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Bioschema metadata discussion in the biohackathon #672

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NRayya opened this issue Dec 11, 2022 · 7 comments
Closed
4 tasks done

Bioschema metadata discussion in the biohackathon #672

NRayya opened this issue Dec 11, 2022 · 7 comments
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@NRayya
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NRayya commented Dec 11, 2022

  • Project
    • conform to ISA
  • Study
    • conform to ISA
    • Re-define the structure the output json. May be the study details can be displayed first followed by project and dataset details. May be isPartOf is something we can use.
  • Dataset
  • use "variableMeasured" for NMRium info and results
@NRayya NRayya self-assigned this Dec 11, 2022
@NRayya NRayya added this to nmrXiv Dec 11, 2022
@NRayya NRayya moved this to 📝Backlog nmrXiv-app & nmrium-react-wrapper in nmrXiv Dec 11, 2022
@NishaSharma14
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NishaSharma14 commented Dec 13, 2022

DataCatalogue -

  • Fetch the below values from env
    Provider name
    Provider URL
  • Measurement technique - we should have a persistent URL not from OLS.
  • Keywords - As defined terms.

Project -

  • Add condition check in API to just fetch public project.
  • Extend the scope of API to accept project-name, right now its just returning result for project-slug.
  • Use env wherever possible.

Study

  • Sample - Bioschema will deprecate Sample soon in favor of [BioSample] (https://bioschemas.org/types/BioSample/0.1-RELEASE-2019_06_19).
  • Add condition check in API to just fetch public project.
  • Extend the scope of API to accept project-name & identifier, right now its just returning result for project-slug.

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@NishaSharma14
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NishaSharma14 commented Dec 14, 2022

As per Steffen,
This Bioschema Validator tool can help in providing some additional validation apart from schema.org.
https://bioschemas-validator.herokuapp.com/ - currently down
The code is in https://github.com/ElixirTeSS/bioschemas-validator and how to run the web app locally is mentioned in ElixirTeSS/bioschemas-validator#7 (comment)

Note that there are the branches main, web and develop, with various states of working.

Output
I tried to spin up the instance locally and tried to validate the DataCatalogue response, but failed to do do due to some unknown error. For more info please track here

After discussion we got to know the above is deprecated now, an alternate could be
https://fair-checker.france-bioinformatique.fr/check

@NishaSharma14 NishaSharma14 self-assigned this Dec 14, 2022
@NishaSharma14
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NishaSharma14 commented Dec 14, 2022

@NishaSharma14
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In case you want to join the main channels for Bioschemas, which would be a good idea to follow the community discussions and so:
Subscribe to the mailing list
Get involved in discussions on GitHub
Join the slack space
There is also a community call once a month and reminders will be sent to the mailing lists

@NishaSharma14
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To look for json schemas:

  1. Go to https://discovery.biothings.io/registry
  2. Go to the tab "Browse by Namespace"
  3. If you are looking for a release you can go to "Bioschemas" (https://discovery.biothings.io/view/bioschemas)
  4. If you are looking for a draft you ca go to "BioschemasDrafts" (https://discovery.biothings.io/view/bioschemasdrafts)
  5. Find the profile you are interested in, for instance Dataset (released version at https://discovery.biothings.io/view/bioschemas/bioschemas:Dataset) and navigate to the page
  6. On the top right, there is a link "View Source"

For markup examples

  1. Go to https://bioschemas.org/
  2. Navigate to the profiles list from the menu Specifications-Profiles (https://bioschemas.org/profiles/)
  3. Stay on the tab "Release" or go to the tab "Draft" depending on the profile you are interested in
  4. For instance, if you are interested in Dataset, you would end up at https://bioschemas.org/profiles/Dataset
  5. On the top, go to the tab "Links" (https://bioschemas.org/profiles/Dataset/1.0-RELEASE#nav-links)
  6. Look for the "Examples" link and there you will find some examples, commonly corresponding to the minimum properties

Alternative

  1. Go to Live Deploys and navigate by Profile (https://bioschemas.org/developer/liveDeploys#nav-profile)
  2. Find the profile you are interested in
  3. Open the page for any of the listed resources
  4. Use Developer Tools in your browser and locate the piece in the HTML corresponding to a script "application/ld+json"
  5. You should get the JSON-LD markup which you can copy to an editor to have a better look

@NRayya
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NRayya commented Dec 14, 2022

Using the fair checker: https://fair-checker.france-bioinformatique.fr/check with the end point https://dev.nmrxiv.org/api/v1/schemas/bioschema/

The result was:
image

Many of the principles are actually met, which requires more discussion in the hackathon

NRayya added a commit that referenced this issue Dec 16, 2022
add NMRium info as property values to variableMeasured
create function for tags, authors, citations.
add percentage compositions to molecules
Fixes:  #672
NRayya added a commit that referenced this issue Dec 22, 2022
NRayya added a commit that referenced this issue Dec 29, 2022
@NRayya
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NRayya commented Jan 2, 2023

closed in favor of Bioschema controllers and API #698
#697
#696

@NRayya NRayya closed this as completed Jan 2, 2023
@github-project-automation github-project-automation bot moved this from 📝Backlog nmrXiv-app & nmrium-react-wrapper to ✅Done in nmrXiv Jan 2, 2023
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