of syntactic rules to
extract this information from the Latin and French text (39 rules for French and
10 rules for Latin). For instance the Latin verbs curare (heal) or sanare (cure)
with an animal name as subject are used to identify the therapeutic topic; the
verbs comedere or pascere or deglutire (eat) are used to identify the diet topic.
Evaluation The analysis of the results of the automatic annotation process
was conducted by knowledge engineers and validated by philologists involved
in the manual annotation. For the evaluation of the extraction of zoonyms we
considered chapters 1 to 53 of book 4 of Hortus Sanitatis. We compared the
results of the automatic annotation with those of the manual annotation of
zoonyms conducted within the past Ichtya project. F-measure equals to 0.93
for both the annotation of the Latin text and the French text. Most missing
annotations are due to the fact that the parsing tool is unable to deduce the exact
lemma of some words, especially for Latin words. Among 65 missing annotations,
51 (rare) fish names were not annotated because TreeTagger does not recognize
them (e.g., loligo). Other missing annotations concern composed names and are
due to a mismatch between the complete fish name in the reference lexicon and
the short name used in the text to be annotated (e.g. locusta instead of locusta
marina). Conversely, most annotation errors are due to ambiguities between
marine animal names and terrestrial animals. For instance, lemma lupus (wolf)
is present in the provided lexicon of fish names (wolffish) and there are some
comparisons in the text with the (terrestrial) wolf6 .
For the evaluation of the automatic extraction of animal properties, we man-
ually annotated the 25 first chapters of Hortus Sanitatis to use it as a reference
version. F-measure is above 0.7 for both the annotation of the Latin text and the
French text. Most wrong annotations are related to anatomy. These annotations
are due to a confusion between human and animal anatomical parts appearing
in the text, when the text deals with the therapeutic power of some animal on
a human organ. For instance, the detection of lemma dentes (tooth) in the text
leads to the annotation of the text with the anatomy topic, whereas, in some
cases, the text describes a therapeutic effect of the animal on (human) teeth7 .
4 From Unstructured Data to Semantic Data
The extracted knowledge has first been used to enrich the available XML anno-
tation of Hortus Sanitatis. Then we translated the whole XML annotation (text
structure, source authors, zoonyms and animal properties) into an RDF dataset
and vocabularies and exploited it with SPARQL queries.
6
“And although this is the case for all fishes, it is however more obvious in him
(wolffish), as it is also for the wolf and the dog among the beasts”
7
“[Human] teeth are cleaned using conch shell ash.”
10
4.1 RDF Dataset
An RDF dataset describing Hortus Sanitatis has been automatically generated
by writing an XSL stylesheet to be applied to its XML annotation. Listing 1.1
presents an extract of it describing quotation 4 of paragraph 3 of chapter 20.
It is a citation of Aristotle, refering to the crocodile zoonym and addressing the
therapeutics and anatomy topics.
< http :// zoomathia . unice . fr / HortusSanitatis / FR . hs .4.25.3/ cit4 >
a tei : Citation ;
tei : hasHead " FR . hs .4.25.3. cit4 ";
tei : hasBibliography [ a tei : Bibliography ;
tei : hasAuthor < http :// zoomathia . unice . fr / auteurs / Aristote >;
tei : hasReference
< http :// zoomathia . unice . fr / oeuvres /612 _a_21 -25 N_MS >. ];
tei : hasCitationText "...";
zoo : hasZoonym < http :// zoomathia . unice . fr / Crocodile >;
dcterms : subject
< http :// zoomathia . unice . fr / subject / therapeutique > ,
< http :// zoomathia . unice . fr / subject / anatomie >. ] ].
Listing 1.1. RDF annotation of an Aristotle’s citation on crocodiles
4.2 Vocabulary
Based on the lexicon initially provided by Historians involved in the Ichtya
project, we built a SKOS thesaurus for zoonyms and we aligned it with both
the cross-domain DBpedia ontology and the Agrovoc thesaurus specialized for
Food and Agriculture8 . In a near future we intend to align it with the TAXREF
taxonomy specialized in Conservation Biology and integrating Archaeozoological
data9 . Listing 1.2 presents an extract of the thesaurus describing taxon Garfish.
< http :// zoomathia . org / Orphie > a skos : Concept ;
skos : prefLabel " orphie " @fr ;
skos : closeMatch < http :// fr . dbpedia . org / resource / Orphie > ;
skos : closeMatch < http :// dbpedia . org / resource / Garfish > ;
skos : closeMatch < http :// aims . fao . org / aos / agrovoc / c_5102 > ;
skos : altLabel " gwich " .
Listing 1.2. Extract of the Zoomathia thesaurus of zoonyms
We built an RDFS ontology of zoology-related sub-disciplines and animal
properties, based on the results of interviews with Historians and the properties
extracted from texts. This is a preliminary modelisation which has to be further
developed.
8
http://aims.fao.org/vest-registry/vocabularies/agrovoc-multilingual-agricultural-
thesaurus
9
http://inpn.mnhn.fr/programme/referentiel-taxonomique-taxref?lg=en
11
Fig. 1. Relative importance of zoological topics in Hortus Sanitatis
4.3 Reasoning on Historical Zoological RDF Data
In order to exploit the extracted RDF knowledge base, we built a set of SPARQL
queries enabling to answer questions such as “What are the zoonyms studied in
this text?”, “What are the topics covered in this text?”, “Where can we find
these topics?”,“What are the zoonym properties (in which chapter or paragraph
or citation)?”. Let us note that it is the semantics captured in the constructed
vocabularies which make it possible to answer these queries: multiple labels
associated with a taxon in the thesaurus of zoonyms, hierarchy of zoology-related
sub-disciplines, denoted by various terms.
We went a step further in the exploitation of the RDF dataset by writing
SPARQL queries of the construct form to construct new RDF graphs captur-
ing synthetic knowledge. When graphically visualized, they support the analyt-
ical reasoning of historians on texts. For instance, Figure 1 presents the RDF
graph capturing the relative importance of zoology-related sub-disciplines in the
Hortus Sanitatis and their location in it. At a glance, it shows that anatomy
occupies a predominant place in this text, far ahead of therapeutics and fishing.
5 Conclusion and Future Work
We presented a preliminary work conducted in the context of the Zoomathia
network, on the zoological mediaeval encyclopaedia Hortus Sanitatis. This work
combines NLP techniques to extract knowledge from texts, and knowledge engi-
neering and semantic web methods to build a linked RDF dataset of zoological
annotations of this scientific text. It exploits this dataset to support the analysis
of the Ancient zoological knowledge compiled in the encyclopaedia.
The next step will be to apply the presented process on a classical Latin
book on fishes (Pliny, Historia Naturalis, book 9, 1st century AD), which is a
major, though indirect, source of the Hortus Sanitatis, to deal with the historical
12
perspective of zoology, and end up with comparing the data of the two selected
works, to appraise the density of the transmission and the evolution of the zoolog-
ical knowledge on an epistemological point of view. We intend to systematically
compare the two texts, with the aim of evaluating the loss, distortion or enrich-
ment of information, and comparing the relative importance in the books of the
different zoological perspectives (anatomical, ethological, geographical, etc.) and
of the different animal species.
Acknowledgments. Zoomathia is an International Research Group (GDRI)
supported by the French National Scientific Research Center (CNRS).
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