2023-02-16

This is PMAS's COMMONS Lab daily Open Notebook.

Today is 2023.02.16

Todo today

Have a look at the XXXX discussion forum

- https://github.com/orgs/XXXXX/discussions

Doing

4th and last day of the #swat4hcls (Private)

Program is here

https://www.swat4ls.org/workshops/basel2023/hackathon/

Hacking Scholia for custom SPARQL endpoints discord

https://github.com/SWAT4HCLS/Biohackathon-SWAT4HCLS-2023/issues/4 This hack project is following up efforts of other to repurpose the Scholia platform for other SPARQL endpoints, like custom Wikibase installations or Wikidata subsets. In this project we will explore how we can make the Scholia code base configurable for the aspects to show, and which panels to show. If the project is successful, we have a custom Scholia instance around any of the existing public SPARQL endpoints (e.g. ChEMBL, UniProt/NextProt, etc).

Expertise needed SPARQL coding, and/or Python coding (Flask experience particularly welcome)

https://en.wikipedia.org/wiki/Flask_(web_framework)

https://github.com/wdscholia/scholia

Leyla Jael Castro

http://guide.biohackrxiv.org/

https://nanopub.net/

https://linkml.io/

https://www.semantic-web-journal.net/content/onegraph-vision-challenges-breaking-graph-model-lock-0

Check in WikiBase

http://guide.biohackrxiv.org/

From Egon

good morning. I am finishing some teaching before we start around 9am CET hacking ideas for this project include:

global configurable SPARQL endpoint URL

configurable subset of aspects to run

mappings between Wikibase properties and classes with Wikidata equivalents (so that SPARQL can be in the "Wikidata language" but translated to the "Wikibase language" before being run)

extract mapping of Wikidata classes (Q-ids) to Scholia aspects into a config file

oh, and yes, this project will write a BioHackrXiv report https://biohackrxiv.org/

Creating life science fom WD

Discussion with Tarcisio, Ana & Marco

small sized RDF (see PCM molecules) are a thing to investigate
check into Wikibase installs
have a RDF with no GraphDB dependenat specification (should easily go to GraphDb and Virtuoso for ex)
nonopubs website changed its now at https://nanopub.net/ https://arxiv.org/pdf/2203.01608.pdf

A startup is beeing build Knowledge Pixels https://knowledgepixels.com/

Knowledge Space https://gist.github.com/tkuhn/a3842683b810f1e0dbc72a021083ea31

Peta Pico https://github.com/peta-pico