=Paper=
{{Paper
|id=None
|storemode=property
|title=A Lattice-based Query System for Assessing the Quality of Hydro-ecosystems
|pdfUrl=https://ceur-ws.org/Vol-959/paper18.pdf
|volume=Vol-959
|dblpUrl=https://dblp.org/rec/conf/cla/BraudNGB11
}}
==A Lattice-based Query System for Assessing the Quality of Hydro-ecosystems==
https://ceur-ws.org/Vol-959/paper18.pdf
A lattice-based query system for assessing the
quality of hydro-ecosystems
Agnès Braud1 , Cristina Nica2 , Corinne Grac3 , and Florence Le Ber?3,4
1
LSIIT, CNRS-UdS, Strasbourg, France
2
University Dunărea de Jos, Galati, Romania
3 ›
LHYGES, CNRS-ENGEES-UdS, Strasbourg, France
4
LORIA – INRIA NGE, Nancy, France
Abstract. Concept lattices are useful tools for organising and querying
data. In this paper we present an application of lattices for analysing
and classifying stream sites described by physical, physico-chemical and
biological parameters. Lattices are first used for building a hierarchy of
site profiles which are annotated by hydro-ecologists. This hierarchy can
then be queried to classify and assess new sites. The whole approach
relies on an information system storing data about Alsatian stream sites
and their parameters. A specific interface has been designed to manipu-
late the lattices and an incremental algorithm has been implemented to
perform the query operations.
Keywords: incremental lattice, lattice-based query system, classifica-
tion, information system, biological quality of water-bodies
1 Introduction
Concept -or Galois- lattices are useful tools for organising, mining, and querying
qualitative data in various application domains [14, 10, 24]. However when de-
veloping a domain specific lattice-based tool -to be used by domain analysts, a
main problem is to define the proper approach and tool that fit the requirements
of the experts and other users involved in the project. This paper presents an
application of Galois lattices to the hydro-ecological domain, focussing on how to
assess and monitor the ecological state of streams or water areas. These questions
are currently major problems in Europe, as underlined by the recent European
Water Framework Directive (2000). Assessing the ecological quality of streams
requires to take into account various data such as physico-chemical measures on
sites, but also taxonomic statements or qualitative information on species. Fur-
thermore tools are needed to summarise all these data and to provide a global
and reliable information on the ecological state of streams and water areas. Fol-
lowing this aim we have developed an information system to collect data on
Alsatian streams (North-East of France) [17] and implemented a lattice-based
query system to help hydro-ecologists to compare and assess the ecological state
?
Corresponding author, florence.leber@engees.unistra.fr.
2 A. Braud, C. Nica, C. Grac, F. Le Ber
of streams. Concepts lattices are used: (1) to organise data, i.e. stream or water
area sites with similar parameters are clustered within concepts; (2) to embed
expert knowledge, i.e. concepts are annotated with an expert qualification or
comment; (3) to perform queries, i.e. the annotated concepts are used to help
assessing new sites of streams or water areas.
The paper is organised as follows. First (Section 2) we present the application
domain. Section 3 is devoted to the principles of lattice-based querying. Sections
4 and 5 describe the principles and the implementation of our proposition. Sec-
tion 6 compares our approach to other lattice-based tools and the last section is
a conclusion.
2 Assessing the quality of hydro-ecosystems
The European Water Framework Directive (2000) requires the development of
new tools for monitoring and assessing the quality of water-bodies (i.e. rivers,
lake, gravel pits,...). Such an assessment is built on various information: informa-
tion about the species living in the streams and physical, chemical and biological
data collected on the sites. From these information are built several numerical
indices that are synthetic indicators for assessing the physico-chemical or bio-
logical quality of an hydro-ecosystem.
More precisely, in France, five biological indices have been normalised to
assess the quality of running water. They are based on three faunistic groups: the
invertebrate index [1], the oligochaete (small worms living in sediments) index [3],
the fish index [5], and on two floristic groups: the diatom (microscopic algae)
index [2], and the macrophyte (macroscopic plants living in water) index [4].
Illustrations of the taxa used for these indices are given in Figure 1.
(a) Invertebrate(b) Oligochaete (c) Fish (d) Diatom (e) Macrophyte
Fig. 1: Taxa examples for the five biological indices
According to AFNOR (French organism of normalisation) [1, 3, 5, 2, 4] each of
them gives a different estimation of the water ecosystem quality. The macrophyte
index estimates the trophic level of water, the diatom index gives the global water
quality, the oligochaete index gives an evaluation of the sediment quality, and
the fish index allows to classify the chemical and physical water quality quite
like the invertebrate index. Therefore, their answers on a same site, with a same
undergone pressure, at the same time can be really different but the simultaneous
Lattice-based assessment of hydro-ecosystems 3
application of these five indices is not common and work comparing their answers
are not frequent [20].
Furthermore, indices based on physical (e.g. width and slope of the stream
bed) and physico-chemical (e.g. pH, temperature, nitrates, organic matters, pes-
ticides) data give an other estimation of the ecosystem quality.
Thus, it is necessary to combine the various indices to assess the quality
of a whole water ecosystem. Such an approach, called the ecological ambiance
system, has been proposed in [20, 21] based on the five French biological indices.
Our objective is to develop this concept and to propose a concretely applicable
tool. We therefore rely on a large database collecting data on Alsatian streams
and water areas [18]. The database contains 38 tables and it suits the SANDRE1
French national format for aquatic data. It is implemented within the MySQL
Database Management System.
The data are either issued from samples, synthetic data or general informa-
tion issued from the literature. They are qualitative and quantitative, and suit
the current standards about protocol sampling and indices computation based on
thresholds [1, 3, 5, 2, 4, 22, 23]. Data issued from samples correspond to raw data.
Synthetic data are produced from these samples, in particular taxonomic lists
are used to compute biological indices. Data issued from the literature are used
for the analysis and synthesis of the preceding data (for example they provide
the thresholds for the classification of physical, physico-chemical and biological
results into classes ranging from 1 (very good quality) to 5 (very bad quality)).
We have gathered information on 700 sites in the Alsace Plain, the oldest one
being collected 20 years ago. Details on this database and how it is used are
given in [17].
3 Using lattices for querying databases
Galois lattices are useful tools for organising data and building knowledge bases [7,
14, 24]. Furthermore, they are very interesting for information retrieval since they
allow both direct retrieval and browsing [16]. Primarily, concept lattices have
been used for information retrieval within texts [25, 11]. More recently lattice-
based approaches have been used to build query or information retrieval systems
on various data: e.g. information retrieval within photos or personal data [13],
geographical data [8], or museum collections [26]. The underlying hypothesis is
that a concept extent represents the result of a query which is defined by the
conjunction of its intent. The query can be easily refined or enlarged following
the edges starting from the concept into the lattice hierarchy.
Practically, the query (a A set of attributes) can be performed as follows: the
lattice is looked for a matching concept that is a concept which intent equals
the A set -if it exists- or the most general concept which intent is larger than A.
This concept can also be characterised as the infimum (greatest lower bound) of
all the concepts containing at least one of the attributes of A. This can be done
1
http://sandre.eaufrance.fr
4 A. Braud, C. Nica, C. Grac, F. Le Ber
with various algorithms and the queried lattice does not have to be modified.
Furthermore, a local view can be displayed to the user.
However, when the query represents a new object that is to be incorporated
within the lattice, an incremental algorithm has to be used [15, 10]. This is the
case in our application, since the user has got data about real stream sites which
she/he wants to confront to the sites represented in the existing lattice. Further-
more, she/he can add the new sites to the lattice and thus modify its structure.
We have implemented therefore two incremental algorithms proposed in [10], and
roughly described in section 5.1. These algorithms have been chosen because they
allow to build the Hasse diagram of the lattice, contrarily to most of incremental
algorithms (see [19] for a comparison on these algorithms). Furthermore, we did
not look for performance, since in this first step of our work only small data sets
(40 sites) have been considered.
4 Using lattices for assessing hydro-ecosystems
Lattices have been used in two ways: firstly to cluster stream sites into concepts
that are used by hydro-ecologists to define profiles of these sites; secondly, the
lattices are annotated with the profiles and used into a query-system to help
the assessment of new sites. The proposed tool includes the two stages (see
Section 5.2).
4.1 A lattice-based clustering of Alsatian stream sites
Stream sites are described by different numerical attributes, biological indices on
the one hand, physico-chemical data on the other hand. Those attributes are con-
verted into ordinal scales leading to quality classes. The whole context contains
about 40 stream sites, described with 5 biological indices, 10 physico-chemical
indices and 5 physical indices. In the following, we focus on the biological indices.
Table 1 gives the values of these five indices restricted to seven sites. Each site is
denoted by a code: for example, the BW2 site (Brunnwasser downstream) has a
good quality (class 2) for the IBGN (invertebrate), IBD (diatom) and IPR (fish)
indices, a bad quality (class 4) for the IBMR (macrophyte) index and an average
quality (class 3) for the IOBS (oligochaete) index. The multi-valued context rep-
resented in table 1, denoted C7 in the following, can be converted into a binary
one by using a linear scale [14].
The general idea is to gather similar sites and to allocate them a profile
describing their ecological state, combining the quality estimations of all com-
partments, with respect to the different classes of indices. This work is based on
the approach described in [20]. The process is as follows:
– Step 1: Lattice construction on the data. To facilitate the expert analysis,
the context size is reduced by focussing on a small number of indices or
by identifying sub-lattices with respect to classes of indices. For example,
Lattice-based assessment of hydro-ecosystems 5
Site code IBGN IBMR IOBS IBD IPR
BW2 2 4 3 2 2
IL1 3 3 3 2 3
MO1 1 4 3 3 4
MS2 2 4 5 2 2
RT2 2 5 4 2 2
ST1 1 3 4 3 2
ZN4 1 4 4 3 2
Table 1: Quality classes of the five biological indices for 7 stream sites
Figure 2 presents the lattice obtained from the context C7 (the lattice was
built with ConExp2 ) .
– Step 2: Analysis by the experts of the lattice hierarchy and its implication
rules in order to select relevant concepts (or site profiles). In this step, the
expert may identify profiles which are not present in the lattice and create
virtual sites to be represented in the lattice.
– Step 3: Qualification of the concepts by the experts. For example, the con-
cept ({IBGN 2, IBD 2, IPR 2, IBMR 4, IOBS 3},{BW2}) (down on the lat-
tice, Figure 2) is interpreted as follows: Brunnwasser downstream: low sed-
iment degradation, high eutrophication, good general potential of resilience
and possible resilience for sediments, various habitats.
Once a suitable annotated lattice has been built following this process, it
can be used to determine the profile of a new site based on its values for the
corresponding indices. This is explained in the next section.
4.2 Assessing a stream site from the lattice
According to the ecological ambiance system described in [20], several lattices
have been built for clustering sites with similar average values (or alteration
degrees3 ) on the five biological indices. The underlying hypothesis is that global
state of an hydro-ecosystem can be assessed on the basis of the five biological
indices and synthesised by the alteration degree. Sites with similar alteration
degrees can be compared even if they represent various profiles. The intervals of
similarity have been defined by the hydro-ecologists [18]. For example, the lattice
in Figure 2 was obtained from a set of sites with an alteration degree belonging
to [2.5 ; 3] (see C7 context in table 1). The classes of indices in the lattice vary
between 1 and 5. Each site is represented alone in an atom of the lattice, which is
coherent with the choices done in the project, trying to represent all the variety
of streams or water areas in the Alsace plain.
2
http://conexp.sourceforge.net/
3
The alteration degree is computed as the average value of the five biological in-
dices, e.g. the alteration degree of BW2 equals 13/5. Currently the physico-chemical
parameters are not taken into account.
6 A. Braud, C. Nica, C. Grac, F. Le Ber
Fig. 2: The lattice based on the context of table 1 (linear scale)
Let us now suppose that we have got a partial information on a new stream
site, denoted Q, defined by the following values: IBGN 2 IBMR 4 IOBS 3 IPR 2
(IBD missing). Its alteration degree is 2.75 ∈ [2.5 ; 3], Q can thus be compared
to the stream sites represented in the C7 lattice. This is done by classifying Q
within this lattice, as shown in Figure 3.
Looking at the lattice in Figure 3, one can see that the Q site-query has four
common values with only the BW2 site (Brunnwasser downstream). The expert
qualification of BW2 (except for the IBD index) can thus be used to assess the Q
site. The Q site could thus be assessed as follows: the habitat quality and the water
physico-chemical quality are good, expect for nutriments (nitrate and phosphor
mineral forms) which quality is medium; the sediment quality is medium, the
resilience potential of the general ecosystem is good, while the resilience potential
of sediments is deteriorated.
5 Implementation
5.1 Algorithms
As explained before, the built lattices have to be queried for assessing new sites.
Furthermore, they could have to be updated, by adding a new site, or by modi-
fying an existing site. The new/updated object is described by attributes which
can exist in the context of the lattice or not. In this paper we only consider the
case where the attributes already exist. Two algorithms described by Carpineto
and Romano [10] have been implemented, the first one allows to add a new object
in a lattice, while the second one allows to delete an object from a lattice.
Lattice-based assessment of hydro-ecosystems 7
Fig. 3: The C7 lattice with the Q site-query inserted
The first algorithm allows to add a new object into an existing Galois lattice,
which can be interpreted as classifying a new object. It takes as input a Galois
lattice and the new object with its attributes. The output is the updated Galois
lattice of the new context. The mechanism of the algorithm is as follows. The
set of the concepts is divided into subsets according to their intent cardinality,
and then analysed in ascending order. For each concept of a subset, if the intent
is included in or equal to the set of the new object attributes then the current
concept extent is augmented by the new object; otherwise a new concept is
created, after verifying that such a concept is not in the initial set of concepts
or among the new added ones. The intent of this new concept is determined
by the intersection of the current concept intent and the new object attributes;
its extent is defined by the current concept extent augmented with the new
object. After the addition of a new concept a new link between this concept and
the current concept is created. The links with neighbouring concepts are also
updated.
The second algorithm allows to delete an object from a lattice. It takes as
input a Galois lattice and the object to be removed. The output is the updated
Galois lattice of the new context. The mechanism of the algorithm is as follows.
For each concept, if the object to be deleted is included or equal to the current
concept extent, then it is removed from this extent. If the modified concept has
then the same extent as one of its children, it is deleted. When a concept is
removed the links among the concepts are updated.
8 A. Braud, C. Nica, C. Grac, F. Le Ber
The modification of an existing object in a Galois lattice is performed in
two steps: (1) deleting this object using the second algorithm; (2) adding the
updated object using the first algorithm. The whole process could be improved
with a third algorithm for adding attributes into the lattice context, allowing to
enrich the initial lattice with new information.
5.2 User interface and manipulation
The user interface allows to use a lattice either stored in the database or stored in
a XML file with the structure used in the software Galicia4 . Three main functional
views are provided to the user. The first one allows to qualify concepts, i.e. to
describe the profile of a set of sites. The second one allows to define a query,
i.e. a new site to be assessed according to an existing lattice. The third view
allows to explore the result of the query, i.e. to compare the characteristics of
the new site to those of the already assessed sites. Currently texts appearing on
the interface views are written in French since the target users are French. Other
languages could be used in the future.
The functional view for qualifying concepts is presented on Figure 4. Once a
lattice is chosen, it is possible to select a given concept in a list and to see its
description (intent, extent, and comment). The lists of the parents and children
of that concept are also shown, and by a click on one of them, we see its related
information. These information may help the experts in qualifying the concept.
The comment is then stored in the database.
Fig. 4: Qualifying the concepts of the site lattice
4
http://www.iro.umontreal.ca/~galicia/
Lattice-based assessment of hydro-ecosystems 9
The functionality for classifying a new site based on its values (for one or
several indices) is presented on Figure 5. One has first to select a lattice and to
give a name for the new site, and then to provide a description of this new site by
choosing indices and their values. Once this is done, it is possible to classify the
site, that is to integrate it in the lattice, either temporarily or to save it in the
lattice. The button “Classer” allows this classification. To interpret the result,
the button “Visualiser le résultat” can be used to see the new lattice with the
modifications shown in a specific colour. The button “Explorer le treillis” also
helps in the interpretation by giving access to a third view (Figure 6) where it is
possible to navigate within the concepts and see the description of the parents
and children of the current concept.
Fig. 5: Definition of the Q site-query
More precisely, the third view allows to explore only the modified or new
concepts of the lattice, i.e. the concepts where the site-query is represented.
These concepts can be commented and the modified lattice can be stored in the
database. Eventually, the commented lattices can be exported in various formats
to be further analysed.
6 Discussion
We decided to implement a specific tool for several reasons:
1. the tool has to be interconnected with a database and to offer a user-friendly
interface for hydro-ecologists, allowing them to annotate the concepts;
2. the purpose of the tool is not navigating throughout the whole database;
3. this is a two-stage tool: the first stage organises a specific information within
a lattice; the second stage allows the user to explore and possibly modify
this lattice.
10 A. Braud, C. Nica, C. Grac, F. Le Ber
Fig. 6: Analysing the classification result of the Q query
Regarding the first point, lattice-builder tools like Galicia, ConExp, or the
Toscana suite5 cannot be used, since they do not fit the requirements of hydro-
ecologists. Actually, as said before, we have used Galicia to build the lattices
which are then recorded in the database to be annotated and explored by hydro-
ecologists. Besides, the lattices built through our tool can be exported into a
Galicia format.
Regarding the second point, our approach differs from those used in search
or browsing tools like Camelis [13], Abilis [6], D-SIFT [12] or in the Virtual
Museum of the Pacific [26]. Indeed we did not try to implement a lattice-based
approach to explore the whole database, but only specific information from this
database. This information was chosen by hydro-ecologists as a synthetic view
of the database. Furthermore, the lattice is used as a basis to record expert
knowledge (the annotations) that can be involved in further investigations.
Regarding the last point, our tool can be compared to Ulysses [9] which is
a visual interface allowing to access a lattice structure organising information
from a database. Ulysses allows the user to search the retrieval space both by
browsing or querying, whereas our tool only allows querying. Nevertheless, the
originality of our tool is the user possibility of modifying and annotating the
lattice concepts.
Finally, the underlying aim of our approach is to build an ontology, gather-
ing the knowledge of various experts on hydro-ecosystems. Each expert indeed
focuses on a specific compartment of the hydro-ecosystems (e.g. fishes, macro-
5
http://toscanaj.sourceforge.net/
Lattice-based assessment of hydro-ecosystems 11
phytes, diatoms...) and a generic tool is needed to combine their expertises and
produce a global assessment of the ecological state of a stream site.
7 Conclusion
This paper presents a lattice-based query system for helping the assessment of
hydro-ecosystems. The approach relies on a database storing various information
on stream sites of the Alsace plain. These data are summarised within qualitative
indices, biological indices or physico-chemical and physical indices. Based on
these indices and their own expertise, hydro-ecologists can perform a global
evaluation of the functioning of a stream ecosystem. Furthermore, they want to
define quality profiles of streams or water areas that could be used to assess new
sites. Eventually a tool is needed to help the whole process.
Our work aims at building such a tool. Concept lattices appeared as a good
approach since they allow both to build hierarchical clustering of sites, to nav-
igate through the clusters, and to perform queries for helping the assessment
of a new site. The clustering aspects already proved to be interesting, and the
user interface allowing to comment and query the lattices is currently being ex-
perimented by hydro-ecologists. In the future, several lattices have to be built
including various sets of indices (physico-chemical and physical indices). Fur-
thermore, the whole approach will be tested with stream or water area data
from other regions in France.
Regarding the implementation aspects, the system should be improved in two
ways: allowing the integration of new attributes in an existing lattice and allow-
ing the navigation through bigger lattices. Finally improvements can be done to
provide self-building comments on the site-queries, based on the comments of
the neighbouring concepts.
Acknowledgements
The Indice project (2006-11) was supported by the Agence de l’Eau Rhin-
Meuse. We also acknowledge the scientific and technical help of the Cemagref
Centre in Lyon, the Gabriel Lippmann Public Research Centre in Luxembourg
and the regional delegation of ONEMA (Office National de l’Eau et des Milieux
Aquatiques). Cristina Nica’s stay in France was supported by the Erasmus Eu-
ropean program. We acknowledge the anonymous reviewers who helped us to
improve our paper.
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