M.P. Cuellar, M. Delgado, W. Fajardo, R. Pérez-Pérez*
Escuela Superior de Ingeniería Informática, University of Granada,C. Periodista Daniel Saucedo, s/n, Granada 18072, Spain
Keywords: Information System, Botanist, Biodiversity, Multi-Agent System, Semantic Web, Service Ontology
Abstract: This paper presents the development of BioMen (Biological Management Executed over Network), an
t-managed system. By using service ontologies, the user is able to perform services remotely from a
web browser. In addition, artificial intelligence techniques have been incorporated so that the necessary
information may be obtained for the study of biodiversity. We have built a tool which will be of particular
use to botanists and which can by accessed from anywhere in the world thanks to Internet technology. In
this paper, we shall present the results and how we developed the tool.
A herbarium is defined as a place where collections
of dried, classified plants are stored before being
used as material for the study of botany. The
specimens contained in herbariums are and always
have been the essential base for performing
systematic, floral and biogeographical studies; in
addition, as a collection of perfectly identified and
ordered dried plants these represent a permanent
record of biodiversity.
It is currently calculated that more than 2.5 billion
ecimens are to be found in natural history museum
collections and herbariums throughout the world
Biological diversity research and study requires
satisfactory access to this biological information. As
this complex information is currently distributed
among herbariums all over the world, this makes it
practically inaccessible (BERENDSOHN et al.,
Therefore, by its own nature, the herbarium once
again bec
omes an essential piece for the
development of these objectives and those in charge
of it are responsible for providing the response
called for by the research community.
Consequently, one of the prime current needs is to
uire updated, relevant, scientifically contrasted
and easily accessible information as the basis for
conservation, the handling and the sustainable use of
biodiversity. However, the complexity and
variability of studies carried out in this field has
forced these institutions to adopt new techniques and
protocols which are capable of responding to the
ever growing demands (BERENDSOHN, 2001).
Actualy, there are some syste
m that solves the
herbarium management problem: Hebar (Pando,
1991), Virtual Herbarium Express (The New York
Botanical Garden, 1996), Brahus (University of
Oxford, 2002). The following characteristics are
common to all of the above software packages:
- Free s
- Use
of not particularly powerful database
managers (Access, Dbase).
- Data en
tered using templates.
- Inform
ation filtering.
- Lab
el creation.
- Decent
ralized use of software.
These systems show a set of deficiencies:
- The
have no user supervision neither the
operations they perform.
- Th
ey don’t incorporate powerful DBMS
that allow a great amount of registries
neither concurrency access of the users.
- They
don’t have a friendly interface.
After analyzing a herbarium’s needs, it can be seen
hat the systems developed so far have not been able
to incorporate a large number of requirements. For
this reason, BioMen was developed, and by taking
P. Cuellar M., Delgado M., Fajardo W. and Pérez-Pérez R. (2005).
In Proceedings of the Seventh International Conference on Enterprise Information Systems, pages 91-99
DOI: 10.5220/0002512400910099
advantage of modern communication technologies,
the information is available online.
A herbarium, as we have already mentioned, is a
place where collections of dried, classified plants are
stored, so that these can later be used as material for
botanical study. From this definition, we can
highlight the concepts of storage and study. The
stored material is studied in order to obtain
information which will be used for the conservation,
handling and sustainable use of biodiversity.
The need therefore arises for the information to be
available in a suitable, standardized form so that it
may be studied by researchers.
We shall show some features of BioMen:
- Management of loans (information about
specimens that are bellow minimum
- Management of Taxonomic (new
information, revisions of folds, … ).
- Supervisión of the Users.
- Information consultation (Folds, etc.)
- Multimedia Administration.
- Report Creation.
- Issuing of labels.
Another of the most important points for a
herbarium, besides administration, is to be able to
satisfy the demands of biodiversity studies. These
studies use databases, and this can at times pose
quite a complex task because of the way the data is
displayed. We should therefore point out that the
system must provide a series of services so that
studies may be obtained about:
1. Specific richness (this is the number of
species in a certain region or location)
2. Taxonomic complexity (complexity when it
comes to identifying a specimen)
3. Study of the alpha/beta/gamma diversity
(diversity within the habitats: alpha
diversity; between the habitats: beta
diversity; and for all the habitats being
studied: gamma diversity) (Rosenzweig,
4. Orientation in the collection campaigns.
Among all the possibilities which currently exist to
tackle the problem, the convenience of information
systems was thought of because of the intrinsic
nature of the problem. According to Henry C. Lucas
(1987), we can define information system as a set of
organized procedures, which when performed,
provide information for decision-making and/or
control of the organization. The general theory of
systems on which the information system analysis
and design is based, indicates that it is necessary to
consider the system to comprise smaller subsystems.
The connection of the smaller systems with the
larger systems forms a hierarchy which is
characteristic of the theory of systems. It also shows
us that we must have an overall view of the system,
knowing that all the system components are
interrelated and interdependent, with this being one
of the most important tasks.
We can therefore say that BioMen is an information
system with a client-server architecture (Figure. 1)
designed for herbarium management. Researchers
and those interested in this subject matter can gain
online access to a virtual center which models the
real behavior of the units which comprise the
research center, and they are able to obtain all the
information offered totally dynamically. The virtual
users request (remote and/or hybrid) services which
will enable them to perform all the intended
operations within the system.
Figure 1: Client/Server Architecture of the System
BioMen offers a series of services which enable the
users to have:
- All the centralized information
- Security protocols
- Greater computational power
The services offered might be:
1. Remote services: remote execution of
processes and return of the results to the
2. Hybrid services: interaction between local
and remote processes. e.g. integration of
barcode readers.
The majority of the services are remote, although
there are some multimedia services which will need
hybrid services (remote image processing and
As BioMen needs a representation of the domain
knowledge, our system uses a service ontology
described by means of the DAML+OIL
terminological system, and the services are
described using OWL-S (OWL-S is an OWL-based
web service ontology). This enables us to organize
the services on a graph and to provide a description
of the services including the characteristics of each
service (Figure 2).
The ontology is used by the system to enable the
user to select the desired service, provide the
necessary parameters, and the system is therefore in
charge of executing the selected service. Due to the
characteristics of the system, implementation has
been carried out using agent technology (Figure 3).
In the last 25 years, we have seen the appearance of
several paradigms to design software systems such
as procedural programming, structured
programming, object orientation and component-
based software. Agents (Weiss, 1999; Wooldridge,
2002) are now being championed as the next
generation paradigm to design and build complex
and distributed software systems. An agent-based
architecture provides additional robustness,
scalability, flexibility, and is particularly appropriate
for problems with a dynamic, uncertain, and
distributed nature. In particular, they seem to be the
ideal computational model for developing software
for Internet, and open networked system with no
single controlling organization (Jennings, 2000).
Lastly, architectures allow the incremental
development of modular systems not only because
of the modular nature of the agents, but also because
of the possibility to incorporate legacy code by
wrapping it within an agent interface.
Figure 3: Way system acts given user interaction
In a multi-agent system (MAS), agents interact with
one another to achieve their individual objectives by
exchanging information, cooperating to achieve
common objectives, or negotiating to resolve
conflicts. Alternative flexible patterns of interaction
have been used such as the Contract Net Protocol
(Reid & Smith 1980), where a task is advertised by a
coordinating agent and is assigned to the agent that
makes the best bid. However, details of all possible
interactions between agents cannot be foreseen a
priori and consequently:
1. Agents need to be able to make decisions
about their interactions at run-time, and
2. the organizational relationships between
agents need to be represented explicitly
(e.g. peer member in a team, manager,
coordinator) by means of constructs such as
roles, norms, and social laws.
Figure 2: Hierarchy of services
An agent is anything which can be observed sensing
its environment using sensors and acting on this
environment by means of effectors/actuators. The
programming language which has been used is Java,
enabling us to include a greater number of mobile
devices and operating systems.
Figure 4: Way of action in a remote operation
The way the user interacts with the user is even
simpler. The user interacts with the server using the
HTTP protocol, performing the operations desired
by means of a totally pleasing interface and without
needing to have any additional tool installed. Once
the web server has gathered the user’s request, it
interacts with the multi-agent system in order to
carry out the service requested by the user (Figure 4)
and returns the results of the service. The multi-
agent system is made up of the following agents:
- User
- Request manager or coordinator
- Service execution agents:
i. Remote
ii. Hybrid
The agents which form the multi-agent system use a
blackboard architecture (Nii 1986ª, 1986b)(Hayes-
Roth,1985)(Kowalski & Kim, 1991) for
communication. The blackboard is implemented by
a series of tables. The agents use the blackboard to
exchange the necessary information.
Having looked at the operational logic of the system,
we shall describe the characteristics of the system
and how the requirements of a system for a
herbarium have been solved.
2.1 From the client’s point of view
As we have already mentioned, the client
communicates with the server using the HTTP
protocol in order to execute the desired (remote
and/or hybrid) services. In addition, the HTTP
protocol will show the desired information and enter
the parameters.
There are two ways to access the system:
- without identification: the system is
accessed as an Internet user and therefore
access to the information is severely
- with identification: the system controls the
different authenticated user types using
login/password and allows more or less
sophisticated services to be carried out
according to the level of security allocated
by the managers.
The identified users access the system from the
authorization window (see Fig. 6), beginning a new
session. Having been identified in the system, menu
systems are created which show the services allowed
according to the level of security (see Fig. 7).
Through the menu systems and the I/O interfaces,
the system will receive requests and will provide the
user with the requested information.
Figure 5: Different options according to the user
2.2 From the server’s point of view
From the server, pages are dynamically generated
for each of the users, enabling all of the services
required of the center to be performed. By
maintaining a client/server structure, we provide
solutions to the location problems which have
previously been mentioned. Therefore, the server
will act as a virtual center enabling as many services
as those allowed to each user by the center
All these services are carried out and are
managed by the multi-agent system totally
transparently to the user so that a dynamic system is
obtained with excellent features from the client’s
and the server’s point of view.
Bellow we shall describe a few of the more
important tasks which can be carried out within the
virtual center.
2.2.1 Multimedia management
As we have already mentioned, one of the features
of the service which distinguishes it from others is
the incorporation of a multimedia service which
enables the user to obtain much more detailed
information. There is a multimedia element
associated to each fold, for example, fold images,
video of the habitat, etc. which any authorized user
can consult. This service would require the
execution of local services (reproducer, image
viewer, etc.).
From the point of view of information
management and incorporation, users can pre-
process the information which they wish to
incorporate for a given fold. For example, scanning
the center’s folds and associating an identifier with
the scanned image, recording a video about the
collection of the specimen in the field, etc.
This is one of the solutions offered by the system
to improve the work of the center’s staff. This
multimedia service is available to all system users.
In this way, the multimedia consultation of a
specimen is made possible without the need for a
corresponding loan request. Therefore,
1. The researcher can consult the specimen’s
multimedia information the moment the
center’s staff carry out the operation in the
2. There is a reduction in the number of loans
which the center must make to the
3. In turn, there is a better conservation of the
center’s material.
2.2.2 Advanced consultation and/or consultation
of folds
If we make a consultation using the fold’s identifier,
we will only obtain information about that fold, but
what happens with the information contained in
these? From the researcher’s point of view it is much
more necessary to be able to make a consultation
using the information contained within a fold than
for the existence of a fold. For example, existing
specimens for a UTM and/or above a certain height,
This is, as we have already mentioned, the main
distinction between a library and a herbarium, in that
the information which is useful to the researcher is
the information which there is within the fold and
not the fold in itself. It is therefore as if we were
asking about the information contained in each book
in a library. From this service, any type of
information existing in the system can be searched
for, and the result can be obtained both in HTML
and PDF so that it can be easily exported. The online
access to the information when consultations are
made bestows the power that the herbarium staff and
researchers need.
From the advanced consultation, the center’s staff
can begin to make a loan to the center requesting it.
If the center needs to lend all the folds containing
the specimen Pinaceae Pinus baciano, in a normal,
non-computerized process, the staff would need to
go to the storeroom, look through the folds one by
one in order to select those requested by the
researcher. If the system is used, the fold identifiers
containing this specimen can be obtained and in
turn, the loan service of the system can be activated
merely by entering the loan recipient’s data and
recording this in the system.
2.2.3 Treatment for biodiversity
By means of a series of remote services, the user can
request information about:
1. Taxonomic complexity (Magurran,
Moreno)(Halffter et al)
2. Specific richness (Magurran, Moreno).
3. Orientation in collection campaigns
4. Study of the alpha/beta/gamma diversity
These remote services show the user the desired
information, using the information provided by other
agents who are constantly processing the data
contained in the databases.
We shall now see how this information can be
obtained and we solve the existing problems.
As we have mentioned already, there is a large
amount of interesting information in the center’s
databases. This information enables important
improvements to be made in the quality of botanists’
Nevertheless, the information is not usually
directly accessible since it needs to be processed
from the database. As a first approach to the solution
of this problem, we can recover and process
information in order to obtain new knowledge and
1. Taxonomic complexity (Magurran,
Moreno)(Halffter et al)
2. Specific richness (Magurran, Moreno).
3. Orientation in collection campaigns
4. Study of the alpha/beta/gamma diversity
The main disadvantages of obtaining the
taxonomic complexity are:
1. Existence of a large volume of data
2. Redundancies present in the information
3. The existence of synonyms in the database
Because of these problems, it is not possible to
perform the taxonomic complexity studies directly.
In order to look at this problem in more detail, we
shall consider the following example:
Below we shall show the identification of a
small sample of the specimens contained in the
database. The specimen’s name, in this case,
comprises the family, genus and species:
- Cruciferae Alyssum spinosum
- Cruciferae Hormathophylla spinosa
- Cruciferae Ptilotrichum spinosum
If we want to know the number of different
specimens, when the count is made in the database,
we would obtain 3 specimens. However, according
to Flora Ibérica (1996), the three names refer to the
same specimen (Cruficerae Hormathophylla
spinosa). In addition, the order by which the name
(identification) has evolved (Alyssum Æ
Ptilotrichum Æ Hormathophylla) is established. For
this reason, as we mentioned before, there are
synonyms in the database. This makes it impossible
for us to obtain the information necessary for
biodiversity studies (different number of specimens
in one area e.g. for specific richness studies).
Below, and in view of the importance which the
problem of synonymy has within the research center,
we shall attempt to resolve the problem. In order to
do so, there are two possible courses of action:
1. By creating a synonym database. This
alternative accelerates the processing work.
However, it offers a series of drawbacks:
a. The size of the synonym table is
very large, since there is a great
variety of species.
b. The table would have to be
compiled by an expert. The expert
would have to carry out a
repetitive and tedious task.
2. By studying the evolutions. The name we
give to the change in the denomination of a
specimen is evolution. We shall explore
this in greater depth later. This task can be
carried out without an expert having to
intervene and enables us to obtain the
sequence of the change in the identification.
Another piece of extremely interesting
information relates to orientation in the collection
campaigns. This provides the center with advantages
both in terms of finances and documentation. The
idea is to provide information about the types of
specimens needed for the center to be complete and
well represented. For example, if the number of
specimens in the center is low, it might be that:
1. there really are few specimens.
2. the specimen has been lent to other research
It is therefore necessary to inform the center of
the specimens which need to be collected so that the
center is complete and well-represented. The
information might be:
1. specimens which are not particularly
represented and/or below minimum levels.
2. the best path to follow in order to collect
the specimens.
In order to obtain this knowledge, three
intelligent agents have been used (according to
Wiener’s definition of intelligence) which will act in
turn within the multi-agent system described above.
These agents would constantly be observing the
media (databases), acquiring and processing the
information in order to achieve the necessary
information. The agents deposit the information in
the system, using the blackboard, so that the users
who so desire can access it by means of the
previously described corresponding services.
The first of the agents, called the revision agent, is
responsible for studying all the revisions for a
specimen. This result is taken advantage of by the
agent called the specific richness agent. This agent
obtains the set of synonyms contained in the
database. This information is necessary in order to
count the different specimens which there are in the
database. In turn, the information obtained by the
two previous agents is used by the agent called the
collection campaign orientation agent. This agent
issues a report of those little represented specimens
in the center.
We found the solution to the synonymy problem by
studying the evolutions which a certain specimen
goes through. We shall present the concept using an
example (see Figure 6):
Figure 6: Example of Synonyms
The different blocks determined as A, B, C, D and E
are the different determinations through which a
specimen passes. The arrows indicate the evolution
to another determination.
Specimen 1 was first determined as A but is later
determined as B, C and D. These determinations are
processed as evolutions and therefore, the
determinations, A, B and C are synonyms of D.
These values are inserted into EvolutionAlert table.
This table is managed by the agent. The following
information is entered:
Specimen 1: AÆD, evolution 0.
Specimen 1: BÆD, evolution 0.
Specimen 1: CÆD, evolution 0.
The agent enters the following fields:
- Taxon: indicates the number of the specimen. In
this case 1.
- Antecedent: Previous denominations of the
specimen, for example A, B or C.
- Consequent: indicates the denomination of the
evolution. In this case D.
- Evolution. This field can take 2 values:
· evolution is 0: this indicates that the
specimen will not be determined in another
· evolution is 1: this indicates that if the
specimen is studied, it may change its
determination to the one indicated by the
Consequent field. This enables us to inform
the botanist of the specimens to be revised
so that the center material is totally
updated. This information centers on the
revisions which have already been made to
other specimens.
We shall now put this knowledge on the blackboard,
and in particular, the taxones table, so that it may be
consulted by other agents. The following taxon is
therefore entered in the table:
Specimen 1: D.
Specimen 2 is a synonym as there is another
specimen in which it has gone from a state C to a
state D.
We would therefore enter the following in the
EvolutionAlert table:
Specimen 2: CÆD, evolution 1.
In this case, the evolution value to 1 indicates that if
Specimen 2 were studied, it would probably be
determined as D. We therefore enter it as a possible
Specimen 1 A C D
Specimen 2
Specimen 3
Specimen 4
The following Specimen, Specimen 3, has some
revisions determined as A and B. As in the
EvolutionAlert table, the fact that state B can pass to
state D is stored, due to the sequence of evolutions
which Specimen 1 possesses. We therefore add the
following tuple to the EvolutionAlert table:
Specimen 3: BÆD, evolution 1.
We should remember that in the taxones table, there
is only one tuple, which indicates that of the
specimens studied, there is only one different taxon.
In the next specimen, number 4, we can see that
state D is revised to state E, and therefore state D
becomes a synonym of E and consequently, it is
necessary to revise the data stored in the
EvolutionAlert table, and in turn, to update the
taxons identified. The tables would therefore remain
as follows:
- EvolutionAlert table:
Specimen 1: AÆE, evolution 0.
Specimen 1: BÆE, evolution 0.
Specimen 1: CÆE, evolution 0.
Specimen 1: DÆE, evolution 1.
Specimen 2: CÆE, evolution 1.
Specimen 3: BÆE, evolution 1.
Specimen 4: DÆE, evolution 0.
- taxones table:
Specimen 4: E.
Having taken a general look at the example, we
shall use the data which we have shown previously
in order to see how the agents would act:
- Fold GDAC2745:
o Revision 1: Cruciferae
Ptilotrichum spinosum (L.) Boiss.
o Revision 2: Cruciferae
Hormathophylla spinosa (L.)
- Fold GDA28909:
o Revision 1: Cruciferae Alyssum
spinosum L.
o Revision 2: Cruciferae Alyssum
spinosum L.
o Revision 3: Cruciferae
Ptilotrichum spinosum Boiss.
When the multi-agent system acts, we would obtain
the following final situation:
AlertaEvolución Table:
- Fold GDA28909: Cruciferae Alyssum
spinosum Æ Cruciferae
Hormathophylla spinosa, evolution 0.
- Fold GDA28909: Cruciferae
Ptilotrichum spinosum Æ
Hormathophylla spinosa, evolution 1.
- Fold GDAC2745: Cruficerae
Ptilotrichum spinosum Æ Cruciferae
Hormathophylla spinosa, evolution 0.
Taxa table:
- Fold GDAC2745: Cruciferae
Hormathophylla spinosa
As we can see, we obtain the desired result without
needing to produce any table which contains these
synonyms and which would involve a great deal of
work for the specialist.. So far, all the solutions
provided for the synonymy problem have involved
the construction of the synonym table Species2000.
We therefore believe that we have provided an easy
and innovative way for the researcher to obtain very
important information which does not entail any
expense for the center using it. This information
determines the taxonomic complexity and the
richness of species for any area and consequently
enables biodiversity studies to be made.
If we combine the information obtained by the
existing agents, we can obtain yet more advantages.
We obtain the necessary specimens to be collected
so that we may have a complete center. The systems
issues reports filtering the synonymy problems.
In order to achieve a complete center, both on a
geographical level and in terms of plant groups, we
cross the information obtained by the agents with a
Geographical Information System. This fact offers a
number of advantages which will enable the center
to obtain better results from the information
provided by the multi-agent system.
In this paper, we have described our experiences of
constructing BioMen, an information system
executed on Internet and developed for herbariums.
The constructed system incorporates all the center’s
needs, uses a multi-agent system which makes the
system much more dynamic and easy to maintain. In
addition, this is done entirely independently of the
user who does not need to know how an ontology
operates or how the agents must communicate with
one another.
BioMen is a totally operational system which
uses the newest technologies:
- Access to the system by means of a web
- Java™ Servlet technology (Sun
Microsystems Corporation, 2001; Hall,
- Apache Server (The Apache Software
Foundation, 2001a)
- Apache Jakarta Proyect Tomcat (The
Apache Software Foundation, 2001b)
- Java Agents.
- JDBC for communication with the
The majority of software tools are free and this
makes the system much more attractive and enables
it to be more standardized.
This work was founded through Project TIC2003-
08807-C02-01 from the Spanish Ministry of Science
and Technology (MCYT).
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