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Introduce BioSchemas terms into pending#2863

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danbri merged 172 commits intomainfrom
issue-2862
May 21, 2021
Merged

Introduce BioSchemas terms into pending#2863
danbri merged 172 commits intomainfrom
issue-2862

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@RichardWallis
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Implements issue #2862 which in turn implements proposed bioschemas terms from PR #2711.

#2711 introduced data/ext/bio for them definitions, this moves those definitions into pending

ljgarcia and others added 30 commits November 16, 2018 11:07
Not as an extension yet...
And fix hasSequence domains and ranges
and missing property sources
so the unit can be included as well
so the unit can be specified
adjusting domains and ranges when needed. And updating temperature range from Text to Quantity
and add inverseOf statements and links
Commented out classes that fail to work
- Tweaks to wording of terms
- Fixes to make valid HTML
- Omitting keywords property
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@AlasdairGray and I met today to go through these line by line.

We're merging this, and note for future improvements:

  • linking to design discussions would be very useful, and to works e.g. Darwin Core that have inspired the choices here.
  • acknowledge that the communities brought together around bioschemas can reasonably be expected to be kept in the loop for changes, tweaks, and improvements
  • expect to move Taxon under DefinedTerm, and anticipate potential changes in that area to ensure that other non-lifesci forms of taxonomy can be addressed coherently within schema.org.
  • note that /potentialUse needs clarification and an example.
  • suggest adding /MediaObject as a potential value for /hasRepresentation, to allow mime-typed formats to be easily described.
  • Note that BioChemEntity is a kind of organizational construct rather than an upper level ontology sort of a type.
  • We'll establish quarterly check-ins to review progress, collect implementation experience, review new vocabulary suggestions especially those motivated by data-consuming implementations.

@danbri danbri merged commit 13f9dcf into main May 21, 2021
@danbri danbri mentioned this pull request Jun 22, 2021
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danbri commented Jun 25, 2021

https://webschemas.org/hasStatus is too general a property name, we should refine this. Suggestions, @AlasdairGray ?

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@danbri, in order to not delay the release, we would suggest dropping the property.

We had a discussion about this in our telcon today. We can't find the original motivation for the hasStatus property and those present noted several issues with the current proposal. However, we also saw the benefit of having a property to capture this sort of information, e.g. to capture if the Gene has been 'knocked out'.

We've created an issue in the Bioschemas tracker (Bioschemas:512) to come back with a more detailed proposal in a future iteration.

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danbri commented Jun 29, 2021

Thanks, I'll comment it out for now!

danbri added a commit that referenced this pull request Jun 29, 2021
danbri added a commit that referenced this pull request Jun 29, 2021
@RichardWallis RichardWallis deleted the issue-2862 branch November 23, 2021 15:26
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9 participants