Lmst

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

Screenshot of part of a page of the paper PDF, showing a fragment of XML with metadata, the Zenodo API section, and the "Virtuoso as a system container" section header.

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).

https://biohackrxiv.org/c724r/

Workflow diagram from preprint, showing multiple possible sources of plant phenotyping data on the left (FAIRDOM-SEEK and PHIS or PIPPA communicating over BrAPI; DataPLANT; and standalone template data) feeding into an Investigation-Study-Assay model organised as an Annotated Research Context (ARC), which can then be packaged using RO-Crate or fed into a repository." title="Workflow diagram from preprint, showing multiple possible sources of plant phenotyping data on the left (FAIRDOM-SEEK and PHIS or PIPPA communicating over BrAPI; DataPLANT; and standalone template data) feeding into an Investigation-Study-Assay model organised as an Annotated Research Context (ARC), which can then be packaged using RO-Crate or fed into a repository.

On my way home from #BioHackEU22 in Paris. Over thirty projects, great interactions, inspiration and so many new things learned. Thanks #ELIXIREurope ! Nice progress towards FAIRer ML models, curation and deposition in #biomodels at #emblebi Some initial work on #lipids shorthand names in #wikidata and some more insight into semantic web. @fzj #denbi

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/

Project #10: this one I have to see in practice, but more work on RDM in Galaxy, DSW, using RO-Crates.

Project #11: working on subsets of #wikidata. First subsets created showed some bugs, and some successes (lipids and GeneWiki). Tried publishing on TriplyDB and data.world, but free accounts allow too few triples.

Project #12: more work on improving notebooks for the MGnify microbiome analysis workflows

#BioHackEU22 5/

Project #7: fixed a big, had a meeting with @bridgedb, worked on Rhea, and Bgee. They're still looking for more databases to integrate. (Check out https://togoid.dbcls.jp/ !) Btw, "Togo = integration in Japanese" (from the slide)

Project #8: Developing a lesson for the ELIXIR Software Management Plan.

Project #9: FAIR comp models via BioModels. Curated 3 ML models and identified issues. Automated extraction of metadata to server "F"-indable. Using ONNX

#BioHackEU22 4/

Project #4: Enhancing BioHackrXiv with OSF.org, Zenodo.org, EuropePMC indexes BioHackrXiv articles, and @opencitations tracks citations. There is a new template (https://github.com/biohackrxiv/publication-template), and the Preview Server is updated

Project #5: Bioschemas and the DAta Discovery Engine (DDE). Profiles are already easier to update. 22 profiles already have.

Project #6: Assembly for non-model eukaryotes. updated workflows, annotations with funannotate ongoing. And started evaluation.

#BioHackEU22 3/

Project #1: using data from ZOOMA, peraring data for user queries, and preparing a RShiny app

Project #2: APICURON is still looking for curators to show them their solutions. @ORCID_Org being integrated.

Project #3: BioINForm has defined learning paths, created an app to visualize it

#BioHackEU22 2/

people at #BioHackEU22 are making the last preparations for the midterm update presentations. These sessions are always fun and give a great insight in all the life science hacking happening here. More integration, more open, better, higher impact. I will cover it again and try to keep up.

Day three of #BioHackEU22 just starting. Project 9 for FAIRer ML models support in EMBL-EBIs BioModels database rolling along nicely. #DOME recommendations and thanks to #onnx https://github.com/elixir-europe/biohackathon-projects-2022/tree/main/9

Day 3 "Even the candy is in pumpkin theme now" of #BioHackEU22 :)

Project #26 sign post with two orange pumpkin colored/shaped candy in front on it, on the white table hacking table.

okay, time to close the laptop. Day 2 of #BioHackEU22 has been busy. Lot's of talk. FAIR chemical structures (x2), BioHackrXiv, Bioschemas, Rhea, SBML, WikiPathways, LIPID MAPS, CiTO. no wonder I'm tired.

Day 2 at #BioHackEU22 !

https://galaxyproject.org/events/2022-11-b-h2022/ lists all projects being worked on with a connection to #UseGalaxy.

the #BioHackEU22 hashtag also works on other platforms, e.g. GitHub: https://github.com/topics/biohackeu22

#BioHackEU22

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