Wikidata: A large-scale collaborative ontological medical database

Abstract

is a flexible biomedical semantic knowledge-base  It has the potential to perform a much better role as a large-scale biomedical semantic resource  Tools are available to query, enrich, verify and process the biomedical knowledge Abstract: Created in October 2012, Wikidata is a large-scale, human-readable, machine-readable, multilingual, multidisciplinary, centralized, editable, structured, and linked knowledge-base with an increasing diversity of use cases. Here, we raise awareness of the potential use of Wikidata as a useful resource for biomedical data integration and semantic interoperability between biomedical computer systems. We show the data model and characteristics of Wikidata and explain how this database can be automatically processed by users as well as by computer methods and programs. Then, we give an overview of the medical entities and relations provided by the database and how they can be useful for various medical purposes such as clinical decision support

Standardised Data on Initiatives – STARDIT: Beta Version

“…STARDIT is the first system that enables sharing of standardised data about initiatives across disciplines. By using Wikidata, STARDIT will make use of existing infrastructure capable of co-defining types of data in multiple languages 37,84,85 . It is important to note that access to Wikidata is actively blocked by governments or internet service providers in some countries.…”

“…The terms used in this paper are working terms, which will be progressively standardised over the lifetime of the project. The current Beta Version of STARDIT maps terms and concepts using the Wikidata initiative (part of the Wikimedia Foundation) 36 , which includes definitions (taxonomy), a way of describing relationships between concepts (ontology) 37 , and a system to translate definitions and ontology between many languages. Examples of existing taxonomies include the National Library of Medicine's Medical Subject Headings (MeSH), which are used extensively in multiple kinds of literature reviews 38 .…”

Wikidata as a FAIR knowledge graph for the life sciences

“…Wikidata also 9 became the first Wikimedia project that surpassed one billion edits, achieved by its community of 20 10 thousand active users and 80 active computational 'bots'. Since its inception in 2012, Wikidata has a 11 proven track record for leveraging the crowdsourced efforts of engaged users in building a massive 12 knowledge graph [8]. Wikidata is run by the Wikimedia Foundation (https://wikimediafoundation.org), an 13 organization that has a long track record of developing and maintaining web applications at scale.…”

“…23 24 In previous work, we seeded Wikidata with content from public and authoritative resources on 25 structured knowledge on genes and proteins [10] and chemical compounds [11]. Here, we describe 26 progress on expanding and enriching the biomedical knowledge graph within Wikidata, both by our 27 team and by others in the community [12]. We also describe several representative use cases on how 28…”

“…We then coded each bot to 9 perform data retrieval from a primary resource, data transformation and normalization, and then data 10 upload via the Wikidata application programming interface (API). 11 12 We generalized the common code modules into a Python library, called Wikidata Integrator (WDI), to 13 simplify the process of creating Wikidata bots [37]. Relative to accessing the API directly, WDI has 14 convenient features that improve the bot development experience.…”