=Paper=
{{Paper
|id=Vol-1364/paper2
|storemode=property
|title=Towards a Shared Reference Thesaurus for Studies on History of Zoology, Archaeozoology and Conservation Biology
|pdfUrl=https://ceur-ws.org/Vol-1364/paper2.pdf
|volume=Vol-1364
|dblpUrl=https://dblp.org/rec/conf/esws/CallouMFMM15
}}
==Towards a Shared Reference Thesaurus for Studies on History of Zoology, Archaeozoology and Conservation Biology==
https://ceur-ws.org/Vol-1364/paper2.pdf
Towards a Shared Reference Thesaurus for
Studies on History of Zoology,
Archaeozoology and Conservation Biology
Cécile Callou1 , Franck Michel2 , Catherine Faron-Zucker2 , Chloé Martin1 , and
Johan Montagnat2
1
Archéozoologie et archéobotanique (UMR 7209), BBEES (UMS 3468),
Sorbonne Universités, Muséum National d’Histoire Naturelle, CNRS, France
2
Univ. Nice Sophia Antipolis, CNRS, I3S (UMR 7271), France
Abstract. This paper describes an ongoing work on the construction
of a SKOS thesaurus to support multi-disciplinary studies on the trans-
mission of zoological knowledge throughout historical periods, combining
the analysis of ancient literature, iconographic and archaeozoological re-
sources. We first describe the I2AF, a national archaeozoological and
archaeobotanical inventory database integrating data from archaeologi-
cal excavation reports. Then we describe the TAXREF taxonomical ref-
erence designed to support studies in Conservation Biology, that was
enriched with bioarchaeological taxa from I2AF. Finally we describe the
TAXREF-based SKOS thesaurus under construction and its intended
use within the Zoomathia research network.
Keywords: I2AF, TAXREF, SKOS, History of Zoology
1 Introduction
Animal bones and plant remains from archaeological excavations are a rich and
original source of information on the history of biodiversity and its interac-
tion with human societies. When compared with the knowledge about diversity
and current locations of human populations, these remains help to figure out
the scenarios of past extinction, biological invasions and anthropic impact. This
is particularly true during the Holocene, when the influence of human activ-
ities overrode that of climatic factors. Therefore, gathering archaeozoological
and archaeobotanical data in a sustainable bioarchaeological database, publicly
available, represents a major challenge for Natural Sciences and Conservation
Biology. Archaeozoological and Archaeobotanical Inventories of France database
[1] (I2AF) aims to address this challenge.
Historians address a related challenge. Identifying the reported species in an-
cient literary and iconographic resources, and assessing the documentation is a
momentous issue of the History of Zoology. An increasing amount of primary ma-
terial (such as textual or iconographic resources) is encoded in domain-specific
15
digital formats. For instance, the SourcEncyMe3 and Ichtya4 projects aim to
encode mediaeval encyclopedias in the XML-TEI standard5 while adding man-
ual annotations with regards to mediaeval compilers, author sources and taxa.
These works succeed in making material about mediaeval scientific knowledge
more easily exploited by a broad scientific community, and support researchers
studying e.g. the transmission of zoological knowledge throughout historical pe-
riods. Yet, the sharing with related scientific communities remains hampered by
the lack of formal semantic reference and terminological standards. For instance,
the dolphin is a research topic for modern studies on biodiversity, for archaeozo-
ologists, as well as for studies on Greek mythology wherein the dolphin played an
important symbolic role [2]. Nevertheless, when the dolphin is identified in the
TEI annotation of the Hortus Sanitatis mediaeval encyclopedia6 or in Pliny the
Elder work (Historia Naturalis), how to know whether this refers to the same
animal? How to know which species is targeted, since the Latin word delphinus
is used in the textual tradition at least for all Mediterranean regular species of
Delphinidae, and labels many different modern taxa (Tursiops truncatus, Del-
phinus delphis, Stenella coeruleoalba, etc.)? How to relevantly relate those terms
with the Delphininae subfamily of modern zoological taxonomy, or even upper
terms in the classication (family Delphinidae, order Cetacea)? More generally,
how to simultaneously query various archaeozoological, zoological and historical
data sources, crosscheck the evidences and make sure that concepts share the
same meaning across data sources?
Those challenging questions can be addressed through the use of controlled
and widely accepted semantic references. A reference thesaurus shared by sibling
scientific disciplines would help to clear the many misinterpretations or confla-
tions made by ancient authors and debated at length in modern critic literature
referring to Ancient sources (from P. Belon, 1551, to I. Geoffroy Saint-Hilaire,
1841). The Zoomathia research network7 addresses this challenge, specifically on
the study of rich mediaeval compilation literature on Ancient zoological knowl-
edge, supported by archaeological and iconographic knowledge. The Semantic
Web provides powerful models and technologies for connecting and sharing pieces
of data while making their semantics explicit. RDF facilitates the combination
and sharing of different data sets thanks to the underlying Web technologies
and the subsequent Linked Data paradigm. Zoomathia intends to leverage those
technologies to annotate and link together various medieval compilations such as
the Hortus Sanitatis 8 , archaeozoological data (I2AF database) and iconographic
material. In this context, we chose the TAXREF [3] zoological and botanical
3
http://atelier-vincent-de-beauvais.irht.cnrs.fr/encyclopedisme-
medieval/programme-sourcencyme-corpus-et-sources-des-encyclopedies-medievales
4
http://www.unicaen.fr/recherche/mrsh/document numerique/projets/ichtya
5
http://www.tei-c.org/index.xml
6
https://www.unicaen.fr/puc/sources/depiscibus/accueil
7
http://www.cepam.cnrs.fr/zoomathia/
8
This very popular text that enjoyed numerous editions and translations between 1491
et 1547 is not only a landmark in the history of encyclopedias, but also, concerning
the naturalistic knowledge, representative of the whole medieval tradition. It provides
16
taxonomy to build a SKOS thesaurus supporting the integration of these het-
erogeneous data sets.
This paper is organized as follows: Section 2 presents the I2AF project. Sec-
tion 3 describes the TAXREF taxonomical reference. Then, section 4 presents
our ongoing work on the construction of a SKOS thesaurus based on TAXREF.
Finally, section 5 concludes and suggests leads for future works.
2 I2AF: Archaeozoological and Archaeobotanical
Inventories of France
During the eighties decade, it was acknowledged that the access to archaeological
data by researchers was increasingly challenged by the growing amount of data
produced, and hampered by its scattering. The risk of permanent loss was even
more worrying. Thus, it appeared obvious that data in archaeological reports
had to be systematically and sustainably collected and inventoried, in a heritage
perspective, while making them available to all potential users. From 2003 on,
several programs supported by multiple French institutes designed, deployed and
maintained such a national inventory database. Today, the I2AF is a collection
of the French National Museum of Natural History (MNHN). It is continuously
and increasingly populated with data on flora and fauna from reports of all exca-
vations performed in French territories, whether the bioarchaeological material
was already studied or not. Since January 2014, the inventory and knowledge
dissemination effort has been actively sustained by a national multi-institute
network of bioarchaeologists9 . When data from excavation reports is imported
into the I2AF, it is aligned on two thesauri: a chronocultural thesaurus provides
temporal terms with regards to cultural periods (the oldest records date back to
the Middle Palaeolithic), and a taxonomic thesaurus of zoological and botanical
names, namely the TAXREF taxonomical reference (see section 3).
As the national reference for nature and biodiversity, the MNHN is responsi-
ble for scientific and technical coordination of the natural heritage inventory. To
this end, it develops and distributes the TAXREF taxonomical reference, and
maintains the National Inventory of Natural Heritage 10 (INPN), an information
system that gathers current (contemporary) occurrence data on fauna and flora
of metropolitan France and overseas departments and collectivities. To date,
INPN gathers data from approximately 800 data sources aligned on TAXREF.
In this context, the I2AF was naturally identified as a potential data contribu-
tor to the INPN. This was however challenging due to the discrepancies between
both databases in terms of temporal periods and inventoried species. Indeed,
while the INPN gathers actual environmental data on wild life, the I2AF also
most of the data available between 1260 and 1320 in western Europe, derived from
the late antiquity compilations.
9
GDR 3644 BioArcheoDat, ”Societies, biodiversity and environment: archaeozoolog-
ical and archaeobotanical data and results on the French territory”.
10
Inventaire National du Patrimoine Naturel: http://inpn.mnhn.fr. Muséum National
d’Histoire Naturelle [Ed]. 2003-2015.
17
provides archaeological data on domestic species, exotic species (not invento-
ried on any French territory, notably imported by menageries as soon as Roman
Antiquity) and possibly extinct species. This issue was solved progressively by
enriching TAXREF with new taxa along with the integration of I2AF data into
the INPN. As examples we can cite extinct species such as the mammoth and
the cave bear, domestic species such as the dog and the ox, and exotic species
such as the Barbary macaque.
3 TAXREF: a Taxonomic Reference in Conservation
Biology
TAXREF[3] is the French national taxonomic reference for fauna, flora and fun-
gus of metropolitan France and overseas departments and collectivities. It is de-
veloped and distributed by the MNHN in the context of the Information System
on Nature and Landscapes11 . TAXREF aims to (i) give an unambiguous unique
scientific name for each taxon inventoried on the territory, that marks a national
and international consensus; (ii) enable interoperability between databases in
(archaeo)zoology and (archaeo)botany, to help the study of biodiversity and sup-
port strategies of natural heritage conservation; and (iii) manage the taxonomic
changes (synonymy, taxonomic hierarchy).
TAXREF can be browsed on the INPN web site, and downloaded in TSV
format (tab-separated values). An on-going work aims to set up a Web service
allowing to query the taxonomy and retrieve results in XML or JSON formats.
TAXREF is organized as a unique, controlled, hierarchical list of scientific names.
Conceptually, it consists of a table wherein one row uniquely describes one sci-
entific name. All taxonomical names are presented in the same way, whatever
their taxonomical rank. Most salient fields are listed below:
– CD NOM : unique identifier of the scientific name.
– CD SUP : identifier of the upper taxon in the classification.
– CD REF : identifier of the reference taxon. This may be either the same as
CD NOM or a different one. In the latter, CD NOM identifies a synonym
of the reference name identified by CD REF.
– Nom: taxon scientific name.
– Nom Vern and Nom Vern Eng: French and English vernacular names.
– Auteur : taxon authority (author name and publication year).
– Rang: taxonomical rank (phylum, class, order, family, gender, species...),
represented by a code of two to four letters.
– HABITAT : type of habitat in which the taxon usually lives marine, fresh
water, terrestrial...) coded as values from 1 to 8.
– A set of biogeographical statuses, one for each geographical region (metropoli-
tan France and overseas departments and collectivities). E.g.: P stands for
present, E for endemic, X for extinct, etc.
11
http://www.naturefrance.fr/sinp/presentation-du-sinp
18
As an example, Listing 1.1 shows a JSON excerpt describing the common
dolphin using its reference scientific name Delphinus delphis, and its synonym
Delphinus tropicalis. Annotation "HABITAT":1 states that it lives in a marine
habitat. Annotation "Rang":"ES" states that the taxon belongs to the species
taxonomical rank (ESpèce in French). Annotation "GUA":"P" states that its bio-
geographical status is P (present) in Guadeloupe, a French overseas department.
A comprehensive description of allowed values for the habitat, taxonomical rank
and biogeographical status is provided in [3].
{ "CD_NOM":60878, "CD_REF":60878, "CD_SUP":191591,
"Nom":"Delphinus delphis",
"Nom_Vern":"Dauphin commun a bec court",
"Nom_Vern_Eng":"Short-beaked common dolphin",
"Auteur":"Linnaeus, 1758",
"HABITAT":1, "Rang":"ES",
"FR":"P", "GUA":"P", "REU":"B", (...)
},
{
"CD_NOM":60881, "CD_REF":60878, "CD_SUP":191591
"Nom":"Delphinus tropicalis",
"Nom_Vern":"Dauphin commun d’Arabie",
"Nom_Vern_Eng":"Arabian common dolphin",
"Auteur":"Van Bree, 1971",
"HABITAT":1, "Rang":"ES",
"FR":"P", "GUA":"P", "REU":"B", (...)
}
Listing 1.1. Example of a JSON representation of TAXREF entries
Currently, more than 450.000 taxa are registered, covering the continental
and marine environments. From the temporal perspective, all current living be-
ings are considered as well as those of the close natural history, that is, from
the Palaeolithic until now. Usage statistics12 attest the large variety of people
using TAXREF, far beyond the research community: botanic conservatories, as-
sociations, public institutions and collectivities, private companies, individuals.
Given its wide adoption in various communities, we chose it to build a SKOS
reference thesaurus that should be published and linked on the Linked Data.
4 A TAXREF-based Thesaurus for the Linked Data
In this section we present our ongoing work on the creation of a SKOS vocabu-
lary faithfully representing the TAXREF taxonomical reference. SKOS13 is the
acronym of Simple Knowledge Organization System; it is a W3C standard de-
signed to represent controlled vocabularies, taxonomies and thesauri. It is used
extensively to bridge the gap between existing knowledge organisation systems
and the Semantic Web and Linked Data.
12
TAXREF usage statistics are not published publicly but can be provided on demand.
13
http://www.w3.org/2009/08/skos-reference/skos.html
19
1 @prefix skc: .
2 @prefix skx: .
3 @prefix tc: .
4 @prefix gn: .
5 @prefix nt: .
6 @prefix taxr: .
7
8 a skc:Concept;
9 skx:altLabel ;
10 skx:prefLabel .
11 skc:broader ;
12 taxr:hasHabitat ;
13 taxr:bioGeoStatusIn [
14 taxr:bioGeoStatus ;
15 gn:locatedIn ];
16 taxr:bioGeoStatusIn [
17 taxr:bioGeoStatus ;
18 gn:locatedIn ];
19 taxr:bioGeoStatusIn [
20 taxr:bioGeoStatus ;
21 gn:locatedIn ].
22
23 a skx:Label;
24 taxr:isPrefLabelOf :
25 skx:literalForm "Delphinus delphis";
26 tc:authority "Linnaeus, 1758";
27 nt:has_rank ;
28 taxr:vernacularName "Dauphin commun a bec court"@fr;
29 taxr:vernacularName "Short-beaked common dolphin"@en.
30
31 a skx:Label;
32 taxr:isAltLabelOf ;
33 skx:literalForm "Delphinus tropicalis".
34 tc:authority "Van Bree, 1971";
35 nt:has_rank ;
36 taxr:vernacularName "Dauphin commun d’Arabie"@fr;
37 taxr:vernacularName "Arabian common dolphin"@en.
38
39 a skc:Concept;
40 skc:prefLabel "Species"@en;
41 skc:exactMatch
42 ;
43 skc:exactMatch
44 .
45
46 a skc:Concept;
47 skc:prefLabel "Marine habitat"@en;
48 skc:relatedMatch
49 ;
50 skc:exactMatch
51 .
Listing 1.2. Example SKOS representation of TAXREF entries
20
Listing 1.2 shows the proposed SKOS representation of the taxon presented
in Listing 1.1, using the Turtle RDF syntax. The keystone of our modelling of
TAXREF in SKOS is as follows. Each taxon is represented by a SKOS con-
cept (line 8); its URI is in namespace http://inpn.mnhn.fr/taxref/taxon/,
which local name is CD NOM, the TAXREF taxon identifier (see section 3). The
skc:broader property is used to model the relationships between a taxon and
the upper taxon in the classification (CD SUP). The reference scientific name of
a taxon and its synonyms are defined as values of properties skx:prefLabel
and skx:altLabel respectively (lines 9 and 10). They are URIs in names-
pace http://inpn.mnhn.fr/espece/cd nom/. These URIs have been defined
by INPN; today they are dereferenced to a Web page providing a HTML descrip-
tion of the taxon. The label literal values themselves are defined with property
skx:literalForm (lines 25 and 33). The habitat and biogeographical status are
represented by a property value which subject is the URI representing the taxon
(lines 12 to 21), while the authorities, taxonomical rank, and vernacular names
are attached to labels (lines 26 to 29 and 34 to 37).
We identified existing vocabularies that can be reused in our context, keeping
in mind that we wish to link the TAXREF thesaurus with existing, well-adopted
data sets, in particular within the Linking Open Data cloud. We first focussed on
classes and properties that represent taxon characteristics (habitat, taxonomical
rank, name authority, etc.). For example, taxonomical ranks are defined in var-
ious ontologies such as the NCBI taxonomic classification14 and the GeoSpecies
ontology15 . Similarly, the type of habitat is commonly defined in several ontolo-
gies such as the ENVO16 environment ontology. To keep full control over the
TAXREF vocabulary, we chose to define terms (SKOS concepts) for the taxo-
nomical ranks (lines 39 to 44), types of habitat (lines 46 to 51) and biogeographi-
cal statuses in a specific TAXREF namespace (http://inpn.mnhn.fr/taxref/),
and align them with concepts of existing vocabularies using the skc:exactMatch
or skc:closeMatch properties. In future works, we intend to align the TAXREF
taxa themselves with taxa in other well-adopted taxonomies.
To perform the translation of TAXREF into a SKOS vocabulary, we use
xR2RML [4], a declarative mapping language designed to address the mapping of
a large and extensible scope of databases (RDB, NoSQL, XML native database,
object oriented, etc.) into RDF, by flexibly adapting to various data models and
query languages. The produced RDF graph can reuse existing domain vocabu-
laries. A prototype implementation of the xR2RML mapping language, Morph-
xR2RML, supports the translation of data from relational databases and from
the MongoDB17 NoSQL document store. To deal with TAXREF, we import its
JSON version into a MongoDB instance. Then, we write the xR2RML mapping
that describes how to map the result of queries to the MongoDB instance into
RDF triples. Finally, the Morph-xR2RML tool coordinates the whole process: it
14
http://www.ontobee.org/browser/index.php?o=NCBITaxon
15
http://datahub.io/dataset/geospecies
16
http://www.ontobee.org/browser/index.php?o=ENVO
17
http://www.mongodb.org/
21
parses the mapping description, performs the queries against the database and
produces the resulting target SKOS vocabulary according to the mapping.
5 Conclusion and Future Works
In this paper, through a few simple example questions, we have highlighted to-
day’s needs of some scientific disciplines, as diverse as Conservation Biology,
Bioarchaeology, and Ancient literature, to gather and make sense of heteroge-
neous data and material. Then, we have described I2AF, a national archaeozo-
ological and archaeobotanical inventory database integrating data from archae-
ological excavation reports. We have presented the TAXREF taxonomical refer-
ence designed to support studies in Conservation Biology. To meet the needs of
Archaeozoology and Archaeobotany, TAXREF was progressively extended with
taxa from I2AF. It is the first taxonomical reference used to integrate data from
Bioarchaeology and Conservation Biology[5].
Then we have presented our ongoing work on the construction of a SKOS
thesaurus based on TAXREF. In the context of the Zoomathia research net-
work, we aim to use this thesaurus to support multi-disciplinary studies on the
history and transmission of zoological knowledge throughout historical periods,
combining the analysis of ancient and mediaeval literature, iconographic and
archaeozoological resources. This will require the enrichment of the TAXREF-
based thesaurus with philological and cultural information and its geographical
extension to other Mediterranean areas (Greece, Italy, etc.). Besides, in order for
a large community to benefit from this work, and to spur its adoption by linked-
data based applications, future works target the automatic creation of links with
other well-adopted open data sets and thesaurus, may they be non-specialized
like DBpedia, or domain-specific like the NCBI taxonomical reference.
References
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22