scholarly journals Challenges, Solutions, and Workflows Developed for the Taxonomic Backbone of the World Flora Online.

Author(s):  
William Ulate ◽  
Sunitha Katabathuni ◽  
Alan Elliott

The World Flora Online (WFO) is the collaborative, international initiative to achieve Target 1 of the Global Strategy for Plant Conservation (GSPC): "An online flora of all known plants." WFO provides an open-access, web-based compendium of the world’s plant species, which builds upon existing knowledge and published floras, checklists and revisions but will also require the collection and generation of new information on poorly known groups and unexplored regions (Borsch et al. 2020). The construction of the WFO Taxonomic Backbone is central to the entire WFO as it determines the accessibility of additional content data and at the same time, represents a taxonomic opinion on the circumscription of those taxa. The Plant List v.1.1 (TPL 2013) was the starting point for the backbone, as this was the most comprehensive resource covering all plants available. We have since curated the higher taxonomy of the backbone, based on the following published community-derived classifications: the Angiosperm Phylogeny Group (APG IV 2016), the Pteridophyte Phylogeny Group (PPG I 2016), Bryophytes (Buck et al. 2008), and Hornworts & Liverworts (Söderström et al. 2016). The WFO presents a community-supported consensus classification with the aim of being the authoritative global source of information on the world's plant diversity. The backbone is actively curated by our Taxonomic Expert Networks (TEN), consisting of specialists of taxonomic groups, ideally at the Family or Order level. There are currently 37 approved TENs, involving more than 280 specialists, working with the WFO. There are small TENs like the Begonia Resource Center and the Meconopsis Group (with five specialists), medium TENs like Ericaceae and Zingiberaceae Resource Centers or SolanaceaSource.org (around 15 experts), and larger TENs like Caryophyllales.org and the Legume Phylogeny Working Group, with more than 80 specialists involved. When we do not have taxonomic oversight, the World Checklist of Vascular Plants (WCVP 2019) has been used to update those families from the TPL 2013 classification. Full credit and acknowledgement given to the original sources is a key requirement of this collaborative project, allowing users to refer to the primary data. For example, an association with the original content is kept through the local identifiers used by the taxonomic content providers as a link to their own resources. A key requirement for the WFO Taxonomic Backbone is that every name should have a globally unique identifier that is maintained, ideally forever. After considering several options, the WFO Technology Working Group recommended that the WFO Council establish a WFO Identifier (WFO-ID), a 10-digit number with a “wfo-” prefix, aimed at establishing a resolvable identifier for all existing plant names, which will not only be used in the context of WFO but can be universally used to reference plant names. Management of the WFO Taxonomic Backbone has been a challenge as TPL v1.1 was derived from multiple taxonomic datasets, which led to duplication of records. For that reason, names can be excluded from the public portal by the WFO Taxonomic Working Group or the TENs, but not deleted. A WFO-ID is not deleted nor reused after it has been excluded from the WFO Taxonomic Backbone. Keeping these allows for better matching when assigning WFO-IDs to data derived from content providers. Nevertheless, this implies certain considerations for new names and duplications. New names are added to the WFO Taxonomic Backbone via nomenclators like the International Plants Name Index (IPNI, The Royal Botanic Gardens, Kew et al. 2021) for Angiosperms, and Tropicos (Missouri Botanical Garden 2021) for Bryophytes, as well as harvesting endemic and infraspecific names from Flora providers when providing descriptive content. New names are passed to the TEN to make a judgement on their taxonomic status. When TENs provide a new authoritative taxonomic list for their group, we first produce a Name Matching report to ensure no names are missed. Several issues come from managing and maintaining taxonomic lists, but the process of curating an ever-growing integrated resource leads to an increase in the challenges we face with homonyms, non-standard author abbreviations, orthographic variants and duplicate names when Name Matching. The eMonocot database application, provided by Royal Botanic Gardens, Kew, (Santarsiero et al. 2013) and subsequently adapted by the Missouri Botanical Garden to provide the underlying functionality for WFO's current toolset, has also proven itself to be a challenging component to update. In this presentation, we will share our hands-on experience, technical solutions and workflows creating and maintaining the WFO Taxonomic Backbone.

Author(s):  
William Ulate

In 2013, the World Flora Online (WFO) Consortium Council decided to use version 1.1 of the The Plant List (TPL) to initially populate the WFO taxonomic backbone. TPL is a collaboration between the Royal Botanic Gardens, Kew, Missouri Botanical Garden and other stakeholders to create a comprehensive list of Vascular plant (flowering plants, conifers, ferns and their allies) and of Bryophytes (mosses and liverworts). By combining multiple checklist held by these institutions, TPL 1.1 contained 1,064,035 scientific plant names of species rank, 350,699 of which were accepted species names. TPL provides the Accepted Latin names linked to Synonyms by which that species has been known. It also includes Unresolved names for which the contributing data sources did not contain sufficient evidence to decide whether they were Accepted or Synonyms. Fortunately, TPL keeps track of the provenance of names and links back to the International Plant Names Index (IPNI) repository. This provenance trace has proven crucial when giving proper credit, as well as implementing a reliable curating process in WFO that supports the incorporation of potential new content, updates and further improvements contributed by the source. We will see some examples in WFO where duplication of names is originated from combining different providers and different sources, but also cases where duplication was caused within the same provider and even within a single source. The WFO Council also decided to adopt the software used by eMonocot.org to display and harvest the information of plants. This decision made it possible to take advantage of the efforts previously done by the Monocots group in using already defined standards and existing tools to create and validate the input files harvested. Unfortunately, no technical documentation nor support was available for the eMonocot software and adapting the software code was not an option then. Therefore, a process of reverse engineering was implemented to determine what input was expected, which harvested values were actually stored in the database and what impact, if any, they could have on the Portal function. For example, the eMonocot software always harvests content under a particular hierarchy where an authority, in this case corresponding to a family taxon, holds ownership of the taxa underneath. We will explain how this may become an issue when incorporating new endemic taxa. To ensure a convenient quality control, processes of validation and data curation were implemented. WFO assigns a unique ID to each name in its taxonomic backbone. The guarantee of uniqueness and permanence of such IDs is essential to support a process of cumulative improvement. To obtain this ID, a tool that matches Names was developed, allowing providers to contribute revisions to the taxonomy and descriptive content associated to a taxon. The origin of changes needs to be considered when tracing and correcting errors, implementing modifications or rolling back them later. A report about the result of requested changes in the taxonomy needs to be approved by the provider before any actual change is implemented in the taxonomic backbone. Programmatically, any process that performs quality assessment or makes data modifications must be implemented as parameterized algorithms to allow replication of the process whenever new or updated data is available from the source. Single-use scripts are quick but not very scalable. Finally, having defined a schema to use when providing content doesn’t necessarily imply that the values provided in each field are correct. Even with standardized values, the semantics associated could cause unforeseen behavior in the process implemented by the software. When possible, an additional step was required to convert harvested data from different localized vocabularies for standardized fields. Examples in Portuguese and Turkish will be given.


2020 ◽  
Vol 8 (2) ◽  
pp. 431-445
Author(s):  
Leandro do Nascimento Martinez ◽  
Francisco Lurdevanhe da Silva Rodrigues ◽  
Nairo Brilhante da Silva ◽  
Ediana Vitor dos Santos ◽  
Joana D'Arc Neves Costa

O Brasil alberga uma incontestável diversidade de plantas utilizadas com potencial medicinal para o tratamento de várias doenças, vale ressaltar que muitas espécies ainda não têm sua comprovação quanto o seu real potencial terapêutico. A partir de um levantamento etnobotânico na região de Porto Velho - Rondônia objetivou-se verificar para qual finalidade é usada as espécies das famílias Lamiaceae e Asteraceae. Para a confirmação cientifica utilizou-se as plataformas SciELO, PubMed, ScienceDirect e LILACS, foi utilizada a base de dados Internacional Plant Names Indes (IPNI), Tropicos Missouri Botanical Garden, para a confirmação dos nomes científicos atualizados. Das plantas mais citadas da família Asteraceae apenas a Acmella olarecea L. não foi encontrado nenhum estudo para problemas cardiovasculares e nem para patologias respiratórias, como os entrevistados havia indicado, seus estudos centrados para cicatrização de ulceras, a família Lamiaceae dentre as mais citadas todas confirmam a sua efetividade na literatura, entretanto o Plecanthus barbatus Andrew. Demonstrou não ser eficaz contra a malária, os estudos até o momento corroboram com a indicação popular, evidenciando a importância de aliar o conhecimento empírico com os estudos científicos.


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