BIODIVERSITY INFORMATION SYSTEMS

USING GEOREFERENCING AND PHYSICAL IDENTIFICATION

Tiago Lira

Faculdade de Engenharia da Universidade do Porto, Porto, Portugal

Cristina Ribeiro, Jo

ao Correia Lopes

DEI - Faculdade de Engenharia da Universidade do Porto / INESC Porto, Porto, Portugal

Keywords:

Biodiversity informatics, Web applications, Georeferencing, Physical object identiﬁcation, Data standards.

Abstract:

Biodiversity information can be found in diverse information systems, ranging from large technical repos-

itories for research purposes to dedicated databases supporting the web presence of natural sites. To deal

with individual botanical objects, it is important to adopt the established scientiﬁc taxonomy. Providing a

satisfying experience with current interface devices is also mandatory. Two problems have been addressed

in this work: the unique identiﬁcation of the objects and the representation of their physical location. The

former has been tackled with QR code, a two-dimensional barcode standard, and the latter with the use of a

PostgreSQL/PostGIS spatial database.

The paper describes the development and test of a Web information system integrating physical identiﬁcation

and geo-referencing. The application in biodiversity information management shows that low-cost, state-of-

the-art technologies can provide appropriate solutions even for small- and medium-sized natural sites, incor-

porating existing scientiﬁc information on species and contributing for a growing record of their occurrences.

The system was tested on a university garden and can be used by site maintainers, visitors and researchers. The

dataset collected in the site can be exported according to the Darwin Core biodiversity standard for research

purposes.

1 INTRODUCTION

The year of 2010 was declared International Year of

Biodiversity by the United Nations, both as a celebra-

tion and as an invitation to safeguard the variety of

life on earth

Biodiversity informatics is gathering researchers

from biology and from several information and com-

puter science domains to handle the collection, anal-

ysis, search and application of information regarding

biological diversity. The massive amounts of data in

this ﬁeld are being organized by international organi-

zations (ITIS, 2010; Wikispecies, 2010; IPNI, 2010;

Smithsonian Institution, 2010). In the near future, it is

reasonable to expect that application developers will

have access to high-quality information on species

that they can explore at a convenient level of detail.

There are ongoing international initiatives promo-

Introduction to the International Year of Biodiversity,

http://www.cbd.int/2010/about/.

ting the organization of large digital botanical re-

sources. The Global Biodiversity Information Facil-

ity (GBIF) is an example of an organization aimed at

providing an informatics infrastructure to support bio-

diversity applications (GBIF, 2006). The concept of

an individual, as an instance of a species, is present

in the Darwin Core biodiversity standard proposed by

GBIF. Gathering information on individuals is very

important when dealing with applications where the

representation of a natural site requires the identiﬁca-

tion of specimens.

Many existing biodiversity repositories tend to be

narrow in scope and have very specialized informa-

tion on some categories. They may cover just one

genus, the ﬂora from a region, or a set of endangered

species. They are therefore not suitable for services

aimed at lay users, where it is necessary to have non-

specialized descriptions of a broad range of species.

In this work we focus on the management of

botanical information in natural sites. The people in

255

Lira T., Ribeiro C. and Correia Lopes J..

BIODIVERSITY INFORMATION SYSTEMS USING GEOREFERENCING AND PHYSICAL IDENTIFICATION.

DOI: 10.5220/0003300102550262

In Proceedings of the 7th International Conference on Web Information Systems and Technologies (WEBIST-2011), pages 255-262

ISBN: 978-989-8425-51-5

 2011 SCITEPRESS (Science and Technology Publications, Lda.)

charge of a site want to represent the data about their

specimens, to manage their evolution and to present

them to the public in appropriate ways. We have as-

sumed also as requirements the use of rigorous botan-

ical data and the association of geo-referencing infor-

mation to each object. Currently, it is hard for small

and medium-sized natural sites to get botanical in-

formation covering their specimens and aimed at lay

users, and it is also not common for a site to contribute

the data it gathers to some larger repository. As a con-

sequence, these sites release little information about

their collections to visitors, as promotional resources

are expensive to maintain, and they rarely share their

data with other organizations.

The proposed system provides the tools for pro-

motion and scientiﬁc contribution, therefore increas-

ing the public interest in them. The concept of in-

formation systems for a natural site can be redeﬁned

with the application of current technologies. We pro-

pose the integration of geo-referencing and physical

object identiﬁcation features to improve the useful-

ness of these systems. This creates a new approach,

both in the way they manage their specimen collec-

tion and in the way they interact with site maintainers,

visitors and the scientiﬁc community. Our system is

supported by a spatial information platform and ge-

ographical data visualization applications. Its contri-

bution for Biodiversity Informatics research is on two

main aspects: the integration of tools that contribute

to a more accurate representation of specimens and

the ability to share standardized information. The sys-

tem is demonstrated using the capabilities of modern

mobile devices to bring relevant content to the site

users.

This work explores the capabilities of information

systems for efﬁcient management of objects on large

spaces, creating a collection of geo-referenced and

physically identiﬁed elements, making them search-

able and making their information immediately ac-

cessible. While this approach can be useful in

many ﬁelds, the signiﬁcant dispersion of specimens

in botanical collections makes them a challenging ap-

plication domain.

1.1 Contributions

The main contributions of this work are:

• the evaluation of physical identiﬁcation methods

in botanical collections;

• the integration of spatial information in the

database supporting a natural site;

• the development of an information system for

small and medium-sized natural sites that offers

innovative features for object identiﬁcation and

geo-referencing;

• the use of a data model for natural sites account-

ing for both the botanical information and the site-

speciﬁc management information;

• the use of biodiversity information standards for

exporting data from a natural site;

• the instantiation of the system in a real-world

botanical site in order to evaluate its functional-

ity.

2 EXISTING SYSTEMS

Biodiversity information platforms are being created

to support the storage and access to large biodiversity

datasets. The systems that manage information on bi-

ological specimens range from large scientiﬁc repos-

itories, used in research, to the databases that support

the management of natural sites, to informal collec-

tions of information contributed by amateurs.

Large scientiﬁc repositories are supported by

powerful databases and are now focusing on the shar-

ing of information between organizations. A prob-

lematic barrier is found in taxonomic differences and

data model inconsistencies (Chavan et al., 2005); for

this reason many repositories are contributing to the

deﬁnition of standards to share and transfer their in-

formation. The use of spatial data is also becom-

ing common, as the information on the location and

distribution of specimens is valuable for research in

this ﬁeld. As for the services presented to users,

the research-oriented systems focus more on search

functions to retrieve technical information from their

databases; there usually isn’t much concern about the

details of user interaction (Neale et al., 2007).

The GBIF

network is a good example of a large-

scale repository on biodiversity. This international

initiative displays information from hundreds of or-

ganizations around the world. It includes data from

both natural history collections and from observa-

tional records. Combining information from diverse

sources, it uses the Darwin Core standard as a pre-

ferred format for data exchange.

Repositories are now giving attention to spatial in-

formation, registering the geographic location of the

specimens and allowing its visualization in graphic

format. As an example, the Ocean Biogeographic

Information System (OBIS, 2010) includes in their

search results a distribution map for the specimens

(see Figure 1).

GBIF: Infrastructure, http://www.gbif.org/informatics/

infrastructure/.

WEBIST 2011 - 7th International Conference on Web Information Systems and Technologies

256

Figure 1: Distribution map generated by the OBIS system.

The systems that support the information for nat-

ural sites, on the other hand, are usually less com-

plex in their services, and tend to give simple descrip-

tions of the site with the intention of inviting visitors.

Still, some of these systems present some spatial in-

formation, in the form of dynamic maps of the space,

giving visitors a preview of the site. Graphical pre-

sentation of the information is more important here,

and no great detail on the collection’s specimens is

required. An example with a remarkable graphical

interface for a virtual visit is the Monticello Explorer

website (Thomas Jefferson Foundation, 2010) shown

in Figure 2; the user can navigate the interactive map

and see an interesting description of the highlights in

each area.

Figure 2: Monticello Explorer’s interactive map.

3 AN INFORMATION SYSTEM

FOR NATURAL SITES

The developed information system offers innovative

features for managing and publishing information

about a botanical site. The main characteristic of this

system is the implementation of a data model capable

of combining the internal information of the site, the

visitor-oriented information, and the scientiﬁc infor-

mation in a coherent manner. The approach is based

on current technologies, namely geo-referencing and

physical identiﬁcation.

The Darwin Core biodiversity standard (Dar-

win Core Task Group, 2009) is used for exporting

datasets, contributing them to the scientiﬁc commu-

nity and making it easy to share information with

other organizations.

The proposed information system is designed for

small and medium-sized natural sites, allowing them

to manage their information in an effective way. It in-

cludes a spatial database and a web application which

presents information on botanical specimens.

3.1 Specimen and Species Information

A major goal in this work is to supply useful descrip-

tive information to visitors and site workers. They

can view information pages, used to display the data

related to the specimens. These pages can be accessed

from the various services of the system. An individual

page focuses on a speciﬁc specimen or set of speci-

mens, and includes its description, photographs, gen-

eral information about the corresponding species and

its taxonomic classiﬁcation. Figure 3 gives an exam-

ple of one of these pages, where species information

uses the scientiﬁc descriptors in Latin.

Figure 3: Information page for an oak tree.

3.2 Spatial Services

This work explored the geo-referencing of the site

specimens, allowing the user to ﬁnd the physical posi-

tion of any specimen. This information can be easily

inserted and corrected by the site staff, and some fea-

tures were developed based on this information.

The main spatial feature is the virtual tour map,

where the user can view a dynamic map of the site,

BIODIVERSITY INFORMATION SYSTEMS USING GEOREFERENCING AND PHYSICAL IDENTIFICATION

257

with specimens represented by markers and specimen

sets by polygons. Clicking in these markers the user

will have basic information in popup windows or go

to the full information page of the specimen. This

feature also includes the suggestion of tour paths (see

Figure 4), formed by sequences of interesting points

chosen by the site staff.

Figure 4: A suggested tour path.

A more demanding use of the spatial database ca-

pabilities is the geographic search feature. Here the

user selects a polygon in the map, which results in

a spatial query that returns the elements contained or

intersected by that polygon (see Figure 5).

Figure 5: Geographic search.

These features are the more obvious examples of

the potential of spatial data for natural sites. Other

services might be developed, depending on the scope

and needs of an individual site.

3.3 Physical Identiﬁcation and Mobile

Services

Physical identiﬁcation allows a user to see a speci-

men and access its information (and even update it)

on site. The QR code (Denso Wave, 2010), a two-

dimensional barcode standard, was chosen for this

purpose because it can be read by most mobile de-

vices with standard software. Any user with a com-

mon cell phone equipped with a camera and basic In-

ternet access can use this service.

For visitors, the local tour assistant feature is sup-

ported by this technology. The user identiﬁes the

specimen with his mobile phone (see Figure 6), and

the device connects to the corresponding information

page in the Web application. This supplies casual vis-

itors and researchers with relevant information during

their visit to the site, instead of having to search for

it later. For the site staff, there are other uses for this

technology. They can edit the specimen’s information

when they are working, register operations they did

or upload photos of the specimen, all from their mo-

bile phones and using the identiﬁcation codes. This

ability to easily identify a specimen and access its re-

lated contents creates a richer interaction with the sys-

tem, making it more useful. The code tags are gener-

ated automatically, using an external API, ready to be

printed (Google, 2010b).

Figure 6: Identiﬁcation using a QR code.

To offer these features, the Web application must

be suited for mobile devices. There are several op-

tions to solve this problem (Ekris and Vugt, 2010;

Mehta, 2008; Harris, 2008). In this case, as all the

services are intended to work in the mobile version

as well, a separate stylesheet was created to format

the pages according to the speciﬁcation of mobile de-

vice screens. The system detects the kind of device

being used, either by the browser properties or the

screen size and selects the correct stylesheet. This

directs the user to the services in his mobile browser

(see Figure 7). The support of the different features

depends on the speciﬁcations of each device; while

the basic features like information pages can be used

even in low-end mobile phones, the more resource-

consuming features like the dynamic map will re-

WEBIST 2011 - 7th International Conference on Web Information Systems and Technologies

258

quire more powerful devices to work correctly (cur-

rent smartphones should be able to use all the features

in the mobile version).

Figure 7: Mobile version of the Web application.

Mobile technologies are constantly evolving and

its use will predictably continue to grow in the near

future (Kendrick, 2010). The combination of mo-

bile technologies with QR codes makes information

in large open spaces easily available to visitors.

3.4 Scientiﬁc Information

While the above features are sufﬁcient for casual vis-

itors, researchers have a need for more formal and

organized information. The support for the Darwin

Core biodiversity standard allows the site to export its

datasets in a format that can be read by other orga-

nizations, thus making it possible to contribute to the

ongoing efforts on botanical repositories. Researchers

can download the site’s data in the speciﬁed format,

either for research or for integration in larger reposi-

tories.

When the user requests the data for a selected

specimen, the system provides an XML ﬁle with the

relevant terms of the Darwin Core description

. This

includes specimen identiﬁcation, details on its geo-

graphic location, the scientiﬁc name of the species

and its taxonomic classiﬁcation (see Figure 8).

3.5 Search and Additional Features

To fulﬁll the needs of the system, some additional

features were implemented, including various search

options. Apart from the above mentioned geo-

graphic search, the user can search by names (speci-

men description, common and scientiﬁc names of the

Darwin Core XML Guide, http://rs.tdwg.org/dwc/

terms/guides/xml/index.htm.

Figure 8: Excerpt from the Darwin Core description of a

specimen.

species), and attributes (the user selects one or more

characteristics from the available options, and the sys-

tem retrieves the specimens that verify them). Basic

user-related features were also implemented, includ-

ing authentication, access control, and user manage-

ment, to achieve a complete application that can be

put to real use.

4 ARCHITECTURE

The system is implemented as a web application de-

veloped in the PHP language and using the Zend

Framework. Zend is a ﬂexible framework that fea-

tures the Model-View-Controller design pattern and

an extensive library of classes. Its use leads to the

creation of a solution with good portability, meaning

that it can be easily adapted to any natural site, requir-

ing only a suitable web server and little conﬁguration.

From the available choices, the Zend Framework was

selected for its ﬂexibility of use and good documenta-

tion (Lapsha, 2008).

The data model for natural sites comes from the

work of Jo

ao Silva (Silva, 2009), and was reﬁned to

better suit the current needs. As shown on Figure 9,

it can be divided into 4 main parts: the Park pack-

age includes classes related to the site and its users,

the Identiﬁcation package focuses in the data about

specimens, the Taxonomy package deals with classi-

ﬁcation and species information, and the Geography

package holds the spatial data.

The spatial database is based on this model. The

PostgreSQL/PostGIS technology is used for support-

ing the geographical information. PostgreSQL is an

open-source database system renowned for its relia-

bility, stability and scalability. PostGIS (Obe and Hsu,

2010; PostGIS, 2010), its spatial extension, is a solu-

tion for storing and managing geographic data certi-

ﬁed by the Open Geospatial Consortium (OGC).

Geographical information visualization, using a

JavaScript-based dynamic map, uses the Google

Maps service (Google, 2010a). Its combination with

BIODIVERSITY INFORMATION SYSTEMS USING GEOREFERENCING AND PHYSICAL IDENTIFICATION

259

Figure 9: Package diagram of the data model structure.

the spatial database provides geo-referencing, mak-

ing it possible to insert and visualize the specimen’s

physical location in an intuitive way, and allowing

for other operations like the spatial search feature.

The required spatial calculations are accomplished by

PostGIS functions (BostonGIS, 2010), making use of

the capabilities of the database; the results are re-

turned as text coordinates to be used for visualization

in the dynamic map.

As an identiﬁcation method, the system uses the

previously mentioned QR code. There are various

alternatives for specimen identiﬁcation. RFID tags

(Smith and Konsynski, 2003; Want et al., 1999) can

be an effective solution, but require costly equipment

and would be usable only by the park maintainers.

The barcode system, on the other hand, is inexpensive

and readable on most mobile phones

, extending the

service to the visitors of the natural site. The QR code

standard was compared to other barcode types and

chosen for its efﬁciency and for being supported in

the majority of mobile devices (Kato and Tan, 2005;

Susono and Shimomura, 2006).

QR-Code Readers, http://www.mobile-barcodes.com/

qr-code-software/.

5 DATA COLLECTION

A practical aspect which has required some con-

cern was how to populate the database with accurate

species information. Users should not be forced to

create information such as species taxonomies, which

are well established in the scientiﬁc community, or

even generic descriptors such as specimen size or

shape, which are typically already described else-

where. We have collected general data on taxonomy

and species descriptions that can be applied to any

natural site. A case study was used to test the system

on a real garden.

5.1 Species and Taxonomic Information

After contacting various organizations, the Illinois

Plant Information Network (Iverson et al., 1999) al-

lowed the use of their data, which included common

and scientiﬁc names and various descriptive botani-

cal information on plant species. The data was dis-

tributed on thousands of text ﬁles with organized for-

matting but somewhat variable content. A small Java

application was developed to extract the information

and prepare it for insertion in the database. Data was

obtained for more than 3000 natural species.

The taxonomic information for the Plantae king-

dom was imported from a previous work (Silva,

2009). With this data, the system shows the taxo-

nomic classiﬁcation for each species in the site.

All this information is associated with the plant

species, and can be used for any natural site, indepen-

dently from its specimens. While not all the species

have a description, many are covered by the collected

data, and others can be completed manually.

5.2 Case Study

The system was applied to one of the university gar-

dens, which is in the process of expanding its speci-

men collection. The garden has several species and is

large enough to take advantage of the developed ser-

vices.

This deployment of the system allowed us to test

its features in a real situation. For that purpose data

was collected on various specimens of the garden, in-

cluding descriptions and photographs, which were as-

sociated to the corresponding species. Some of the

species were not in the system yet and were inserted

with data from various sources (Fernandes and Car-

valho, 2003). The geographical coordinates were col-

lected for each specimen, using a GPS device. As the

device presented signiﬁcant precision errors, part of

WEBIST 2011 - 7th International Conference on Web Information Systems and Technologies

260

the data was corrected using the application’s dy-

namic map. The collected spatial data was tested in

the virtual tour service, visiting the specimens for the

frontal area of the garden (as shown on Figure 10).

Identiﬁcation codes were also printed for some of the

specimens allowing us to test the local tour assistant

and related mobile Web contents.

Figure 10: Virtual tour of FEUP’s gardens.

6 EVALUATION

The goal of this work was not only the creation of a

solution, but also an evaluation of the applicability of

the selected technologies in this domain.

Physical identiﬁcation proved to be an effective

service when associated with mobile device contents.

The QR codes in particular can be easily generated

and printed, and the tests suggest that most common

mobile phones can use them. With the evolution of

mobile Internet and devices, this service is expected

to become even more practical in the future.

The geo-referencing of specimens is a useful fea-

ture both for visitors and for site workers, and spatial

data can also be important for research purposes. The

value of this data increases for larger spaces, where

the difﬁculty of locating a specimen is much more sig-

niﬁcant.

Exporting data in Darwin Core format is relevant

for specialized users and can be valuable for research

purposes. The usefulness of the data will depend on

its content, the amount of information collected, and

the interest of the species in the collection. Neverthe-

less, the system allows for easy sharing of the data in

a standardized format supported by large global orga-

nizations.

The success of any system is, of course, dependent

on the reaction of its users; therefore, a more detailed

evaluation with different user groups would be useful

to better assess its practical value. A group of users in

the ﬁelds of Biology and Botany would be specially

relevant, to test the developed features and identify

possible points for improvement. The virtual tour and

the local tour assistant features should be tested with

visitors.

7 CONCLUSIONS

Biodiversity information systems are evolving in the

direction of spatial information. The Darwin Core

standard is also becoming more common in the shar-

ing of scientiﬁc data. Information systems for natural

sites are starting to use new technologies and there are

still vast opportunities for improvement.

The work explores two technologies for natural

sites. Physical identiﬁcation of specimens supplies

visitors with relevant content in an easy way and

improves the efﬁciency of information management

tasks for the staff. Geo-referencing allows the collec-

tion and storage of precise information on the local-

ization of the specimens, which can then be visualized

by the users. The support of the Darwin Core standard

enables the site to share datasets with the scientiﬁc

community.

This work has resulted in a Web information

system focused on improving specimen information

management and offering distinct services for visi-

tors, with the support of current technologies. The

system is ﬂexible and can be applied to botanical gar-

dens and other natural sites. Hopefully the result will

have an impact on biodiversity information systems.

These technologies can improve the services of nat-

ural sites and their use in this context can be further

explored.

The broad scope of the study also creates opportu-

nities for continuation, expanding the work for differ-

ent uses and related areas. One possibility is to con-

nect the application to a biodiversity repository (some

of which already provide APIs for data retrieval),

to get relevant information on species or taxonomy

whenever necessary. The application might also up-

load its data periodically to the repository, making it

available for research. Another possibility is to ex-

pand the system to the animal kingdom, for example

in a small zoo, with some modiﬁcations on the iden-

tiﬁcation and geo-referencing methods. The spatial

capabilities of the database can be further explored as

well; global maps may show the origin of the collec-

tion’s species, or the retrieval place of the specimens.

Additionally, the increasingly common GPS capabil-

ities of mobile phones can be used in a location-

oriented tour assistant that will point interesting el-

ements near the user’s position, or help the staff to

BIODIVERSITY INFORMATION SYSTEMS USING GEOREFERENCING AND PHYSICAL IDENTIFICATION

261

geo-reference a specimen using the coordinates of the

device.

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