AN INFORMATION SYSTEM TO PERFORM SERVICES

REMOTELY FROM A WEB BROWSER

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

Interne

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.

1 INTRODUCTION

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

(DUCKWORTH, GENOWAYS & ROSE, 1993).

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.,

1999).

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

acq

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

oftware.

- 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).

AN INFORMATION SYSTEM TO PERFORM SERVICES REMOTELY FROM A WEB BROWSER.

In Proceedings of the Seventh International Conference on Enterprise Information Systems, pages 91-99

DOI: 10.5220/0002512400910099

 SciTePress

advantage of modern communication technologies,

the information is available online.

2 SYSTEM ANALYSIS AND

DESIGN

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

levels).

- 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,

1995).

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

user.

ICEIS 2005 - ARTIFICIAL INTELLIGENCE AND DECISION SUPPORT SYSTEMS

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

inclusion).

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.

AN INFORMATION SYSTEM TO PERFORM SERVICES REMOTELY FROM A WEB BROWSER

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

limited.

- with identification: the system controls the

different authenticated user types using

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.

ICEIS 2005 - ARTIFICIAL INTELLIGENCE AND DECISION SUPPORT SYSTEMS

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

managers.

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

system.

2. There is a reduction in the number of loans

which the center must make to the

researchers.

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,

etc.

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

AN INFORMATION SYSTEM TO PERFORM SERVICES REMOTELY FROM A WEB BROWSER

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.

3 BIODIVERSITY

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’

work.

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

determine:

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:

ICEIS 2005 - ARTIFICIAL INTELLIGENCE AND DECISION SUPPORT SYSTEMS

1. there really are few specimens.

2. the specimen has been lent to other research

centers.

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

way.

· 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

evolution.

Specimen 1 A C D

Specimen 2

Specimen 3

Specimen 4

A B

E D

AN INFORMATION SYSTEM TO PERFORM SERVICES REMOTELY FROM A WEB BROWSER

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.)

Küpfer

- 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

Cruciferae

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.

4 CONCLUSIONS

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:

ICEIS 2005 - ARTIFICIAL INTELLIGENCE AND DECISION SUPPORT SYSTEMS

- Access to the system by means of a web

browser.

- Java™ Servlet technology (Sun

Microsystems Corporation, 2001; Hall,

2001a,b)

- Apache Server (The Apache Software

Foundation, 2001a)

- Apache Jakarta Proyect Tomcat (The

Apache Software Foundation, 2001b)

- Java Agents.

- JDBC for communication with the

databases.

The majority of software tools are free and this

makes the system much more attractive and enables

it to be more standardized.

ACKNOWLEDGEMENTS

This work was founded through Project TIC2003-

08807-C02-01 from the Spanish Ministry of Science

and Technology (MCYT).

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AN INFORMATION SYSTEM TO PERFORM SERVICES REMOTELY FROM A WEB BROWSER