LeafLive-DB: Classification and Data Storage of Botanical Studies
Abstract
:1. Introduction
Literature Survey
2. Materials and Methods
2.1. Overview of Leaflive-DB
- (a)
- Classification;
- (b)
- Taxonomies;
- (c)
- Images;
- (d)
- Geolocation information;
- (e)
- Scientific articles (scientific productivity and published data, resulting from studies on various species).
- (a)
- Administrative Module: the administrative panel or control dashboard allows the total management of the system, the database of users and hierarchical access profiles, and the approval of organism registration. This module’s template was designed to have an adequate level of abstraction, thus allowing the reuse of some functions common to all users (header, footer, sidebar, and slide bar, among others). In the business layer, which is responsible for the administrative panel, functions were created to be loaded according to each user’s access profile.
- (b)
- Organism Registration Module: considered the main module of the system, since it provides the interfaces for feeding the system, it allows data insertion related to a particular species and its related information, such as its taxonomy. The module is divided into five levels:
- (i)
- Taxonomic Classification Level: allows the insertion of the entire taxonomic hierarchy of the organism. It was built to enable a dynamic search in the database and return the results by similarities in an auto-complete form. Consequently, if the taxonomy entered by the user already exists, it is not necessary to make a new registration and duplicate the data, allowing only a new relationship with the pre-existing taxonomy. When selecting a pre-existing taxonomy, the database query’s return was treated in a form that will enable a new taxonomy to be registered in case of non-existence.
- (ii)
- Image Level: at this level, the function that allows uploading the registered plant’s image is programmed, allowing the user to correlate the information visually. The upload is done asynchronously using the “fineuploader” plug-in. The images are visualized as a slide show, together with a preview of the organism’s registered information, when registration is finalized.
- (iii)
- General Information Level: at this level, there are text fields for the insertion of information for each plant species, where a “leaf map” is made available to assist the user in the precise identification of the species during the moment of registration.
- (iv)
- Indexing Level: this level includes registering academic papers related to the recorded species. After the article’s registration, relationships are created between all registered species that have been studied and described in the paper. For this purpose, the user needs to mention the plants that were considered using keywords. All information provided is grouped, and references (link or article) are inserted on the main registration page of each organism. The articles to be uploaded on this platform must be from the authors themselves and with open access. Otherwise, the user can share the official publication webpage.
- (v)
- Geolocation level: this level was built to insert geographic location information of the identified species (Google Maps API). This should eliminate errors at the origin (where the plant was located) and allow easy mapping of the Brazilian biome species.
- (c)
- Consultation Module: the consultation module allows, with a combination of specific filters, the location of registered bodies and related works (articles). Currently, this module has a base of 56 thousand records, with a response time per query in the order of milliseconds. Date and time functions on the insertion and manipulation of data registered on the platform are part of this module.
2.2. Description of the Architecture
- (a)
- Interface layer (view) is restructured with a new interface control class, coupling the Dwoo PHP Template Engine. Incorporating the template allows efficient recovery of structures encoded in HTML and makes dynamic replacements with data received from the control layer. The result is an agile construction of interfaces, keeping the code organized and eliminating the mix of languages. In this same interface layer, the routing class “Bootstrap” is called, which has direct communication with the control layer. In this class, all application execution control is performed. All the framework routing is done based on the URL used, either by the user or the application itself. Using the URL, the Bootstrap class identifies which controllers, models, and views should be instantiated and which function must be executed.
- (b)
- Control layer (controllers or Business Layer) was restructured and segmented into three levels. At level 1, specific control is performed by reducing the set of specific business rules for a given controller. At level 2, an abstraction class called ControllerCrud is developed, which implements and executes automatically without the developer’s need to code them. The basic functionalities of a CRUD (function) are to create, read, edit, and delete entries. At level 3, the most common control methods used by the lowest levels of operation are grouped, such as access to the functions of the interface layer (view) and data (model).
- (c)
- Data layer (model) is restructured and segmented into two levels. At level 1, there is the specific model, and at level 2, the general model. The abstractions performed by both levels follow the same line of operation as the control layer. At level 1, it is possible to encode specific and more complex queries, and level 2 automatically takes care of the most common queries to be used.
- (a)
- Interface layer: built following a hybrid programming model, using HTML5, PHP, JavaScript, and CSS3 languages. As a language for styling content at the interface level, the latter is part of the platform specification. The JavaScript language allows the performance of the dynamic control of HTML and CSS3, making changes to the layout in real-time according to user interaction, and to change the behavior and information displayed on the page.
- (b)
- Business Layer: responsible for validating, processing server-side data, applying business rules, and communicating with the data layer. In its implementation, the framework called FelideoMVC was used, a component of the MVC framework. It was chosen due to its simplicity in the development and study routines, initially relying on the basic implementation of an MVC architecture, communication with the database, URL routing, and user login system. In addition, it is also an intuitive administrative panel. Improvements in the MVC framework allowed for better code organization, greater agility in coding the platform’s functionalities, and, finally, greater stability to the system.
- (c)
- Data Layer: it follows a relational structure currently composed of 22 tables. Six tables are essential to the framework’s functioning, and sixteen tables refer to the structure for storing data and images of organisms and scientific articles.
3. Results
Accessing Leaflive-DB Services
4. Conclusions and Future Works
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
- Neto, L.M.; Furtado, S.G.; Zappi, D.C.; de Oliveira Filho, A.T.; Forzza, R.C. Biogeography of epiphytic Angiosperms in the Brazilian Atlantic forest, a world biodiversity hotspot. Braz. J. Bot. 2016, 39, 261–273. [Google Scholar] [CrossRef]
- de Almeida, R.F.; Mamede, M.C.H. Checklist, conservation status, and sampling effort analysis of Malpighiaceae in Espírito Santo State, Brazil. Braz. J. Bot. 2014, 37, 329–337. [Google Scholar] [CrossRef] [Green Version]
- Rahul, J.; Jain, M.K. Floristic assessment of the important least concern plant species with taxonomic descriptions along the National Highway. Braz. J. Bot. 2015, 38, 851–864. [Google Scholar] [CrossRef]
- David, B.; Wolfender, J.; Dias, D.A. The pharmaceutical industry and natural products: Historical status and new trends. Phytochem. Rev. 2015, 14, 299–315. [Google Scholar] [CrossRef]
- Wu, X.; Zhu, X.; Wu, G.; Ding, W. Data mining with big data. IEEE Trans. Knowl. Data Eng. 2014, 26, 97–107. [Google Scholar] [CrossRef]
- Hasanin, T.; Khoshgoftaar, T.M.; Leevy, J.; Seliya, N. Investigating Random Undersampling and Feature Selection on Bioinformatics Big Data. In Proceedings of the 2019 IEEE Fifth International Conference on Big Data Computing Service and Applications (BigDataService), Newark, CA, USA, 4–9 April 2019; pp. 346–356. [Google Scholar] [CrossRef]
- Jäntschi, L.; Sestras, R.E. Local Using of Integrated Taxonomic Information System (ITIS). Bull. Univ. Agric. Sci. Vet. Med. Cluj-Napoca Hortic. 2011, 68, 62–67. [Google Scholar] [CrossRef]
- Benson, D.A.; Clark, K.; Karsch-Mizrachi, I.; Lipman, D.J.; Ostell, J.; Sayers, E.W. GenBank. Nucleic Acids Res. 2015, 43, D30–D35. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Arctos Database. Available online: https://arctos.database.museum/SpecimenSearch.cfm (accessed on 1 August 2020).
- CalPhotos: Plants Database. Available online: https://calphotos.berkeley.edu/flora/ (accessed on 5 May 2020).
- Encyclopedia of Life. Available online: https://eol.org/ (accessed on 5 May 2020).
- Global Biotic Interactions. Available online: https://www.globalbioticinteractions.org/ (accessed on 10 May 2020).
- Plants USDA. Available online: https://plants.sc.egov.usda.gov/java/ (accessed on 10 May 2020).
- Plants of de World Online. Available online: http://www.plantsoftheworldonline.org/ (accessed on 10 May 2020).
- International Plant Name Index. Available online: https://www.ipni.org/ (accessed on 10 May 2020).
- TreeBase. Available online: https://www.treebase.org/ (accessed on 10 May 2020).
- World Register of Marine Species. Available online: http://www.marinespecies.org/ (accessed on 11 May 2020).
- Plants of the Americas. Available online: http://www.tropicos.org/Project/VPA (accessed on 11 May 2020).
- iPhylo. Available online: http://iphylo.org/linkout/Main_Page (accessed on 11 May 2020).
- The Plant List. Available online: http://www.theplantlist.org/ (accessed on 3 February 2021).
- World Flora Online. Available online: http://www.worldfloraonline.org/ (accessed on 3 February 2021).
- Global Biodiversity Information Facility—GBIF. Available online: https://www.gbif.org/ (accessed on 3 February 2021).
- Jiang, W.; Ji, C.; Zhu, H. Fractal Study on Plant Classification and Identification. In Proceedings of the 2009 International Workshop on Chaos-Fractals Theories and Applications, Shenyang, China, 6–8 November 2009; pp. 434–438. [Google Scholar] [CrossRef]
- Gopal, A.; Reddy, S.P.; Gayatri, V. Classification of selected medicinal plants leaf using image processing. In Proceedings of the 2012 International Conference on Machine Vision and Image Processing (MVIP), Coimbatore, India, 14–15 December 2012; pp. 5–8. [Google Scholar] [CrossRef]
- Pooja, V.; Das, R.; Kanchana, V. Identification of plant leaf diseases using image processing techniques. In Proceedings of the 2017 IEEE Technological Innovations in ICT for Agriculture and Rural Development (TIAR), Chennai, India, 7–8 April 2017; pp. 130–133. [Google Scholar] [CrossRef]
- Sathwik, T.; Yasaswini, R.; Venkatesh, R.; Gopal, A. Classsification of selected medicinal plant leaves using texture analysis. In Proceedings of the 2013 Fourth International Conference on Computing, Communications and Networking Technologies (ICCCNT), Tiruchengode, India, 4–6 July 2013; pp. 1–6. [Google Scholar] [CrossRef]
- Leff, A.; Rayfield, J.T. Web-application development using the Model/View/Controller design pattern. In Proceedings of the Fifth IEEE International Enterprise Distributed Object Computing Conference, Seattle, WA, USA, 4–7 September 2001; pp. 118–127. [Google Scholar] [CrossRef]
- Felideo, M.V.C. Framework. Available online: https://github.com/felideo/FelideoMVC (accessed on 26 August 2020).
- FelideoTrine Model. Available online: https://github.com/felideo/FelideoTrine (accessed on 26 August 2020).
No | Name | Species | Functions | Tools | Catalog | DB Portable | Platform | References |
---|---|---|---|---|---|---|---|---|
01 | ITIS | Plants, animals, fungi, and microbes. | Taxonomic classification | Not | Text/Alphabetical | Yes | Web | [7] |
02 | GenBank | Humans, animals, sequences. | Genome, analysis, diseases, sequences. | Blast/Primers | Text/Alphabetical | Not | Web | [8] |
03 | ARCTOS database | Various animal species | Taxonomic classification | Linked to Genbank | Text and Sequences | Not | Web | [9] |
04 | CalPhotos: Plants | Plants | Image Repository | Not | Image | Not | Web | [10] |
05 | Encyclope-dia of life | Various animal species, plants | Online encyclopedia | Not | Text/Image | Not | Web | [11] |
06 | Global biotic Interactions | Various bodies | Species interaction | Search in other databases | Text | Not | Web | [12] |
07 | Plants USDA | Plants | Plants Database | Classification | Text | Not | Web | [13] |
08 | Plants of the world online | Plants | Information (description and location) | Not | Text | Not | Web | [14] |
09 | International Plant Name Index | Plants | Search (classification and location) | Search in other databases | Text | Not | Web | [15] |
10 | TreeBase | Plants | Repository of phylogenetic information | Not | Text | Not | Web | [16] |
11 | World register of marine species | Marine species | Repository of marine organisms | Not | Text/Image | Not | Web | [17] |
12 | Vascular Plants of the Americas | Native species/America | Repository/Classification/Searches | Not | Text/Image | Not | Web | [18] |
13 | iPhylo | Plants | NCBI taxonomy repository | Not | Text | Not | Web | [19] |
14 | World Flora Online | Plants | Plants Database | Not | Text/Image | Not | Web | [20] |
15 | GBIF | Biodiversity in Plants and Animals | Biodiversity Database | Yes | Text/Image | Not | Web | [21] |
16 | The Plant List | Plants | Plants Database | Not | Text/Image | Not | Web | [22] |
Name | Functions | Method | Description | Technic/Technology | Platform | Operational |
---|---|---|---|---|---|---|
[23] | Classification | Pixel-covering method | Calculate the fractal dimension of leaves from 102 plant species. | Image Processing | Not specified | No |
[24] | Identification | Learning algorithms | Processing with images of plant leaves as a basis of classification. | Image Processing–Deep Learning | Not specified | No |
[25] | Identification of diseases | SVM Classifiers | Conventional processing–region of interest–extraction–classification vectors. | Image Processing–Machine Learning | Not specified | No |
[26] | Identification and classification | Texture analysis/approximation | The software identifies and returns the closest match of the query image from the database based on its texture features. | Image Processing | Matlab | No |
FelideoTrine | MySQL |
---|---|
$query->select(‘ hhh.*, rel_pop_name.id_nome_popular, popular.nome, geografica.latitude, geografica.longitude, rel_imagem.id_arquivo, imagem.hash, imagem.nome, imagem.endereco, imagem.extensao, rel_trabalho.id, rel_trabalho.id_organismo, rel_trabalho.id_trabalho, rel_trabalho.ativo, trabalho_arquivo.hash, trabalho_arquivo.nome, trabalho_arquivo.endereco, trabalho_arquivo.extensao, ‘) ->from(‘organismo hhh’) ->leftJoin(‘organismo_relaciona_nome_popular rel_pop_name ON rel_pop_name.id_organismo = hhh.id AND rel_pop_name.ativo = 1′) | SELECT rel_pop_name.id_nome_popular AS rel_pop_name__id_nome_popular, popular.nome AS popular__nome, geografica.latitude AS geografica__latitude, geografica.longitude AS geografica__longitude, rel_imagem.id_arquivo AS rel_imagem__id_arquivo, imagem.hash AS imagem__hash, imagem.nome AS imagem__nome, imagem.endereco AS imagem__endereco, imagem.extensao AS imagem__extensao, rel_trabalho.id AS rel_trabalho__id, rel_trabalho.id_organismo AS rel_trabalho__id_organismo, rel_trabalho.id_trabalho AS rel_trabalho__id_trabalho, rel_trabalho.ativo AS rel_trabalho__ativo, trabalho_arquivo.hash AS trabalho_arquivo__hash, trabalho_arquivo.nome AS trabalho_arquivo__nome, trabalho_arquivo.endereco AS trabalho_arquivo__endereco, trabalho_arquivo.extensao AS trabalho_arquivo__extensao FROM organismo hhh LEFT JOIN organismo_relaciona_nome_popular rel_pop_name ON rel_pop_name.id_organismo = hhh.id AND rel_pop_name.ativo = 1 |
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Beingolea, J.R.; Ramos-Pires, D.; Rendulich, J.; Zegarra, M.; Borja-Murillo, J.; da Fonseca, S.A.S. LeafLive-DB: Classification and Data Storage of Botanical Studies. Data 2021, 6, 29. https://doi.org/10.3390/data6030029
Beingolea JR, Ramos-Pires D, Rendulich J, Zegarra M, Borja-Murillo J, da Fonseca SAS. LeafLive-DB: Classification and Data Storage of Botanical Studies. Data. 2021; 6(3):29. https://doi.org/10.3390/data6030029
Chicago/Turabian StyleBeingolea, Jorge Rodolfo, Diego Ramos-Pires, Jorge Rendulich, Milagros Zegarra, Juan Borja-Murillo, and Simone A. Siqueira da Fonseca. 2021. "LeafLive-DB: Classification and Data Storage of Botanical Studies" Data 6, no. 3: 29. https://doi.org/10.3390/data6030029