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NOTE: THE WIKI HAS NOT BEEN MAINTAINED, INFORMATION MIGHT BE OUTDATED
The goal of ''Annotate them all'' is to create an easy to use Graphical User Interface for annotation of scientific manuscripts to Wikidata IDs.
Wikidata is a knowledge base that represents more than 80 million concepts, from cell lines and taxons, to Brazilian footballers and european laws. It is free to use, and anyone can edit. And the concepts are matched to many external databases that represent the same entities.
Using Wikidata, we can have a broad scope of annotations, so the annotator doesn't need to invest a lot of time understanding the rules and schemas of the tens (or hundreds, or thousands) of different IDs / ontology terms needed.
These annotations, in a first momment, would be gathered for some time and later updated to EuropePMC's Annotation API, enabling researchers to both visualize annotations (via EuropePMC's SciLite System) and programatically access them.
Annotation of biomedical texts is the foundational steps for accurately representing biomedical information in a semantic format (i. e. in a knowledge graph compatible way). It also can provide a base for specific curation efforts, such as UniProt and POMBase.
During the eLifeSprint, we will build a prototybe of this crowd annotation system. Something that allows annotation and saves it in an EuropePMC-compatible format.
The ideas presented here are to be seen as a template: the input of participants is really neded to shape this project, making it useful for the community.
Also, this is a voluntary, free, open project. It should be fun, and it should be educative. And of course, it has to be a friendly space. This is as important (if not more) than actually building the prototype.
I (Tiago) really believe that an open base for annotation of scientific articles can profoundly benefit the community. I plan to continue working on this project (alongside anyone that wants to chime in) for the next few years.
The idea is to keep improving the platform, making it more user friendly, developing incentives and integrations.
However, for it to persist after the sprint, one thing is more important than all else. The community has to see value in this. Feedback, ideas, proposals, little helps, debugging here and there, all this.
So, if you hobe something to add, or something that you want to clarify, or just want to say hi, just leave an issue!
And, of course, the more people contributing to the actual code, testing, design, and so on, the better. Following Wikipedias motto, '''be bold''' and join us!
There have been other community annotation projects. If you are intested, you can check them at the Related works page.
If you are looking for relevant bibliography, the Bibliography page is the place for you.