Headnote
ABSTRACT
Objective: Describe the digitization process of the xylarium of the Federal University of Amazonas, detailing the steps, methodologies and technologies used in the creation of an accessible and functional digital repository for the collection of Amazonian woods.
Theoretical Framework: The study is based on the scientific and educational importance of wood collections as biological collections that contribute to wood identification, ecological research, biodiversity conservation, and the fight against illegal trade. It highlights the need for digitization as a strategy to expand access to and management of these collections.
Method: The free software Tainacan, integrated with WordPress, was used to structure the repository. The data from the 1,024 samples in the reference sub-collection were converted from manual records to standardized metadata (41 fields), with the scientific nomenclature updated and new features included, such as QR codes and search filters.
Results and Discussion: Digitalization has expanded remote access and enabled advanced searches, physical-digital integration through QR codes, inclusion of geographic coordinates, scientific synonyms and anthropic uses. The platform now offers intuitive navigation, promoting research, teaching and environmental monitoring. The adoption of Tainacan has proven to be effective and replicable.
Research Implications: The repository promotes the democratization of knowledge, fosters environmental education, strengthens the management of biological collections and can be replicated by other institutions. It also anticipates the use of artificial intelligence in the organization and cross-referencing of data on biodiversity.
Originality/Value: The project is innovative because it adapts an open-source tool to the reality of a collection of Amazonian wood, creating an accessible, scalable and replicable digital system that combines technology with the conservation of scientific and biological heritage.
Keywords: Xylarium, Digital Curation, Systematization of Collections, Amazon Rain Forest.
RESUMO
Objetivo: Descrever o processo de digitalização da xiloteca da Universidade Federal do Amazonas, detalhando as etapas, metodologias e tecnologias utilizadas na criação de um repositório digital acessível e funcional para a coleção de madeiras amazônicas.
Referencial Teórico: O estudo se apoia na importância científica e didática das xilotecas como coleções biológicas que contribuem para a identificação de madeiras, pesquisas ecológicas, conservação da biodiversidade e combate ao comércio ilegal. Destaca-se a necessidade de digitalização como estratégia para ampliar o acesso e a gestão desses acervos.
Método: Foi utilizado o software livre Tainacan, integrado ao WordPress, para estruturar o repositório. Os dados das 1.024 amostras da subcoleção de referência foram convertidos de registros manuais para metadados padronizados (41 campos), com atualização da nomenclatura científica e inclusão de novas funcionalidades, como QR codes e filtros de busca.
Resultados e Discussão: A digitalização ampliou o acesso remoto e permitiu buscas avançadas, integração física-digital por QR codes, inclusão de coordenadas geográficas, sinonímias científicas e usos antrópicos. A plataforma passou a oferecer uma navegação intuitiva, promovendo pesquisas, ensino e fiscalização ambiental. A adoção do Tainacan mostrou-se eficaz e replicável.
Implicações da Pesquisa: O repositório promove a democratização do conhecimento, fomenta a educação ambiental, fortalece a gestão de coleções biológicas e pode ser replicado por outras instituições. Também se antecipa ao uso de inteligência artificial na organização e cruzamento de dados sobre biodiversidade.
Originalidade/Valor: O projeto é inovador por adaptar uma ferramenta de código aberto à realidade de uma coleção de madeiras amazônicas, criando um sistema digital acessível, escalável e replicável, que alia tecnologia à conservação do patrimônio científico e biológico.
Palavras-chave: Xiloteca, Curadoria Digital, Sistematização de Acervos, Amazônia.
RESUMEN
Objetivo: Describir el proceso de digitalización de la xiloteca de la Universidad Federal del Amazonas, detallando los pasos, metodologías y tecnologías utilizadas en la creación de un repositorio digital accesible y funcional para la colección de maderas amazónicas.
Marco Teórico: El estudio se basa en la importancia científica y educativa de las xilotecas como colecciones biológicas que contribuyen a la identificación de la madera, la investigación ecológica, la conservación de la biodiversidad y la lucha contra el comercio ilegal. Resalta la necesidad de la digitalización como estrategia para ampliar el acceso y la gestión de estas colecciones.
Método: Se utilizó el software libre Tainacan, integrado con WordPress, para estructurar el repositorio. Los datos de las 1024 muestras de la subcolección de referencia se convirtieron de registros manuales a metadatos estandarizados (41 campos), con la nomenclatura científica actualizada y nuevas funciones, como códigos QR y filtros de búsqueda.
Resultados y Discusión: La digitalización ha ampliado el acceso remoto y ha permitido búsquedas avanzadas, la integración físico-digital mediante códigos QR, la inclusión de coordenadas geográficas, sinónimos científicos y usos antrópicos. La plataforma ahora ofrece una navegación intuitiva, lo que promueve la investigación, la docencia y el monitoreo ambiental. La adopción de Tainacan ha demostrado ser eficaz y replicable.
Implicaciones de la investigación: El repositorio promueve la democratización del conocimiento, fomenta la educación ambiental, fortalece la gestión de colecciones biológicas y puede ser replicado por otras instituciones. Además, prevé el uso de inteligencia artificial en la organización y el cruce de datos sobre biodiversidad.
Originalidad/Valor: El proyecto es innovador porque adapta una herramienta de código abierto a la realidad de una colección de madera amazónica, creando un sistema digital accesible, escalable y replicable que combina la tecnología con la conservación del patrimonio científico y biológico.
Palabras clave: Xiloteca, Curaduría Digital, Sistematización de Colecciones, Amazonía.
1 INTRODUCTION
The xylotheque, a term derived from the Greek words xylon (wood) and theka (collection), is a biological collection specialised in woody samples, organised for scientific and didactic purposes (Silva et al., 2020). These collections play a crucial role in the study of forest species, allowing the identification of woods, support for research and biodiversity conservation (Fonseca et al., 2005). In addition, they are essential tools in forensic contexts, such as in the fight against the illegal timber trade (Jiao et al., 2018).
The library of the Federal University of Amazonas (UFAM), created in 1992 and named in honour of Professor Dr. Valmir Souza de Oliveira, is a relevant example of this type of collection. Initially made up of a modest collection of Amazonian samples, today it houses over 3,700 specimens, divided into four main subcollections: reference samples, permanent exhibition, a collection of histological slides and a collection of wood for practical lessons. Its focus is didactic, serving as support for teaching and research in forestry engineering.
Despite its importance, the traditional management of xylotecs faces challenges, such as underutilisation due to the difficulty of accessing and analysing data (Smith and Blagoredov, 2012). Abstract: The digitisation of collections emerges as a solution to optimise the organisation, sharing and updating of information (Schuh, 2012). In the UFAM library, this process began with the migration of manual records to spreadsheets and later evolved into the implementation of a digital repository.
This study, therefore, aims to describe the process of digitisation of the library collection in a free online repository (www.xiloteca.ufam.edu.br), including the steps involved, the technologies used and the methodologies adopted, in order to offer a comprehensive view of the practices and challenges faced during the implementation of this project.
2 THEORETICAL FRAMEWORK
A xylotheque is a biological collection composed of samples of woody species, organised according to local, regional, national or global criteria (Fonseca et al., 2005). Its importance is in the contribution to scientific and economic knowledge about forest species, thus allowing the identification of woods by comparison between specimens of the collection and providing relevant data for the development of new research.
The xylotheques function as a database on wood and represent a powerful consultation tool, allowing the identification of artefacts and ancient sculptures (Kurata et al., 2024), the expansion of knowledge and validation in the identification of tropical species (Abeele et al., 2021). In addition, they contribute to biodiversity conservation and species recognition in forensic contexts, such as illegal logging and trade (Jiao et al., 2018). The analysis of wood samples, organised in a collection and grouped according to their anatomical attributes, allows the investigation of several facets of plant biology. This approach allows exploring species distribution, functional strategies and tree growth and, in addition, contributes to the development of technologies aimed at less common timber species.
There is a significant underutilisation of the libraries when there are difficulties in accessing and analysing data within and between collections, being the biggest challenge to find ways to make this knowledge accessible to users (Smith and Blagoredov, 2012). The traditional model of consultation demands time and resources, since the analyses need to be done in person in the collection (Vieira et al., 2019; Martins-da-silva et al., 2015). The digitalisation and systematisation of specimens, together with their corresponding records, eliminate this obstacle (Smith and Blagoredov, 2012) and facilitate the management, sharing, conservation, updating of identifications and the search for information about the stored samples (Schuh, 2012).
The xylotheque of the Federal University of Amazonas (UFAM) began on July 28, 1992 and is located in the Laboratory of Physics of Madeira, a space inserted in the Faculty of Agricultural Sciences, which integrates the South Sector of the Campus Senator Arthur Virgílio Filho, located in the east zone of the urban area of Manaus. It arose to meet the demand of the Forestry Engineering course, from a modest collection of wood samples predominantly originating from the Amazon region, with a few conifers. In 2009, already consolidated, it was approved by the rectory of UFAM, when it was named Dr. Valmir Souza de Oliveira Collection, in tribute to the professor of wood technology, who died in 2008.
It is considered a collection with didactic purpose, that is, it allows to illustrate theory and complement learning, in a practical way (Lima and Faleiro, 2020). The UFAM collection allows the exploration of the anatomical characteristics of the wood and its relations with the anthropic use, as a means of evaluating the environmental impacts and formulating strategies for the conservation of natural resources. In the space there are scheduled visits to schools and national and international institutions, training in wood identification and conferences that promote multidisciplinary dialogues, these are some of the activities carried out in the library, which serves both the academic community and civil society.
Currently, the collection is divided into 4 subcollections, as shown in table 1.
The subcollection, called "reference samples", with 1024 registered specimens aimed at identification, has always been considered the most important subcollection, due to its diversity, composed of a portion of samples donated by collaborators, while others were collected during forest raids organised by teachers and some obtained through exchanges with xylotheques from other countries (Mady, 2017).
The proposal to transfer existing information to a digital repository began in 2019, with the search for software for managing biological collections. Among the options found, most demanded acquisition costs or monthly payments and were not intended for wood collections, which would possibly result in an improvisation of the project. Others, already used traditionally by some research institutions, did not allow for the level of personalisation desired. However, in the course of these software tests, a free Brazilian system was identified that allows to create and manage collections, in a customised way, called Tainacan - a plugin of the wordpress platform, which is a content management system (CMS or Content Management System) for websites.
Tainacan is a free software developed from a partnership between Medialab, from the Federal University of Goiás, and the Ministry of Culture, in 2014 (Brandão e Silva, 2018). The project originated with the objective of enabling the creation of an online repository of easy use, configuration and implementation, as a free and efficient alternative for cultural institutions that aim to implement thematic and institutional repositories (Martins et al. 2017). The Tainacan is used by several institutions, such as the Science Museum of the Federal University of Goiás, the Museum of Archaeology of Itaipu, the Museum of the Republic, the National Historical Museum and the Culture Film Collection of the Ministry of Culture (Ctav, 2017), among others (Tainacan, 2024).
3 METHODOLOGY
3.1 IMPLEMENTATION OF THE DIGITAL REPOSITORY
The transfer of the records of the samples to a public database, called digital repository, began in 2023. The CMS system chosen was Wordpress, which was installed on the UFAM server at www.xiloteca.ufam.edu.br. After installing Wordpress, the Tainacan plugin was added to store the sample metadata. The spreadsheet containing the information of the wood samples was inserted into the WordPress platform in the Microsoft Excel Comma-separated values (CSV) file format.
The implementation of the repository began with the Reference Samples subcollection, because it was considered the most relevant and contained the most stored data, which would facilitate the identification of wood remotely. The 1024 wood samples that make up the collection are distributed in seven cabinets organised in drawers (Figure 1) and were physically examined to verify the correspondence between the records and the real information.
3.2 DATABASE POWER
3.2.1 Update of the scientific nomenclature
The update of the taxonomic characteristics recorded in the UFAM library was performed, since a large part of the collection had been registered under the Cronquist System. For this phase of the project, consultations were made on the online platforms flora and funga do brasil (floradobrasil.jbrj.gov.br) and plants of the world online (powo.science.kew.org).
3.2.2 Metadata extension
In order to create a new set of metadata for the registration of information that would allow the distinction of current data and the elaboration of new arrangements, the fields used in the record books of the xylotheque were examined, when considering the conformity and contemporaneity of the anatomical, organoleptic, physical and dendrological characteristics of each sample. Other digital repositories of wood collections available online were also examined, in order to verify how these collections have their metadata organised, as in the case of the Library of the Forestry and Forest Products Research Institute, in Japan.
Thus, fields adapted to the identified needs, such as text boxes, fields for multiple selection, drop-down lists of data, among other formats, were incorporated to substantially expand the collection of information per sample, which went from 11 fields to 41 fields (table 2).
With the expansion of the fields intended for filling in information, the register of the existing samples in the digital repository was updated, including the new set of metadata established. For this update, as well as for the registration of new samples, it was necessary to individually examine each sample in the physical collection, in order to confirm the previously documented characteristics and, consequently, add new information or correct data that may have been entered in a wrong or erroneous way.
4 RESULTS AND DISCUSSIONS
4.1 QUANTIFICATION OF THE DIGITISED ACQUIS
Data from all 1024 samples that make up the Dr. Valmir de Souza Library were stored in the digital repository. Each sample was registered following the new metadata set implemented, ensuring the standardisation of information and facilitating the consultation and management of the collection. Digitisation ensured the preservation of data in electronic format and expanded remote access to information, allowing researchers, students and other users to use the collection efficiently and integrated with UFAM's online system.
4.2 VISUALISATION OF THE ACQUIS AND TYPES OF DATA AVAILABLE
The interface of the digital repository is designed to facilitate navigation and consultation of the samples available in the biological collection and offers several functionalities capable of improving the user experience (Figure 2). With filters that allow the customisation of searches, the system offers a structured table for the presentation of metadata. In the table, relevant information is highlighted, such as the date of insertion of the samples into the collection and the place where they were collected. This structure promotes an intuitive and targeted navigation, to serve both researchers and the general public interested in the catalogued woods.
The digital platform of the UFAM library currently offers a simple and effective navigation experience, as evidenced in Figure 3. The page dedicated to each sample, such as that of Mezilaurus sp., provides the relevant information in a clear and concise way, with reference image. This structure facilitates consultation and comparison between the different samples, which makes research and study of the woods feasible.
It is appropriate to inform that the interface of the UFAM Library website is responsive, that is, it automatically adapts to the size and type of screen of the device being used - be it a computer, tablet, smartphone or even a TV. The content, images, and layout elements rearrange to ensure the best possible browsing experience without the need for manual magnification or scrolling of the horizontal bar.
4.3 FUNCTIONALITIES OF THE ADOPTED SYSTEM
One of the challenges when creating a digital repository is choosing the right system to manage the data. Although there are robust systems available - some of them free of charge - for use in biological collections, since the beginning of the project, the desired approach was to develop a personalised environment that would meet the demands of a wood collection, in this case, the Xiloteca of UFAM. The use of the Tainacan Platform has brought excellent results regarding the flexibility to create a secure environment for the storage of information in the form of metadata. It is important to note that the system also has a plugin intended to perform backups, that is, copies of the database that can be recovered in case of a server crash.
The adoption of Tainacan made it possible to create new collections on the same online platform (Figure 4), such as the Permanent Exhibition subcollection. The evaluation is that the choice made by the Xiloteca management team was a correct decision, since the Tainacan plugin allows insertion and search from a faceted classification, and is free, in use in dozens of public and private institutions and also offers support, it is noteworthy that Tainacan was developed by a Brazilian public university.
4.3.1 Accessibility and usability
Among the various functionalities offered by the digital repository of the library, the search in the collection stands out, which allows locating species by the common or scientific name, to return the expected result, if it exists. The search engine can be optimised through filters that select samples based on specific criteria, such as scientific synonyms, botanical family, sample number, and organoleptic properties, such as colour and odour (Figure 5).
The cumulative nature of filters is an interesting feature in online repositories, as it acts as a resource that simplifies the separation of registered items - in this case, woods - in a similar way to the use of dichotomous keys. Soon, new filter options will be accessible to the public, so it will be possible to carry out research that considers the colour of the sample that you have or that you want to find in the collection, such as a yellowish wood, for example. Then a second filter can be added to the first one, such as "wood with a pleasant odour". The system will return all the woods that present aroma within the group of the yellowish woods, and will narrow the options to give opportunity to identify the sample at a distance.
4.3.2 The importance of inserting new fields
It is evident that the adoption of a digital system of registration and storage of data, not only optimises the ability to insert new samples, but also allows to manage a large amount of information simultaneously. When we consider as an example the first thousand samples registered, there were 11 thousand lines of text that housed their respective original records, manuscripts on paper. With the advent of the digital repository, after the effective filling of all the new fields related to the first thousand samples, there will be 41 thousand stored metadata, which, unlike texts, can be electronically manipulated.
The expansion of the fields destined to the storage of metadata will not only result in a significant increase in the volume of information about the stored woods, but will also allow the extraction of textual and graphic information from the collection, such as, for example, the listing of samples that have types or that present stratified radii, as well as the ratio of the samples that contain axial channels. This information could be collated and interrelated to result in new clusters of valuable data on forest species.
The update of the scientific nomenclature brought several changes to the collection, such as the migration of species to different botanical families. This reformulation modernised the collection and enabled the creation of a new field of metadata, called "scientific synonyms". This field was incorporated to make the search easier for users who may use outdated scientific names in their investigations.
More than just creating fields for entering data, the system has also made it possible to create taxonomies, a special type of field that contains terms that allow immediate access to all the samples that have a given characteristic. The user, when selecting the link of a taxonomy, is redirected to other library items grouped under the same classification.
A practical example of this functionality can be observed through the taxonomy established on the pore size of wood samples. Traditionally, this information was stored in textual format, located in a paragraph in the section called "observations" of the old registration model. By designating pore size as a taxonomy, a new field was introduced into the repository that classifies woods into large, medium or small pores. This approach allows to gather all labelled samples similarly within this classification, which enables the identification, quantification and immediate separation of these species.
Among the new metadata, there are some that are quite interesting and innovative, such as geographic coordinates, which allows registering on a map the regions of occurrence of each species (Figure 6). This functionality, originally available on the Tainacan Platform, was adapted to the xylotheque system and may shortly make it possible to analyse how the anatomical characteristics of the woods vary in accordance with their geographical origin.
In some cases, new fields need bibliographic references to be filled in, as in the case of the main anthropic uses associated with each wood. This led to the creation of a new field aimed at registering the reference sources for documentary research, which organises and registers the publications that support these descriptions.
The greater capacity to collect and store data in a biological collection for didactic purposes can have positive impacts on the professional training of academics, since it directly expands the amount of systematised information of each sample and the species in the collection (Teles and Sanches, 2021). It is possible that new fields will be incorporated into the system, to increase the capacity for collecting and integrating information from the collection. The structure of the library repository includes, until July 2025, macroscopic anatomical records.
However, there are dozens of anatomical features that can only be visualised with the use of microscopes and that were not considered in this initial phase, to enable the implementation. Obviously, when there are appropriate technical conditions for this extension, new and relevant metadata fields will be included in the existing list, which will significantly increase the relevance and robustness of this digital repository.
4.4 IMPACT OF DIGITISATION ON KNOWLEDGE SHARING
The sharing of scientific knowledge produced in universities is a necessary practice for the socialisation of information with society, which has been accentuated since the 1990s (Apocalypse and Jorente, 2019). When considering this, the implementation of a digital repository of a biological collection that belongs to a public university is an activity from which relevant, lasting, participatory and interactive results are expected, considering the potential that such a mechanism has to leverage scientific research (Silva et al., 2023; Carréra et al., 2015).
With the advent of artificial intelligences (AIs), the existence of these metadata collections can have a multiplying effect, where AIs will solve problems and streamline the document organisation process (Oliveira and Coelho-Júnior, 2021). It is expected that new plugins for wordpress will be developed that contemplate these optimised search and content generation functionalities from the stored metadata, with the aid and use of AIs, which will certainly be profoundly useful for the library repository.
One of the possibilities of the system is to measure the number of accesses in each one of the pages of the portal. Each access is counted and the sum made available in a table in the administrative area. Thus, it was found that the first 6 months of implementation of this system of metrics, there were more than 9,000 views on the home page of the library, more than 4,000 hits on the content "What is wood" and 1,158 hits on the content "What is a library", as shown in Table 3.
4.5 POST-IMPLEMENTATION OF THE DIGITAL REPOSITORY AND FUTURE CHALLENGES
At the present time, the collection of anatomical information from each wood sample counts on the collaboration of monitors and volunteers associated with the UFAM xylotheque, which is a systematic activity that requires time, adequate training and meticulous attention to anatomical details. It is estimated that, by the end of 2026, all the anatomical characteristics of the samples from the current physical collection will have been transcribed to the digital repository, allowing access to a set of detailed information about wood. However, there is full knowledge that this work will be continuous, since the entry of new samples has been constant and that, when they are registered in the repository, they must go through the same process of collecting and storing metadata.
A fundamental step of the digital registration process is the acquisition, processing, storage and sharing of images of the samples present in the collection. The production of macroscopic images involves a sequence of steps that includes the preparation of a specimen of the sample, polishing the surfaces of the material, capturing the macroscopic images, digital treatment using image editing software, coded storage linked to the corresponding sample and its publication in the repository.
The captured images may not be fully faithful to colour and dimensions, but they continue to illustrate the distinctive appearance of wood surfaces, which can be valuable for many uses (Wiedenhoeft, 2014), such as remote identification by inspection teams. Started in 2024, the production of the images of the current collection should be finalised together with the registration of the other metadata. In the future, it is planned to start a similar process for capturing microscopic images.
The creation of an individual online cadastre for each sample allowed to add to the repository a label system containing a QR-Code (quick response code). In this way, each sample was able to receive an adhesive label with a code that, when scanned with a smartphone device, will send the user to the repository page that contains the metadata set of that sample. This system module is already ready, in the physical implementation phase, such as printing labels and applying on the samples. This will speed up the local query and allow you to quickly access all the metadata of any of the samples.
Given that all the experience in the implementation and management of the library data is recent, there are still many lessons to be learned and tests to be carried out. The certainty is that these scientific collections can be considered excellent sources of information and support for phytogeographic, taxonomic, ecological studies and research related to the conservation and preservation of ecosystems (Nascimento, 2019). Therefore, the efforts around this project of digitisation and sharing of information will continue, with the perspective of its constant improvement and expansion of the collection.
5 CONCLUSION
The implementation of the repository and the availability of the metadata of the wood collection constitute a broad source of public consultation that externalises the knowledge acquired at the university, brings the community closer to the academic environment and sediments a healthy symbiotic learning process. The UFAM library, together with its digital repository, has great potential to offer significant information that can still be extracted from its samples. This includes determining the density - which is considered the most elementary characteristic for technological research into wood - besides supplying the material for extracting DNA. In addition, new generations of artificial intelligence and the ease of development of applications for mobile devices can be complementary tools to develop new possibilities for using the digital repository, by expanding the ways of accessing and combining data to generate secondary information.
The implementation and maintenance of physical and digital collections, imply the existence and availability of resources, the improvement of public policies for biological collections and the recognition of the value of such actions by managers and agents of educational and research institutions. In order for these collections to fulfil their role effectively, it is fundamental to foster a culture of valuing scientific heritage, which stimulates investment in infrastructure, personnel training and technological innovation. The articulation between various sectors, including academia, government and civil society, is the key to enhancing the impact of these collections, since the information produced not only contributes to the development of scientific knowledge, but can also help raise awareness of the importance of biodiversity conservation.
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