Dissecting a methodological framework for the systematic and scientometric assessment of the biotechnological potential of endemic Caatinga plantsAbstract
Endemic plant species of the Caatinga (EPCs) domain represent an important reservoir of biotechnological resources, yet scientific evidence on their potential remains highly fragmented. This study presents a structured methodological framework for a systematic review aimed at consolidating and evaluating the biotechnological prospections of EPCs. The protocol incorporates a refined search strategy, combining population- and intervention-based descriptors, the comprehensive inclusion of taxonomic synonyms, and a hierarchical thematic classification of biotechnological domains. This framework was methodologically designed to include studies indexed in the MEDLINE, Embase, Web of Science, and Scopus databases, covering publications from 2014 to 2024 in Portuguese, Spanish, and English. The protocol follows standardized procedures for search strategy development, screening, data extraction, methodological quality assessment using an adapted Critical Appraisal Skills Programme (CASP) tool, and evidence synthesis. Variables related to publication characteristics, investigated species, collection sites, biotechnological sectors, and experimental models employed were systematically analyzed. By consolidating fragmented evidence, this protocol supports the valuation of Caatinga biodiversity, identifies priority species for technological prospecting, and provides a replicable methodological reference for systematic reviews targeting specific biomes and floras.
Keywords:
interdisciplinarity; systematic review; phytocompounds; plant biotechnology; sustainability
Resumo
As espécies endêmicas do domínio Caatinga (EPCs) constituem um importante reservatório de recursos biotecnológicos, embora as evidências científicas sobre seu potencial permaneçam altamente fragmentadas. Este estudo apresenta um arcabouço metodológico estruturado para uma revisão sistemática voltada à consolidação e avaliação das prospecções biotecnológicas dessas espécies. O protocolo incorpora uma estratégia de busca refinada, combinando descritores baseados na população e na intervenção, a inclusão exaustiva de sinônimos taxonômicos e uma classificação temática hierárquica dos domínios biotecnológicos. Esse framework foi metodologicamente delineado para incluir estudos indexados nas bases MEDLINE, Embase, Web of Science e Scopus, abrangendo publicações de 2014 a 2024 em português, espanhol e inglês. O protocolo segue procedimentos padronizados para elaboração da estratégia de busca, triagem, extração de dados, avaliação da qualidade metodológica com uma versão adaptada da ferramenta Critical Appraisal Skills Programme (CASP) e síntese das evidências. Variáveis relacionadas às características das publicações, espécies investigadas, locais de coleta, setores biotecnológicos e modelos experimentais empregados serão analisadas sistematicamente. Ao organizar evidências dispersas, este protocolo fortalece a valorização da biodiversidade da Caatinga, identifica espécies prioritárias para prospecção tecnológica e oferece uma referência metodológica replicável para revisões sistemáticas voltadas a biomas e floras específicos.
Palavras-chave:
interdisciplinaridade; revisão sistemática; fitocompostos; biotecnologia vegetal; sustentabilidade
1. Introduction
The Caatinga is a phytogeographic domain dominated by seasonally dry tropical forests (SDTF), comprising approximately 3,347 species, 962 genera, and 153 plant families distributed across the Brazilian states of Alagoas, Bahia, Ceará, Maranhão, Pernambuco, Paraíba, Rio Grande do Norte, Piauí, Sergipe, and northern Minas Gerais (Brasil, 2016; Fernandes et al., 2020; Queiroz et al., 2017). Endemism is a key feature of this flora: approximately 15.7% of the Caatinga’s vegetation consists of endemic species, including 29 genera. The families Fabaceae, Euphorbiaceae, Cactaceae, Bromeliaceae, Malvaceae, and Apocynaceae exhibit the highest frequency of endemism (Fernandes and Queiroz, 2018; Fernandes et al., 2020).
Recent studies have demonstrated that EPCs hold significant cultural, ecological, and economic importance, supporting traditional practices and contributing to the livelihood strategies of local communities. Their recognized biotechnological potential includes medicinal properties, bioenergy production, the formulation of nutraceuticals and functional foods, natural fiber production, and applications in furniture and building construction (Reis et al., 2023).
The diversity of plant resources in Caatinga SDTF ecosystems enables multiple forms of use particularly in the nutritional domain, where numerous species present considerable dietary value (Camacam and Messias, 2022). The domain also exhibits considerable forage potential, often serving as the primary source of feed for livestock (Santos et al., 2010). The integration of such multifunctional species into local production systems further reinforces their relevance from both ecological and socioeconomic perspectives.
These biotechnological attributes are closely linked to the remarkable chemical diversity of EPCs, which are rich in secondary metabolites, phytoconstituents, and essential oils (Barros et al., 2023). Many of these species are traditionally used in folk medicine to treat a wide range of conditions, although a significant proportion has not been subjected to systematic chemical, pharmacological, or toxicological evaluation (Pacheco et al., 2022). The scientific investigation of their bioactive compounds offers opportunities for validating traditional knowledge and advancing the discovery of new therapeutic agents (Mesquita et al., 2017; Reis et al., 2023). In ecological restoration efforts, species recognized as useful to local populations tend to be more readily adopted, potentially increasing restoration success through enhanced community engagement (Sena et al., 2022).
Therefore, organizing and consolidating the evidence generated by studies on the bioprospecting of EPCs is essential to establish scientifically grounded assertions, systematically identify knowledge gaps, and clarify the potential benefits associated with these species. Fragmented evidence and heterogeneous methodological practices, reinforce the need for structured syntheses capable of minimizing bias and enhancing interpretability (Grant and Booth, 2009; Haddaway et al., 2015). As part of a broader effort to systematize this knowledge, we undertook a rigorous systematic and scientometric assessment of the biotechnological potential of endemic Caatinga plants. Here, we present a critical appraisal of the protocol designed to guide this review. Review protocol articles play an essential role in scientific research by transparently and systematically defining the objectives, criteria, and methodological decisions that precede the synthesis of evidence. This practice strengthens methodological rigor, enhances reproducibility, and reduces the risk of arbitrary decisions and bias (Kolaski et al., 2023; Gough et al., 2017). Public registration of protocols further promotes transparency, enabling independent scrutiny of planned methods and reducing unnecessary duplication of reviews (Lasserson et al., 2019; Haddaway et al., 2017).
Typically, protocols encompass the clear definition of the research question, inclusion and exclusion criteria, search strategies, methods for data extraction and analysis, as well as plans for assessing study quality (Moher et al., 2015). It is common for articles to rely on review protocol guidelines to support their methodological choices, demonstrating that well-designed protocols serve as pillars for subsequent research (Free et al., 2010; Pulido-Chadid et al., 2023). Thus, the standalone publication of review protocols (an established practice in the literature) enables a depth of methodological detail and transparency that typically exceeds what is feasible in studies driven by a tightly focused research question.
In this context, this framework serves as a critical tool not only to guide the ongoing review but also to offer potential pathways for other researchers focused on species-rich and taxonomically complex biomes. We present and detail the development of the search strategy, explicitly addressing the challenges associated with defining a comprehensive set of terms capable of encompassing the multiple domains of biotechnology, as well as managing the extensive synonymy arising from the taxonomic diversity of EPCs. By publicly defining the research question, search strategy, screening procedures, risk of bias assessment, and data extraction methods in advance, this protocol ensures methodological rigor, transparency, and reproducibility, while reducing the likelihood of arbitrary decisions and duplication of effort. We also expect that the evidence base generated by this review will support subsequent question-driven analyses that further explore and interpret the assembled information.
2. Material and Methods
This protocol follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The full protocol was registered and made publicly available on the Open Science Framework (OSF) (Silva et al., 2025).
2.1. Search strategy development
The research question was formulated using the PICO framework, which supports structured and critical reasoning, leading to the following guiding question: ““What are the biotechnological advances derived from the use of endemic Caatinga plant species in the contexts of health and socio-environmental development?” A preliminary literature search confirmed the absence of studies addressing this specific question.
A comprehensive search strategy aligned with the research question was developed (Table 1). The evidence search was performed in the following databases: Medical Literature Analysis and Retrieval System Online (MEDLINE), Excerpta Medica Database (Embase), Web of Science, and Scopus. These were selected based on their broad coverage and relevance to the research topic.
The descriptors and respective synonyms were defined according to the components of (i) population and (ii) intervention:
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Population: EPCs, whose scientific names were extracted from recently published species lists (Fernandes et al., 2020). Synonyms for each species were identified and quantified using the Flora and Funga do Brasil platform (https://floradobrasil.jbrj.gov.br/).
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Intervention: biotechnological prospecting of these plants. The biotechnological domains and corresponding descriptors were defined based on established terminology used in specialized literature (Mavituna, 1992; Murphy, 2004; Bhatia, 2015; Vijayalakshmi and Kripa, 2016). Synonyms for MeSH terms were obtained from the PubMed MeSH dictionary and Embase’s Emtree thesaurus. Duplicates synonyms were checked and removed.
The search strategy was refined through database-specific adaptations and filters. In Embase, publications overlapping with MEDLINE were excluded. In MEDLINE, filters were configured to retrieve records based on titles and abstracts. In Scopus, searches included titles, abstracts, and keywords. Compound terms were enclosed in double quotation marks, and isolated words were truncated using an asterisk, following a consistent rule across databases. Searches were restricted to publications from the past ten years, and the final strategy was validated by a professional librarian.
Sentinel articles were identified through exploratory searches using the terms “Biotechnological Applications” and “Plants of the Caatinga.” Articles were classified as sentinel when their titles or abstracts contained at least one endemic species and showed high citation counts. These articles were evaluated and compiled to confirm the adequacy of the search strategy. Sentinel references included Moura et al. (2019) and Silva et al. (2014).
2.2. Abstract screening
Before screening, three rounds of double-blind training were conducted to minimize potential discrepancies among reviewers. Divergences were resolved by a third, senior reviewer. Following training, concordance and reliability analyses were performed. Inter-rater agreement was calculated using the Kappa coefficient, which quantifies the extent to which observed agreement exceeds that expected by chance. Screening proceeded only after achieving a Kappa of 0.80, indicating strong reliability (McHugh, 2012).
Articles published between 2014 and 2024 and indexed in MEDLINE, Embase, Web of Science, and Scopus were included. Grey literature, defined as non–peer-reviewed scholarly or technical documents produced outside conventional publishing, was excluded, as the focus was restricted to experimental studies published in peer-reviewed journals.
Retrieved articles were organized in the Rayyan platfor ai. Screening was double-blind. Duplicate records were identified by the software, manually verified, and excluded. General inclusion and exclusion criteria are presented in Table 2.
2.3. Full text screening
Training procedures equivalent to those used in the abstract screening stage were also be applied during full-text screening. Three rounds of double-blind training were conducted. Discrepancies among reviewers were discussed and resolved by an experienced adjudicator. The review were proceeded only after achieving a Kappa coefficient of 0.80 (McHugh, 2012). The inclusion and exclusion criteria applied during this stage remained consistent with those previously applied.
2.4. Risk of bias assessment
Risk of bias and methodological quality of the selected studies were assessed using adaptations of the Critical Appraisal Skills Programme (CASP) checklist (casp-uk.net). This instrument contains ten items designed to evaluate methodological rigor and the validity of study outcomes. For this project, the following eight adapted questions were applied: I. Was the research question clearly defined? II. Was the study design appropriate to address the research question? III. Were sample collections and experimental procedures conducted appropriately? IV. Were the data collected in a manner that adequately addressed the research question? V. Were comparison (control) groups established? VI. Were ethical considerations addressed when necessary? VII. Was the data analysis sufficiently rigorous? VIII. Are the results presented with completeness and clarity?
2.5. Data extraction and organization
Primary data from the included articles were organized using the Airtable platform (airtable.com). The variables extracted from each study were presented in Table 3. When information was missing, corresponding authors were contacted via email, with two attempts made at 20-day intervals. The data extraction workflow comprised four stages: team training, reliability verification, final extraction, and requests for missing data. Inter-rater reliability was assessed using the pacman package (Tyler Rinker and Kurkiewicz, 2017) in RStudio (version 2023.06.0+421). Graphical outputs were generated using ggplot2 (Wickham, 2016). All team members received detailed instructions to ensure strict adherence to the established protocols and were encouraged to raise questions or provide suggestions at any stage of the process.
2.6. Scientometric analysis
The scientometric analysis encompassed frequency analysis, co-authorship networks, institutional collaboration, and citation analysis, using software tools such as VOSviewer and Bibliometrix. The results were consolidated through thematic maps, comparative tables, and graphical representations, providing an integrated overview of the scientific output and biotechnological prospects related to endemic plant species of the Caatinga biome. The variables analyzed from the selected articles were listed in Table 4.
3. Results
3.1. Search strategy development
With regard to the processing of population-related search terms, we identified a particular challenge in integrating the full range of taxonomic synonyms of plant species. Among the 526 endemic plant species, belonging to 63 distinct families, 241 species (45.82%) presented a number of synonyms ranging from 1 to 16. In total, 160 species (30.42%) presented a single synonym, 47 species (8.94%) presented two synonyms, and 14 species (2.66%) presented three synonyms. Cases involving a higher number of synonyms were rare; however, Pilosocereus pachycladus F. Ritter (Cactaceae) stood out by accumulating the maximum number of 16 synonyms (Figure 1).
Ridgeline chart representing the distribution of the number of synonyms per family of endemic species from the Caatinga biome. The ridges indicate frequency density, while the overlaid points represent individual observations. Source: The authors, 2025.
Regarding the processing of intervention-related search terms, we identified additional challenges that extended beyond synonym integration, requiring the careful organization of hierarchical themes and topic structures. We found 460 compound terms and 196 single-word terms. Based on this process, four major biotechnological prospecting areas were established: (i) human health, (ii) animal health, (iii) agriculture and agrobiotechnology, and (iv) industry and bioprocesses.
Within the human and animal health domains, eight main terminological branches were identified, comprising a total of 487 synonyms. The branches with the highest number of associated synonyms were biological activities (330 synonyms) and immunobiotechnology (47 synonyms), followed by therapy-related terms (36 synonyms) (Figure 2). It is important to note that, although human health and animal health were treated as distinct domains, the terms applied to both were conceptually congruent.
Sankey diagram illustrating the flows between the categories analyzed within the human and animal health domains. Nodes represent the source and target categories, while flows indicate the number of associated records (value), with the width of each connection proportional to the magnitude of the observed flows. Source: The authors, 2025.
Within the agriculture and agrobiotechnology domain, six terminological branches were identified, comprising a total of 70 synonyms. The branches with the highest number of associated synonyms were resistance-related terms (35 synonyms), followed by cell and tissue culture (13 synonyms) and genetic engineering and transgenics (12 synonyms) (Figure 3A). In the industry and bioprocesses domain, nine terminological branches were identified, encompassing a total of 99 synonyms. The branches with the greatest number of associated synonyms were proteins and enzymes (23 synonyms), food and nutrition (18 synonyms), and flavors, fragrances, and perfumery (14 synonyms) (Figure 3B).
Sankey diagrams illustrating the flows between the categories analyzed in the agriculture and agrobiotechnology (A) and industry and bioprocesses (B) domains. Nodes represent the source and target categories, while flows indicate the number of associated records, with the width of each connection proportional to the magnitude of the observed flows. Source: The authors, 2025.
By integrating the population- and intervention-related components, we ultimately implemented a highly comprehensive and semantically dense search strategy. The inclusion of taxonomic synonyms resulted in an expansion of approximately 78.71% of the population-related search component relative to the use of accepted species names alone, while the hierarchical organization of intervention-related terms further increased the overall breadth of the strategy by approximately 16,400.00%. Owing to its length and logical complexity, the final search string exceeded 47,533.00 characters, requiring its division into two independent queries. Consequently, platform-specific adaptations were required across the bibliographic databases to ensure the accurate, reproducible, and functionally equivalent implementation of the search strategy within the technical constraints of each search interface.
3.2. Screening of studies
The number of articles retrieved from each database was as follows: 419 (16.19%) from Embase, 201 (7.76%) from MEDLINE/PubMed, 1,318 (50.94%) from Scopus, and 647 (25.00%) from Web of Science. The high number of records retrieved from Scopus is attributable to the need to split the search strategy due to character limitations in the database search interface. Of the 2,587 records identified across the four databases, 1,647 were recognized as duplicates and subsequently removed. As a result, title and abstract screening was conducted in a double-blind manner on 938 records. The screening workflow, exclusion criteria, and final dataset are detailed in Figure 4.
Flowchart of Study Selection According to Recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Source: The authors, 2025.
Prior to abstract screening, three double-blind pilot rounds were conducted, during which disagreements were discussed and resolved by an independent third reviewer. Following these pilot phases, a Cohen’s kappa coefficient of 0.83 and an overall agreement rate of 92.1% were achieved, indicating strong inter-rater reliability according to the standardized benchmarks proposed by McHugh (2012). Subsequently, abstract screening was performed on 938 records, of which 340 were excluded.
The assessment of reliability and agreement during the pre–full-text screening pilot yielded a kappa coefficient of 0.81 and an agreement rate of 90%, enabling progression to study selection. Full-text screening was conducted for the remaining 598 articles, resulting in the exclusion of 206 studies. Consequently, 392 articles were included and proceeded to the data extraction phase.
4. Discussion
The results presented in this protocol illustrate the process of constructing and applying the search strategy and provide guidance for similar studies conducted in related research fields.
The present protocol addresses a critical methodological gap by proposing a systematic and transparent framework to identify, structure, and organize the biotechnological potential of EPCs. Rather than representing a preliminary step toward subsequent analyses, the development of the search strategy and the associated terminological organization constitute the core outcome of this study, providing a reproducible methodological foundation for future evidence synthesis and bioprospecting assessments within this biodiversity-rich domain.
The identification and categorization of biotechnological descriptors across health, agriculture, agrobiotechnology, and industrial bioprocesses are consistent with classical and contemporary frameworks used to define biotechnology as a multidisciplinary field (Mavituna, 1992; Murphy, 2004; Bhatia, 2015; Vijayalakshmi and Kripa, 2016). By organizing these descriptors into well-defined terminological branches and quantifying their associated synonyms, this protocol establishes a reproducible methodological pathway that supports both systematic review and scientometric analyses, thereby enhancing transparency and reducing selection bias.
From a broader perspective, global assessments have emphasized that biodiversity loss directly compromises future opportunities for scientific and technological innovation, particularly in fields dependent on natural resources, such as pharmaceuticals, agriculture, and industrial biotechnology (Costanza et al., 2017; IPBES, 2019; Leclère et al., 2020). In this context, the Caatinga SDTF emerges as an area of strategic relevance, combining high biological singularity with limited representation in global research agendas (Santos et al., 2011). The uneven distribution observed among biotechnological descriptors reflects this imbalance and reinforces the need for targeted research efforts in underexplored domains.
The prominence of health-related terminological branches, particularly those associated with biological activities, immunobiotechnology, and therapy, aligns with the well-established role of plant biodiversity as a source of bioactive compounds and pharmacologically relevant molecules. Despite advances in synthetic chemistry, natural products remain central to drug discovery pipelines, either as direct therapeutic agents or as structural templates for molecular optimization (Harvey et al., 2015; Newman and Cragg, 2020; Atanasov et al., 2021). In this regard, the identification of a high number of synonyms associated with endemic species underscores both the taxonomic complexity of the Caatinga flora and its potential relevance for translational research in human and animal health.
Similarly, the results related to agriculture, agrobiotechnology, and industrial bioprocesses highlight the importance of traits such as resistance, metabolic versatility, and enzymatic diversity. These characteristics are particularly valuable in the context of climate change, food security, and sustainable industrial processes, as widely emphasized in global assessments of biodiversity-based innovation (FAO, 2019; IPBES, 2019). Semi-arid ecosystems host species that have evolved unique physiological and biochemical adaptations, such as drought tolerance, osmotic regulation, and specialized secondary metabolism, which may be exploited through genetic engineering, cell and tissue culture, and bioprocess optimization (Chavarría et al., 2020; Gallardo-López et al., 2022). The structured mapping of these terminological branches provides a foundation for identifying research gaps and guiding future experimental and applied studies, particularly in underexplored drylands that harbor high yet undervalued biotechnological potential (Santos et al., 2011).
Beyond its scientific contributions, this protocol is also aligned with emerging discussions on bioeconomy and sustainable development. Biodiversity-based innovation is increasingly recognized as a pathway to reconcile economic growth with environmental conservation and social inclusion, particularly in regions where traditional knowledge and biological resources coexist (Wittmer et al., 2010; Mackenzie and Dasgupta, 2021; Harrington et al., 2010). By offering a systematic and reproducible framework to assess biotechnological knowledge, this protocol contributes to evidence-based decision-making and may support the formulation of public policies aimed at the sustainable use of endemic plant resources.
In summary, this protocol does not merely organize existing literature but establishes a strategic roadmap for future biotechnological research focused on endemic plant species from the Caatinga. By integrating systematic review methods with scientometric analyses, it enables the identification of dominant research themes, emerging trends, and neglected areas across multiple biotechnological sectors. Ultimately, the outcomes derived from this protocol are expected to strengthen the scientific basis for conservation-oriented innovation and to position semi-arid ecosystems as relevant contributors to the global biotechnological landscape.
Acknowledgements
The authors would like to thank the Coordination for the Improvement of Higher Education Personnel - Brazil (CAPES) - Financial Code 001. Science and Technology Foundation of the State of Pernambuco (FACEPE IBPG, APQ) and the University of Pernambuco - UPE/Campus Garanhuns, Brazil, for funding the project.
Data Availability Statement
The research data analyzed in this study are not publicly available by any means.
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