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The e-Flora of South Africa – restructuring data to comply with Darwin Core standards for inclusion into the World Flora Online

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Fhatani Ranwashe
Fhatani Ranwashe
Fhatani Ranwashe
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Margaretha Marianne Le Roux at South African National Biodiversity Institute
Margaretha Marianne Le Roux
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Abstract

The e-Flora of South Africa project was initiated in 2013 by the South African National Biodiversity Institute (SANBI) in support of the Global Strategy for Plant Conservation (GSPC, 2011-2020). South Africa's flora consists of ca. 21,000 taxa of which more than half are endemic. South Africa will contribute a national Flora towards Target 1 of the GSPC ("To create an online flora of all known plants by 2020"). South Africa's contribution is ca. 6% of the world’s flora of which ca. 3% are endemic and therefore unique. South Africa’s electronic Flora is comprised of previously published descriptions. South Africa’s e-Flora data forms part of the Botanical Dataset of Southern Africa (BODATSA) that is currently managed through the Botanical Research And Herbarium Management System (BRAHMS). To date, South Africa’s e-Flora data (http://ipt.sanbi.org.za/iptsanbi/resource?r=flora_descriptions) represents 19,539 indigenous taxa, 79,139 descriptions of distribution, morphological, habitat and diagnostic data, and 27,799 bibliographic records. The e-Flora data was recently published online using the Integrated Publishing Toolkit and henceforth harvested by the World Flora Online (WFO) into the portal. A series of challenges were encountered while manipulating descriptive data from BRAHMS to be ingested by the WFO portal; from taxonomic issues to data quality issues not excluding compliance to data standards. To contribute to the WFO portal, the taxa in BODATSA has to match with the taxa in the WFO taxonomic backbone. Once there is a match, a unique WFO taxon identifier is assigned to the taxa in BODATSA. This process presented various challenges because the WFO taxonomic backbone and the taxonomic classification system that is used by South Africa (South African National Plant Checklist) does not fully correlate. The schema used to store taxonomic data also does not agree between BRAHMS and WFO and had to be addressed. To enable consistency for future, a detailed guideline document was created providing all the steps and actions that should be taken when publishing an e-Flora, managed in BRAHMS, to the WFO portal. The presentation will focus on matching taxonomic classifications between BRAHMS and WFO; dealing with character encoding issues and manipulating data to meet Darwin Core standards.
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Biodiversity Information Science and Standards 3: e35191
doi: 10.3897/biss.3.35191
Conference Abstract
The e-Flora of South Africa – restructuring data to
comply with Darwin Core standards for inclusion
into the World Flora Online
Fhatani Ranwashe , Marianne Le Roux
‡ South African National Biodiversity Institute, Cape Town, South Africa
§ South African National Biodiversity Institute, Pretoria, South Africa
| Department of Botany and Plant Biotechnology, University of Johannesburg, Johannesburg, South Africa
Corresponding author: Fhatani Ranwashe (f.ranwashe@sanbi.org.za), Marianne Le Roux (m.leroux@sanbi.org.za)
Received: 05 Apr 2019 | Published: 17 Sep 2019
Citation: Ranwashe F, Le Roux M (2019) The e-Flora of South Africa – restructuring data to comply with Darwin
Core standards for inclusion into the World Flora Online. Biodiversity Information Science and Standards 3: e35191.
https://doi.org/10.3897/biss.3.35191
Abstract
The e-Flora of South Africa project was initiated in 2013 by the South African National
Biodiversity Institute (SANBI) in support of the Global Strategy for Plant Conservation
(GSPC, 2011-2020). South Africa's flora consists of ca. 21,000 taxa of which more than
half are endemic. South Africa will contribute a national Flora towards Target 1 of the
GSPC ("To create an online flora of all known plants by 2020"). South Africa's contribution
is ca. 6% of the world’s flora of which ca. 3% are endemic and therefore unique. South
Africa’s electronic Flora is comprised of previously published descriptions.
South Africa’s e-Flora data forms part of the Botanical Dataset of Southern Africa
(BODATSA) that is currently managed through the Botanical Research And Herbarium
Management System (BRAHMS). To date, South Africa’s e-Flora data (http://
ipt.sanbi.org.za/iptsanbi/resource?r=flora_descriptions) represents 19,539 indigenous taxa,
79,139 descriptions of distribution, morphological, habitat and diagnostic data, and 27,799
bibliographic records. The e-Flora data was recently published online using the Integrated
Publishing Toolkit and henceforth harvested by the World Flora Online (WFO) into the
portal.
‡ §,|
© Ranwashe F, Le Roux M. This is an open access article distributed under the terms of the Creative Commons Attribution
License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author
and source are credited.
A series of challenges were encountered while manipulating descriptive data from
BRAHMS to be ingested by the WFO portal; from taxonomic issues to data quality issues
not excluding compliance to data standards.
To contribute to the WFO portal, the taxa in BODATSA has to match with the taxa in the
WFO taxonomic backbone. Once there is a match, a unique WFO taxon identifier is
assigned to the taxa in BODATSA. This process presented various challenges because the
WFO taxonomic backbone and the taxonomic classification system that is used by South
Africa (South African National Plant Checklist) does not fully correlate. The schema used to
store taxonomic data also does not agree between BRAHMS and WFO and had to be
addressed.
To enable consistency for future, a detailed guideline document was created providing all
the steps and actions that should be taken when publishing an e-Flora, managed in
BRAHMS, to the WFO portal. The presentation will focus on matching taxonomic
classifications between BRAHMS and WFO; dealing with character encoding issues and
manipulating data to meet Darwin Core standards.
Keywords
Flora; Darwin Core; e-Flora; Biodiversity Informatics; Data standards; World Flora Online;
WFO
Presenting author
Fhatani Ranwashe
Hosting institution
South African National Biodiversity Institute
Conflicts of interest
None
2Ranwashe F, Le Roux M
... It has also been reported in South Africa. P. hadiensis can grow 10-150 cm high [41,44,45]. Local names in Uganda are as follows: Luganda: mukikimbo [14] and Lusoga: kiraga and kigalama [41]. ...
A Bibliographic Assessment Using the Degrees of Publication Method: Medicinal Plants from the Rural Greater Mpigi Region (Uganda)
Article
Full-text available
  • Jan 2021
  • EVID-BASED COMPL ALT
In ethnopharmacological research, many field assessment tools exist. Yet, these miss that critical point of how to really determine which species merit the costly lab studies, e.g., evaluation of traditional use via pharmacological assays and isolation of bioactive secondary metabolites. This gap can be filled with the introduction of a new tool for literature assessment: the Degrees of Publication (DoPs). In this study, its application is illustrated through an extensive bibliographic assessment of 16 medicinal plant species that were recently identified in the Greater Mpigi region of Uganda as being frequently used by local traditional healers in the treatment of medical disorders (namely, Albizia coriaria, Cassine buchananii, Combretum molle, Erythrina abyssinica, Ficus saussureana, Harungana madagascariensis, Leucas calostachys, Microgramma lycopodioides, Morella kandtiana, Plectranthus hadiensis, Securidaca longipedunculata, Sesamum calycinum subsp. angustifolium, Solanum aculeastrum, Toddalia asiatica, Warburgia ugandensis, and Zanthoxylum chalybeum). These species are suspected to be understudied, and a thorough bibliographic assessment has not been previously performed. Thus, the objectives of our study were to undertake a comparative assessment of the degree to which each of these plant species has been studied in the past, including evaluation of the quality of the journals where results were published in. The determination of the DoPs enabled successful assessment of the degrees to which each individual plant species has been studied so far, while also taking into account the methodological “research chain of ethnopharmacology” from ethnobotanical studies (“traditional use”) to pharmacological assays (“bioactivity”) and finally to pharmacognostic research (“structure elucidation”). The significance of a research paper was assessed by determining whether its journal and publishing house were members of the Committee on Publication Ethics (COPE). In total, 634 peer-reviewed publications were reviewed covering the period of 1960–2019, 53.3% of which were published in journals and by publishing houses affiliated with COPE (338 publications). The literature assessment resulted in the identification of understudied plants among the selected species. The majority of plants reviewed have not been sufficiently studied; six species were classified as being highly understudied and three more as being understudied: C. buchananii, F. saussureana, L. calostachys, M. lycopodioides, M. kandtiana, and S. calycinum subsp. angustifolium and A. coriaria, P. hadiensis, and S. aculeastrum, respectively. The newly introduced DoPs are a useful tool for the selection of traditionally used species for future laboratory studies, especially for pharmacological bioassays, isolation procedures, and drug discovery strategies. 1. Introduction Throughout human history and across the globe, plants were regarded as the major source of medicine and natural remedies. Traditional medicine is defined by the World Health Organization (WHO) as “the knowledge, skills, and practices based on the theories, beliefs, and experiences indigenous to different cultures, used in the maintenance of health and in the prevention, diagnosis, and improvement or treatment of physical and mental illness” [1]. In the developing world, over 80% of the population still rely on traditional herbal medicines for their day-to-day healthcare needs [2–4]. This is largely attributed to their ease of access, affordability, perceived fewer side effects, and cultural appropriateness, among other reasons [5]. Despite the general loss of cultural practices worldwide [6, 7], traditional medicine practices and medicinal plant use are still the predominant form of healthcare services in East and Central Africa today [8, 9]. The global importance of plants as a source of medicine is also often emphasized by scientists worldwide [10–14]. Around 25% of the Western drugs prescribed contain active ingredients that were initially isolated as natural products from plants [10]. Still, the majority of Earth’s plant species has never been screened for pharmacological effects in a research facility [10, 15]. In consideration of this global importance, there are many assessment tools applied when reporting field studies in the science of ethnopharmacology. These include field assessment indices for medicinally used species, such as the frequency of citation, use value, informant consensus factor, and fidelity level, among others. However, none of these take into account how to really determine which species merit the costly lab studies. This is why we introduce the Degrees of Publication (DoPs), providing a standardized way to examine how well studied individual species are (or are not) in an ethnopharmacological context. In this study, 16 medicinal plant species from the Greater Mpigi region were selected to illustrate how the new tool works. Situated in West-Central Uganda, the tropical Greater Mpigi region displays a high abundance of traditional medicine practitioners and diverse use of a vast amount of medicinal plant species [14, 16, 17]. Consequently, local people are still highly dependent on these traditional healers and their medicinal plants in order to secure their primary health care. A recently published ethnobotanical survey from the Greater Mpigi region [14] and an ethnopharmacological study [18] identified 16 medicinal plant species that are often used in the treatment of medical disorders in the local traditional medicine system while displaying high pharmacological activity in our ongoing in vitro evaluation in a lab setting. A preliminary literature review resulted in a few results. Therefore, these 16 plants are suspected to be understudied species, and a thorough literature review using the new DoP method for bibliographic assessment enables the selection of traditionally used species for pharmacological bioassays and drug discovery strategies. Our study, therefore, aims to undertake a comparative literature assessment, applying the DoP method, regarding (a) other reports of these species, (b) the quality of the journals where results were published in (assessment of international standards and best practice in scholarly publication ethics), and (c) the degree to which each plant species has been studied thus far. 2. Materials and Methods 2.1. Study Objects Our study objects are 16 tropical plant species identified to be frequently used by Ugandan traditional healers in treatment of diverse medical disorders in the Greater Mpigi region. This choice of species can be considered taxonomically diverse, representing 13 different plant families. Table 1 lists these species, stating their scientific names, local names at the study site (Luganda language), their plant families, and their Relative Frequencies of Citation (RFC), calculated from absolute values of the ethnobotanical survey (n = 39) previously published by Schultz et al. [14]. Botanical name Local name (Luganda language) Family RFC (%) Albizia coriaria Oliv. Mugavu Fabaceae 100.0 Cassine buchananii Loes. Mbaluka Celastraceae 61.5 Combretum molle R.Br. ex G.Don Ndagi Combretaceae 89.7 Erythrina abyssinica DC. Jjirikiti Fabaceae 100.0 Ficus saussureana DC. Muwo Moraceae 94.9 Harungana madagascariensis Lam. ex Poir. Mukabiiransiko Hypericaceae 97.4 Leucas calostachys Oliv. Kakuba musulo Lamiaceae 43.6 Microgramma lycopodioides (L.) Copel. Kukumba Polypodiaceae 43.6 Morella kandtiana (Engl.) Verdc. & Polhill Mukikimbo Myricaceae 87.2 Plectranthus hadiensis (Forssk.) Schweinf. ex Sprenger Kibwankulata Lamiaceae 97.4 Securidaca longipedunculata Fresen. Mukondwe Polygalaceae 38.5 Sesamum calycinum subsp. angustifolium (Oliv.) Ihlenf. & Seidenst. Lutungotungo Pedaliaceae 87.2 Solanum aculeastrum Dunal Kitengo Solanaceae 71.8 Toddalia asiatica (L.) Lam. Kawule Rutaceae 97.4 Warburgia ugandensis Sprague Abasi Canellaceae 92.3 Zanthoxylum chalybeum Engl. Ntaleyaddungu Rutaceae 46.2
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... -The dataset is composed of the South African National Plant Checklist (SANPC), which currently includes 23,170 taxa (SANPC, 2019), and the Botanical Database of Southern Africa (BODATSA; SANBI, 2016), which contains data related to collections in southern Africa, published floristic data and related bibliographic references and is commonly known as the e-Flora of South Africa (Le Roux & al., 2017). The floristic information was ingested into WFO following a restructuring step (Ranwashe & Le Roux, 2019) to meet the DwC-A standard through the Integrated Publishing Toolkit of GBIF (Robertson & al., 2014). ...
World Flora Online: Placing taxonomists at the heart of a definitive and comprehensive global resource on the world's plants
Article
Full-text available
  • Nov 2020
It is time to synthesize the knowledge that has been generated through more than 260 years of botanical exploration, taxonomic and, more recently, phylogenetic research throughout the world. The adoption of an updated Global Strategy for Plant Conservation (GSPC) in 2011 provided the essential impetus for the development of the World Flora Online (WFO) project. The project represents an international, coordinated effort by the botanical community to achieve GSPC Target 1, an electronic Flora of all plants. It will be a first‐ever unique and authoritative global source of information on the world's plant diversity, compiled, curated, moderated and updated by an expert and specialist‐based community (Taxonomic Expert Networks – “TENs” – covering a taxonomic group such as family or order) and actively managed by those who have compiled and contributed the data it includes. Full credit and acknowledgement will be given to the original sources, allowing users to refer back to the primary data. A strength of the project is that it is led and endorsed by a global consortium of more than 40 leading botanical institutions worldwide. A first milestone for producing the World Flora Online is to be accomplished by the end of 2020, but the WFO Consortium is committed to continuing the WFO programme beyond 2020 when it will develop its full impact as the authoritative source of information on the world's plant biodiversity.
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SACHA: an interactive identification key of Southern African CHArcoals for anthracological research
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Since the 1980s, the field of anthracology has continued to expand in Southern Africa to study the interaction between past human societies and their environments, including plant resources and forest management from prehistoric times. To answer such questions, the need for comparative wood anatomy analyses of the local taxa is of particular relevance in this rich species environment to perform rigorous taxonomic identification. This paper introduces the first computer-assisted identification tool specifically designed for the analysis of archaeological charcoals from Southern Africa. This online database, called SACHA for Southern African CHArcoals, is accessible via the following link: https://sacha.identificationkey.org/ . It currently includes anatomical descriptions, as well as ecological and ethnobotanical information for 68 taxa of modern specimens collected in the Savanna Biome. An identification key is available on the Xper ³ online platform, which is designed for descriptive data management and interactive identification. This article presents a survey of the existing reference collections on Southern African woods and charcoals and proposes an overview of the development of computerised tools for systematic wood descriptions and identification keys. The SACHA database can be easily updated and enriched without requiring computer science skills. Furthermore, it can serve as a training tool for beginners in wood anatomy. The database offers an online interactive key option, a fact sheet catalogue, and conventional dichotomous and tabular keys for offline or printed versions. These functions are facilitated by the various export formats that are available in the database.
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