A repository for brainstorming and prototyping ideas related to the eLifeSprint project Annotate them all (https://sprint.elifesciences.org/annotate-them-all/)
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Create tool to convert Europe PMC Annotations to Wikidata #14
What is your idea?
Articles in the Europe PMC database are already annotated by a range of services (see list here). Maybe we can use this annotations in Annotate Them All!
They can be cross-referenced to Wikidata and used as helper annotations. As they are text-mined, they are not always precise. It will be important to keep separate what users annotate and what is converted from other sources.
What can we do at the Sprint?
A lot of biological databases have been reconciled with Wikidata. One study is:
[ ] Check which annotation providers for Europe PMC are reconciled to Wikidata.
[ ] Select one provider to study in more depth (ex: diseases from DisGeNet).
[ ] Build tool that takes a PMID and converts annotations from one provider to Wikidata items
[ ] Think about ways to use these previous annotations to improve the tool. For example, they can be used to give scores back to users.
What skills does it require?
Familiarity with biological databases and Wikidata,
Some programming/data science skills for automating the conversion.
lubianat
commented
3 years ago
What is your idea? Articles in the Europe PMC database are already annotated by a range of services (see list here). Maybe we can use this annotations in Annotate Them All!
They can be cross-referenced to Wikidata and used as helper annotations. As they are text-mined, they are not always precise. It will be important to keep separate what users annotate and what is converted from other sources.
What can we do at the Sprint? A lot of biological databases have been reconciled with Wikidata. One study is:
What skills does it require? Familiarity with biological databases and Wikidata, Some programming/data science skills for automating the conversion.