Wikidata:WikiProject Elixir
WikiProject Elixir aims to connect ELIXIR-related open data on Wikidata during the BioHackathon Europe 2021 (Q109379355), 13th International SWAT4HCLS conference (Q110499790), and beyond.
ELIXIR (Q12269561) is a European research organisation that brings together databases, software tools, training materials, cloud storage and supercomputers for the life sciences (Q864928) (which includes health (Q12147), medicine (Q11190), biology (Q420), agriculture (Q11451), nutrition (Q2138622)). Wikidata (Q2013) links several ELIXIR-related resources, core data resources like Cellosaurus (Q24691710), ChEBI (Q902623), and UniProt (Q905695), and others from the life-sciences ecosystem, like Complex Portal (Q47196990), Uberon (Q7876491), Bgee (Q54985720), and WikiPathways (Q7999828). This integration has largely been done in independent projects, some (like the ComplexPortalBot) initiated in previous biohackathons and in the context of Wikidata:WikiProject_COVID-19.
So far, it is not simple to get a picture of ELIXIR-related-resources, as they are spread throughout the platform. In the upcoming edition of the biohackathon, we propose to continue these efforts with a focus on reusing existing life science content on Wikidata. In this project we will extend this in-wiki documentation page that gathers the different ELIXIR efforts that included integration bots, Wikidata properties, and writting of SPARQL queries. Additionally, we propose to advance the Wikidata-ELIXIR integration by hands-on activities, such as writing integrative queries that bridge Wikidata and other public databases, developing more intuitive user interfaces, and integrating Wikidata in analysis pipelines (e.g., in R or Python).
Alongside the work to be performed at the hackathon, the WikiProjec|t is open to everyone, and new participants are always welcome!
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ELIXIR Resources edit
This includes:
- ELIXIR Core Data Resource (CDR; ELIXIR Core Data Resource (Q108654442))
- ELIXIR Deposition Databases (DD; ELIXIR Deposition Database (Q108655138))
- ELIXIR Recommended Interoperability Resources (RIR; ELIXIR Recommended Interoperability Resources (Q108655114))
- NS: Node Service (ELIXIR Node Service (Q109476467))
For a list of resources per node, see Wikidata:WikiProject Elixir/Resources by node.
Properties edit
edit
- WikiPathways ID (P2410)
- MetaboLights Compound ID (P3890)
- Reactome ID (P3937)
- Complex Portal accession ID (P7718)
Other properties edit
- ...
Queries for Use Cases edit
- Services and Organizations per ELIXIR Node: https://w.wiki/4N9W
- Copyright status of each database: https://w.wiki/4zxD
- Articles that describe ELIXIR resources and their authors: https://w.wiki/4N9e
- Heads and Coordinators of ELIXIR nodes: https://w.wiki/4zxF
Queries for WikiPathways curation in PathVisio edit
- ...
Other queries edit
- All ELIXIR Nodes and their countries: https://w.wiki/4Mhx
- on a map: https://w.wiki/4gCW
Query ideas/requests edit
- Items were an ELIXIR database is cited as a reference
Related projects on Wikidata edit
Bots edit
- ...
WikiProjects edit
Other edit
- ...
Subpages edit
Open tasks edit
- Gather items of interest as on focus list of Wikimedia project (P5008), including:
- ELIXIR resources on Wikidata
- Researchers associated to ELIXIR databases
- ...
- Gather Wikidata Users that are actively involved with ELIXIR-related data
- Represent the information on https://en.wikipedia.org/wiki/ELIXIR on Wikidata
- Catalog (and represent) the services provided by each ELIXIR Node
- Setup a Toolforge tool for operating ELIXIR-related bots
- Request property for ELIXIR TeSS (Q109494708) topics, either via a general search or via queries like https://tess.elixir-europe.org/materials?tools=BridgeDb
- Represent ELIXIR focus groups
Participants edit
The participants listed below can be notified using the following template in discussions:{{Ping project|Elixir}}
- Andra Waagmeester (talk) 12:26, 20 September 2021 (UTC)
- Egon Willighagen ( * talk) 08:31, 17 September 2021 (UTC)
- TiagoLubiana (talk) 20:38, 22 September 2021 (UTC)
- Martina Summer-Kutmon ( * talk) 15:03, 8 November 2021 (UTC)
- Netbio (talk) 16:14, 8 November 2021 (UTC)
- Toniher (talk) 16:20, 8 November 2021 (UTC)