A protocol for adding knowledge to Wikidata, a case report

@article{Waagmeester2020APF,
  title={A protocol for adding knowledge to Wikidata, a case report},
  author={Andra Waagmeester and Egon Willighagen and Andrew I. Su and Martina Kutmon and Jose Emilio Labra Gayo and Daniel Fern{\'a}ndez-{\'A}lvarez and Quentin J. Groom and Peter J. Schaap and Lisa M. Verhagen and Jasper J. Koehorst},
  journal={bioRxiv},
  year={2020}
}
Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons”. Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases However, Wikidata may not… 

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References

SHOWING 1-10 OF 55 REFERENCES

Wikidata as a knowledge graph for the life sciences

The breadth and depth of the biomedical knowledge contained within Wikidata is described, and the open-source tools built to add information toWikidata and to synchronize it with source databases are discussed.

Reifying RDF: What Works Well With Wikidata?

This paper compares various options for reifying RDF triples, and generates the four RDF datasets pertaining to each model and discusses high-level aspects relating to data sizes, etc.

Wikidata as a semantic framework for the Gene Wiki initiative

This project created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data that enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web.

Introducing Wikidata to the Linked Data Web

New RDF exports that connect Wikidata to the Linked Data Web are introduced and several partial exports are introduced that provide more selective or simplified views on the data.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Various semantic web resources were combined with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API, to highlight the utility of integrating Wiki pathways in the semantic web.

Getting the Most Out of Wikidata: Semantic Technology Usage in Wikipedia's Knowledge Graph

A live SPARQL endpoint, regular RDF dumps, and linked data APIs are now forming the backbone of many uses of Wikidata, and the underlying infrastructure is described and analysed.

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

There is a doubling of the number of annotated metabolite nodes in WikiPathways and an OpenAPI documentation of the authors' web services and the FAIR annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data.

Inference of Latent Shape Expressions Associated to DBpedia Ontology

A prototype which is able to infer shapes of classes in a knowledge graph and used it with classes of DBpedia ontology is developed and serialize the results using ShEx.

The Pfam protein families database in 2019

A significant comparison to the structural classification database that led to the creation of 825 new families based on their set of uncharacterized families (EUFs) was carried out and Pfam entries were connected to the Sequence Ontology (SO) through mapping of the Pfam type definitions to SO terms.

BioGPS and MyGene.info: organizing online, gene-centric information

This article describes updates to BioGPS made after its initial release in 2008, and summarizes recent additions of features and data, as well as the robust user activity that underlies this community intelligence application.
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