Database Management System for Ecological Field Surveys

Overview topo

ECOLOG is a specimen-based, cross-platform relational database management system, aimed at the storage, retrieval and preliminary analysis of data on sites, species, and specimens gathered in ecological field surveys and biodiversity inventories.

The main goal of ECOLOG is to make the data gathered in ecological field surveys readily accessible, providing lists of species collected in the study area and informations on habitat preferences, abundance or rarity of a given species, biometrics, morphology, dominance, and spatial location of each specimen collected in the field. The system also aims at contributing to the adoption of a minimum standard for gathering, storing, and exchanging of data from ecological surveys and biodiversity inventories, avoiding duplication of efforts in different research and environmental management projects and institutions.

Features topo

  • Simple menu-driven, multiple document interface, using familiar terminology and options which reflect the researcher workflow

  • Direct utilization of electronic spreadsheets in several formats (.xls, .xlsx, .ods, .csv, and .tsv), which the user can create and edit is her/his favorite program (Office Excel, LibreOffice/OpenOffice Calc, Gnumeric, etc.)

  • Interactive filter definition for the selection of the records; each data field or combination of fields can be used as criteria for record retrieval, including text-based ones

  • Simple pre-defined reports, including checklists, and collecting labels, with output in HTML format, allowing the automatic production of Web pages from database contents

  • Generation of database statistics, including counts of species per family/genus, with percents, counts of individuals per species, also with percents, rarefraction curves, and several diversity indices for one or more filtered sites; these statistics can then be used to automatically produce simple bar and line graphs

  • Storage of user-defined morphological and biometrical descriptors and environmental variables

  • Flexible import/export of data in several different formats for exchange with other software

  • Support to storage and statistical analysis of short gene sequences for biodiversity inventories using DNA barcode

  • Support to the description of the contents, context, structure, and accessibility of data sets (metadata), based on the Ecological Metadata Language (EML) standard

  • Integration with Google Earth, for generating distribution maps of specimens from spatial coordinate data stored in the database, exported to KML format

  • Methods of multivariate analysis of ecological data (similarity indices,  cluster analysis, ordination)

  • Localized versions in English, French and Spanish, geared towards other countries in Latin America, Caribbean, and Africa

Applications topo

  • Faunistic or floristic surveys
  • Conservation inventories
  • Environmental impact assessments
  • Phytosociological studies

Screenshots topo

Click on the images to enlarge.

Data Table (Windows XP)

Data Table (Ubuntu Linux)

Project Form (Windows XP)

Project Form (Ubuntu Linux)

Report (Windows XP)

Report (Ubuntu Linux)

Database Statistics (Windows XP)

Database Statistics (Ubuntu Linux)

Plots (Windows XP)

Plots (Ubuntu Linux)

Data Import Wizard (Windows XP)

Data Import Wizard (Ubuntu Linux)

History topo

Versions 1.0-3.0

The first version of ECOLOG was developed in 1990 with financial support of the Brazilian National Research Council (CNPq proc. #402372/89-1//FV), Programa Mata Atlântica do Jardim Botânico do Rio de Janeiro/IBAMA (CNPq proc. #407809/84.4), Instituto Brasileiro de Pesquisas e Estudos Ambientais (Pró-Natura), John D. & Catherine T. MacArthur Foundation (proc. #8900-527 Environment) and Shell do Brasil for the "Atlantic Rainforest Database Project".

This version was used until 1991, when it was replaced by another version, incorporating several improvements at the physical project of the database and user interface (Cavalcanti, 1991; Cavalcanti, 1993).

The first versions of ECOLOG were written in Clipper Summer '87, from Nantucket Corporation, with some built-in low-level functions in C and Assembler, running under MS-DOS.

Version 4.0

By the end of the decade of 90, the experimental prototype of a version of the ECOLOG system for the MS-Windows 95/98 operating system was developed using the rapid application development environment Borland Delphi version 4.0, but this prototype was never completed.

From 2003, the need for a specialized software tool for data management on sites, species, and specimens gathered by the biodiversity inventory of Tupé Lake, Central Amazonia, conducted by National Institute of Amazon Research (Biotupé Project), prompted the development of an updated version of ECOLOG (Cavalcanti, 2005).

In its new version, released in 2009, ECOLOG has been entirely re-designed as a cross-platform application for Linux, MS-Windows, and Mac OSX, using the Python programming language, the wxPython GUI library and the SQLite database engine.

Version 5.0

By the beginning of 2014, after a long period in which the development of the software stayed inactive, a detailed analysis of ECOLOG was performed, which made clear that many significative changes could (and should) be done to the system, so that it could have its functionalities explored and expanded.

In this version, a number of changes and improvements were introduced in relation to all previous versions:

  1. The data structure based on a relational database library stored in its own files with a ".db" extension, was entirely replaced by electronic spreadsheets, in the .xls, .xlsx, .ods, .csv or .tsv formats, whch the user can create and edit in her/his favourite program (Office Excel, LibreOffice Calc, Gnumeric, etc.) and read directly into ECOLOG. This eliminates the need to "import" data to ECOLOG and makes data entry and editing much faster and uers-friendly to the user already familiarized to electronic spreadsheets.

  2. The user interface of ECOLOG was re-implemented uing the Qt library, replacing the wxWidgets library used in the previous version. This allows to offering a more uniform interface in all supported operating systems and making easier to install and use the program under GNU/Linux, as all distributions based on the KDE graphic environment (Kubuntu, OpenSUSE, Fedora KDE, Mint KDE) are automatically supported (as the KDE environment is itself based on the Qt library). Moreover, the new interface uses the multiple document model (thus allowing the simultaneous visualization of collection data and environmental variábles in separate windows) and has simpler menus, with familiar terminology and options which reflects in a more "natural" way the researcher workflow.

  3. Integration of ECOLOG with the numerical and scientific libraries available for the Python language (NumPy, SciPy, Matplotlib), thus making possible not only to store and manage the data from ecological field surveys, but also analysing them directly from ECOLOG itself. This strategy has the major advantage of making possible to ECOLOG execute many kinds of ecological data analysis, while avoiding "reinventing the wheel" and the unnecessary (and inefficient) re-implementation of methods and algorithms already available and tested.

  4. ECOLOG is free, open source software, distributed at no cost under the terms of the GNU General Public Licence (GPL), however it is now also considered donationware, meaning that the project accepts donations (via PayPal) that make possible to guarantee the continuing development of the software and  minimize the periods between updates. Not being a commercial product nor counting with long-term financial resources for its maintenance, this is the only way that the ECOLOG development team has to be able to keep in activity.

Use Cases topo

  • The Atlantic Rainforest Research Program at Rio de Janeiro Botanical Garden, collated a database with about 20,000 specimen records and 2,000 records of plant species collected at Macaé de Cima Ecological Reserve, Nova Friburgo, Rio de Janeiro (Dalcin et al., 1997) and another one with about 600 specimen records and 140 plant species from Paraíso State Ecological Station, Cachoeiras de Macacu, Rio de Janeiro (Kurtz & Araujo, 2000).

  • The Jacarepiá State Ecological Reserve Integrated Biological Survey, Saquarema, Rio de Janeiro, conducted by Rio de Janeiro State Foundation of Environmental Engineering, created a database with about 300 specimen records e 200 plant species (Sá et al., 1991).

  • Biotupé Project, at National Institute of Amazon Research, Manaus, Amazonas, geared towards the management and analysis of biodiversity data from Tupé Lake Sustainable Development Reserve (Cavalcanti, 2005).

Publications topo

  1. Cavalcanti, M.J. 1991. ECOLOG: um sistema de banco de dados para levantamentos ecológicos de campo. Resumos do XVIII Congresso Brasileiro de Zoologia, Salvador, p. 557.

  2. Cavalcanti, M.J. 1993. ECOLOG: um sistema gerenciador de bancos de dados para levantamentos ecológicos de campo. Resumos do I Simpósio de Aplicações da Informática em Biologia, Campinas, pp. 44-45.

  3. Cavalcanti, M.J. 1998. Aplicações de Sistemas Gerenciadores de Bancos de Dados em Ecologia e Sistemática. Acta Biologica Leopoldensia, São Leopoldo 20: 5-20.

  4. Cavalcanti, M.J. 2005. Bancos de dados sobre biodiversidade na Amazônia: a experiência do Projeto Biotupé. In: Santos-Silva, E.N., Aprile, F.M., Scudeller, V.V. & Melo, S. (orgs.), BioTupé: Meio Físico, Diversidade Biológica e Sociocultural do Baixo Rio Negro, Amazônia Central. Instituto Nacional de Pesquisas da Amazônia, Manaus, pp. 199-213.

  5. Cavalcanti, M.J. 2011. ECOLOG: um sistema gerenciador de bancos de dados para levantamentos ecológicos de campo e inventários de biodiversidade. In: Santos-Silva, E.N., Scudeller, V.V. & Cavalcanti, M.J. (orgs.), BioTupé: Meio Físico, Diversidade Biológica e Sociocultural do Baixo Rio Negro, Amazônia Central - Volume 3. Rizoma Editorial, Manaus, pp. 291-302.

  6. Dalcin, E., Solano, L. & Pizarro, R. 1997. De banco de dados a centro de informações e serviços: uma experiência para a Reserva Ecológica Macaé de Cima. In: Lima, H.C. & Guedes-Bruni, R.R. (orgs.), Serra de Macaé de Cima: Diversidade Florística e Conservação em Mata Atlântica. Jardim Botânico do Rio de Janeiro, Rio de Janeiro, pp. 307-314.

  7. Kurtz, B.C. & Araujo, D.S.D. 2000. Composição florística e estrutura do componente arbóreo de um trecho de Mata Atlântica na Estação Ecológica Estadual do Paraíso, Cachoeiras de Macacu, Rio de Janeiro, Brasil. Rodriguésia, Rio de Janeiro 51: 69-112.

  8. Sá, C.F.C., Araujo, D.S.D., Lima, H.C., Cavalcanti, M.J., Pereira, M.C.A. & Fontoura, T. 1991. Composição florística e estrutura da floresta de cordão arenoso da Reserva Ecológica de Jacarepiá, Saquarema (RJ): dados preliminares. Resumos do XLII Congresso Nacional de Botânica, Goiânia, p. 527.

Download topo

Version 3.0 topo

Version 4.0 topo

Version 5.0 topo

License topo

GNUECOLOG is distributed as free software, gratis and open source, under the terms of the GNU General Public License (GNU GPL), version 2 or later.

Documentation topo

  • ECOLOG User's Guide (jn Portugues) in PDF format PDF
  • ECOLOG User's Guide (in Portuguese) in ODF format Open Documento Format

License topo

GNUECOLOG User's Guide is distributed under the terms of the GNU Free Documentation License (GNU FDL), version 1.1 or later.

Links topo

Data topo

Software topo

Support topo

Forum topo

A community driven support forum for ECOLOG with free registration is available at Google Groups (ECOLOG-L). It is recommendable to join the forum for participating in discussions and exchanging questions about the software, as well as to get information about updates and bugs.

Frequently Asked Questions topo

P. What are the requirements for using ECOLOG?

R. Minimum requirements:
  • 1.2 GHz processor
  • RAM 1 Gb
  • 50 Mb HD space
  • GNU/Linux (Kubuntu, Fedora KDE, Mint KDE, OpenSUSE), MS-Windows (XP, Vista, 7, 8) or Mac OS X (10.5 "Leopard" or later)

P. How much ECOLOG costs?

R. Nada. Niente. Nothing. Néant. Nichts. Niets. Inget.

P. Is ECOLOG source code available?

R. Yes. ECOLOG is free, open source software, released under the GNU General Public License (GNU GPL).

P. Can I import data from an electronic spreadsheet into ECOLOG?

R. Yes. ECOLOG reads directly data from spreadsheets in .csv (text delimited by commas) and .tsv (text delimited by tabs) formats, as well as in the MS-Excel (.xls, .xlsx) and LibreOffice/OpenOffice (.ods) native formats.

P. Can I export data from ECOLOG to other software?

R. Yes. ECOLOG offers several options to export data, in several formats (CSV, DELTA, FITOPAC, RDE/BRAHMS, KML, CEP, etc.).

P. Can I use ECOLOG for managing the herbarium of my institution?

R. No. ECOLOG is not a software for the management of herbaria or zoological colletions. However, specimen data stored in ECOLOG databases can be exported to the BRAHMS botanical research and herbarium database management system.

P. Can I perform multivariate data analysis with ECOLOG?

R. Yes. It is possible to perform data analysis directly from ECOLOG, by means of the R system for statistical computing and graphics. Data stored in spreadsheets readable by ECOLOG can also be exported to specific software for multivariate analysis of ecological data (FITOPAC, DECORANA, TWINSPAN, CANOCO, PC-ORD, MVSP, etc.).

P. Can I get personal, telephonic, or e-ail support for using ECOLOG?

R. Free user supporte to to ECOLOG is available at Google Groups (ECOLOG-L). To get personal, telephonic, or e-mail support, make a donation to the project or contract the consulting services of the system developer.

P. How to cite ECOLOG in publications?

R. The correct citation suggested for ECOLOG in technical and scientific publications is as follows:

Version 1:

Cavalcanti, M.J. 1993. ECOLOG: um sistema gerenciador de bancos de dados para levantamentos ecológicos de campo. Resumos do I Simpósio de Aplicações da Informática em Biologia, Campinas, pp. 44-45.

Version 2:

Cavalcanti, M.J. 2011. ECOLOG: um sistema gerenciador de bancos de dados para levantamentos ecológicos de campo e inventários de biodiversidade. In: Santos-Silva, E.N., Scudeller, V.V. & Cavalcanti, M.J. (orgs.), BioTupé: Meio Físico, Diversidade Biológica e Sociocultural do Baixo Rio Negro, Amazônia Central - Volume 3. Rizoma Editorial, Manaus, pp. 291-302.

Contact topo

Mauro J. Cavalcanti
Caixa Postal 46521
CEP 20551-970
Rio de Janeiro, RJ, BRASIL
E-mail: maurobio (at) gmail (dot) com

Acknowledgements topo

To Dr. Gustavo Martinelli (coordinator of the Atlantic Rainforest Program, Rio de Janeiro Botanical Garden), for supporting the development of the original version of ECOLOG.

To Dr. Edinaldo Nelson (coordinator of Biotupé Project, National Institute of Amazonian Research), for support the development of the new version and updates of ECOLOG.

To all botanists, represented by Drs. Veridiana Scudeller (Federal University of Amazonas), Eduardo Dalcin (Rio de Janeiro Botanical Garden), and Cyl Farney Catarino de Sá (Rio de Janeiro Botanical Garden), who contributed to the improvement of ECOLOG with constructive criticisms and useful suggestions.

Sponsors topo

Donations topo

Contribute with a donation and help to keep alive the development of ECOLOG. Donations can be made with credit card, using PayPal.

There are no limit to the donations, but according to the donated values, the users may support by e-mail and phone, a press printed user manual, and installation package on mini-CD.


Translation topo

Help to translate the user interface of ECOLOG. Any person with an intermediary level of Portuguese or English can contribute with a translation of the interface to her/his native language. At present, there are translations available for Brazilian Portuguese, English, and Spanish.

© 1990-2016 Mauro J. Cavalcanti