Hypothes.is tagging of articles on EuropePMC for ANN MiniCorpus 0.1

[lubianat]

https://hypothes.is/ is a web annotation platform that enables us to take notes anywhere in the web.

They have a system to export annotations which could be integrated to Europe PMCs annotation API.

The plan here is:

• Select a list of articles for which abstracts will be annotated (maybe around 50?)

• Annotate article abstracts via Hypothes.is on EuropePMC

• Select an article to deep annotate full text

• Annotate article via Hypothes.is on EuropePMC

• Export annotations

• Do some nice analytics in integration with Wikidata

• Make short report with proof of concept

• Create converter to EuropePMC format

• Contact EuropePMC about the publishing of the ANN MiniCorpus 0.1 on SciLite

The idea is to prototype around and gain traction to move ANN forward. Perhaps an wrapper for hypothes.is browser extension would already be pretty usable to recruit people and build an slightly larger corpus.

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[lubianat]

As I am personally interested in the Human Cell Atlas, I think that a good starting corpus is the papers that are part of the Human Cell Atlas: https://www.humancellatlas.org/publications/

• I will list them directly on Wikidata as part of Human Cell Atlas.
• Then I'll figure out a way to get the EuropePMC API
• I'll also figure out a way to count annotations per page.

[lubianat]

List made: https://w.wiki/rrm
First article tagged: https://europepmc.org/article/MED/32079746

[lubianat]

Table to keep track of annotations: https://docs.google.com/spreadsheets/d/1hVSV4IlElqjQWRE55EOD-OrQlLWvlGKzRlD6SCF1FV0/edit?usp=sharing

[lubianat]

Google Colab with code to parse Hypothes.is Wikidata annotations: https://colab.research.google.com/drive/1RjnIvWIEJq4Yg2rrFRvnkKDO3iQUyKdC?usp=sharing

Also working on a visualization query, example: https://w.wiki/3VFM
Hard coded with come concepts of https://europepmc.org/article/MED/32079746