Wikidata

Veen, Theo van

doi:10.6017/ital.v38i2.10886

Cited by 24 publications

(11 citation statements)

References 1 publication

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“…ZINC000034518176, similar to α-amyrin, is a chemical constituent of Vernonanthura chamaedrys [ 187 , 188 ], Mangifera indica [ 189 ], Cadia purpurea [ 190 ], Calendula officinalis [ 191 ], Pinalia leucantha [ 192 ], Ilex aquifolium [ 193 ], I. goshiensis [ 194 ], and Rhodomyrtus tomentosa [ 195 ] according to Wikidata ( (accessed on 15 March 2023)) [ 196 , 197 ]. The organic extract of dried flowers from Calendula officinalis exhibits anti-HIV-1 replication properties and is non-toxic to human lymphocytic Molt-4 cells [ 198 ].…”

Section: Resultsmentioning

confidence: 99%

Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors

Broni

Ashley

Adams

et al. 2023

IJMS

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The Ebola virus (EBOV) is still highly infectious and causes severe hemorrhagic fevers in primates. However, there are no regulatorily approved drugs against the Ebola virus disease (EVD). The highly virulent and lethal nature of EVD highlights the need to develop therapeutic agents. Viral protein 40 kDa (VP40), the most abundantly expressed protein during infection, coordinates the assembly, budding, and release of viral particles into the host cell. It also regulates viral transcription and RNA replication. This study sought to identify small molecules that could potentially inhibit the VP40 protein by targeting the N-terminal domain using an in silico approach. The statistical quality of AutoDock Vina’s capacity to discriminate between inhibitors and decoys was determined, and an area under the curve of the receiver operating characteristic (AUC-ROC) curve of 0.791 was obtained. A total of 29,519 natural-product-derived compounds from Chinese and African sources as well as 2738 approved drugs were successfully screened against VP40. Using a threshold of −8 kcal/mol, a total of 7, 11, 163, and 30 compounds from the AfroDb, Northern African Natural Products Database (NANPDB), traditional Chinese medicine (TCM), and approved drugs libraries, respectively, were obtained after molecular docking. A biological activity prediction of the lead compounds suggested their potential antiviral properties. In addition, random-forest- and support-vector-machine-based algorithms predicted the compounds to be anti-Ebola with IC50 values in the micromolar range (less than 25 μM). A total of 42 natural-product-derived compounds were identified as potential EBOV inhibitors with desirable ADMET profiles, comprising 1, 2, and 39 compounds from NANPDB (2-hydroxyseneganolide), AfroDb (ZINC000034518176 and ZINC000095485942), and TCM, respectively. A total of 23 approved drugs, including doramectin, glecaprevir, velpatasvir, ledipasvir, avermectin B1, nafarelin acetate, danoprevir, eltrombopag, lanatoside C, and glycyrrhizin, among others, were also predicted to have potential anti-EBOV activity and can be further explored so that they may be repurposed for EVD treatment. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area calculations corroborated the stability and good binding affinities of the complexes (−46.97 to −118.9 kJ/mol). The potential lead compounds may have the potential to be developed as anti-EBOV drugs after experimental testing.

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Section: Resultsmentioning

confidence: 99%

Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors

Broni

Ashley

Adams

et al. 2023

IJMS

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“…In order to enrich the ontology, the authors search Wikidata by using ontology class names and then match the results with concepts previously identified thanks to WordNet. More recently, van Veen and colleagues have emphasized the transition from a world made of multiple local identifiers to a world in which the unique knowledge base identifier is provided by Wikidata [34].…”

Section: Related Workmentioning

confidence: 99%

Wikidata Support in the Creation of Rich Semantic Metadata for Historical Archives

et al. 2021

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The research question this paper aims at answering is the following: In an ontology-driven annotation system, can the information extracted from external resources (namely, Wikidata) provide users with useful suggestions in the characterization of entities used for the annotation of documents from historical archives? The context of the research is the PRiSMHA project, in which the main goal is the development of a proof-of-concept prototype ontology-driven system for semantic metadata generation. The assumption behind this effort is that an effective access to historical archives needs a rich semantic knowledge, relying on a domain ontology, that describes the content of archival resources. In the paper, we present a new feature of the annotation system: when characterizing a new entity (e.g., a person), some properties describing it are automatically pre-filled in, and more complex semantic representations (e.g., events the entity is involved in) are suggested; both kinds of suggestions are based on information retrieved from Wikidata. In the paper, we describe the automatic algorithm devised to support the definition of the mappings between the Wikidata semantic model and the PRiSMHA ontology, as well as the process used to extract information from Wikidata and to generate suggestions based on the defined mappings. Finally, we discuss the results of a qualitative evaluation of the suggestions, which provides a positive answer to the initial research question and indicates possible improvements.

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“…can also be added to the Wikidata item. Wikidata items are being decorated with an increasing number of diverse identifiers, hence Wikidata is increasingly playing a role as an "identity broker" enabling cross-links between identifiers from different databases (Veen, 2019).…”

Section: Bibliographic Data In Wikidatamentioning

confidence: 99%

Wikidata and the bibliography of life

Page

2021

Preprint

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Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source - indeed sometimes the only source - of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the “bibliography of life”). This paper argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs (“bots”) adding, editing, and curating that information. The paper also describes a tool to visualise and explore bibliography information in Wikidata and how it links to both taxa and taxonomists.

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Wikidata

Cited by 24 publications

References 1 publication

Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors

Cheminformatics-Based Study Identifies Potential Ebola VP40 Inhibitors

Wikidata Support in the Creation of Rich Semantic Metadata for Historical Archives

Wikidata and the bibliography of life

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