new preprint: "Metadata handling for BioHackathon publications through BioHackrXiv" https://doi.org/10.37044/OSF.IO/QVFTJ
Resulting from the 2022 @elixir_europe BioHackathon Europe, where work was done on automating migration of metadata #BioHackEU22
on my previous account, I posted conference coverage for a few meetings (with a mixed number of posts; I do not know how to list just my posts):
- #epiLipidNet https://akademienl.social/tags/epiLipidNet
- #maasosf23 https://akademienl.social/tags/maasosf23
- #srd23 https://akademienl.social/tags/srd23
- #iwomi2023 https://akademienl.social/tags/iwomi2023
- #DMCM2023 https://akademienl.social/tags/DMCM2023
- the #OpenScienceChallenge https://akademienl.social/tags/OpenScienceChallenge
- #NanoInformaTIX https://akademienl.social/tags/NanoInformaTIX
- #BioHackEU22 https://akademienl.social/tags/BioHackEU22
Preprint released from the #BioHackEU22 #PlantDataExchange session. This tries to link and map between several key data standards and technologies for crop/plant data, including Minimum Information for a Plant Phenotyping Experiment (#MIAPPE), Breeding API (#BrAPI), the Investigation-Study-Array model (#ISA-Tab), RO-Crate, Bioschemas.org and more.
I hope much of this can be applied in work to make data #FAIR at the Australian Plant Phenomics Facility (#APPF).
Project #33: training for systems biology curators, building interoperable and reusable models following the learning paths approach. Collab with Project #32. Feedback for Bioschemas and ELIXIR TeSS pending.
Project #34: integrating cancer data. they need #wikidata, I think.
Project #35: workflow execution service (WES), workflow-run-crate.
And that's a wrap!
#BioHackEU22 11/11
Project #31: a lot of FAIR CookBook work on integration with the RDMKit. More technical: interlinking via shared YAML. Other, strategies for persistent identifiers for RDMkit, and 6 identified representative user journeys
Project #32: more training material, for systems biology, data management, data stewardship, BioiNFORming etc. 16 people "frantically working"
#BioHackEU22 10/
Project #27: making great progess with ISA-JSON to get data into ENA and Biosamples, showing an XML snippet of "ENA Experiment XML" (and more)
Project #28: "One of the most productive BioHackathons for us"
Project #29: lot of progress. NextFlow, GNU Guix, more docs
Project #30: more flexible ELIXIR::GA4GH
#BioHackEU22 9/
Project #25: Tools Ecosystem. They have a bio.tools + EDAM SPARQL endpoint now! Brainstorming, first queries. Working on getting more data in.
Project #26: lot of work. Curation datasets of unknown compounds. Mapping of FAIR chemical structures with Bioschemas. Federated SPARQL queries between IDSM, WikiPathways, Rhea, and MolMeDB, PubChemLite classification.
Their tip: Check out YummyData!
#BioHackEU22 8/
Project #21: updating the operator dashboard.
Project #22: worked on ISA and RO-Crate support and mapping to Bioschemas
Project #23: Bioschemas data dumps for IDP-KB, bio.tools, and Rhea. Dedicated "DataFeed" page created on website.
Project #24: collecting and curating data. Extracted text. Annotation and analysis in progress..
#BioHackEU22 7/
Project #13 - #17 (skipped)
Project #18: mOWL project worked on the ALC dataset, implemented DeppGOZero, and working on usability testing
Project #19: working on https://ebi-webcomponents.github.io/nightingale/#/, bugfixing, docs, migration of key components
Project #20: Identified user stories for onboarding people for Federated EGA nodes, see https://github.com/EGA-archive/FEGA-onboarding
#BioHackEU22 6/
Egon Willighagen
Donald Hobern
TheLipidHoff
Egon Willighagen