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Exploring at the network-level: Related Interactions #988

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Exploring at the network-level: Related Interactions #988

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@jvwong
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@jvwong jvwong commented Jun 15, 2021

This is a prototype. Displays more detail of INDRA search results upon interacting with elements of the network in our Explorer.

The original motivation for this feature was to provide more explicit information about why the papers were being displayed for a given network element.

  • Notes
    • It is backwards compatible in the sense that it displays 'There were no interactions found for the selected item' for element.relatedPapers data with the existing schema, or if in fact none were found
    • 'Show more articles' isn't implemented, not sure if this should be punted til later and how it should be implemented (routing?)
    • I'm showing 'Source' (e.g. Pathway Commons; Human Protein Reference Database) when available but not sure if this is worth including or how to include it (link to PC apps?).

Refs #937

jvwong added 27 commits March 24, 2021 16:47
@jvwong
Map ids to UniProt, otherwise fallback to HGNC, then text
50cae75
@jvwong
Transitioned all but one function to async/await style
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Updating the indra.js module to present lists of evidence with aggreg…
ee80a4d 
…ated text between PMIDS
@jvwong
Filter for statements with non-empty evidence
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@jvwong
Drop testing suite
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@jvwong
Environment variables to control the number of INDRA interactions ret…
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…urned
@jvwong
- expose a search function that accepts element and doc
952e148 
- comment out interaction/doc ranking logic
@jvwong
- Accommodate new indra search function
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- simply do not back-fill interactions with document related papers
@jvwong
Take into account edge case where no dbXref exists
7f8f0ca
@jvwong
- Extend the related papers (doc) to a related interactions component…
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… (selection)

- Create reusable loading and paper components
- first pass at the related interaction list element display
@jvwong
- Ensure component is backwards-compatible
da3425a 
- Make hypertext colored blue
@jvwong
- Make font sizes more consistent
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Pull the 'Show more papers' link right
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- Use string-similarity to ensure that excerpts are unique
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- Improve the readability of the excerpts display
@jvwong
Allow the evidence detail block to take up the remaining space
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@jvwong
Breakpoints for interaction component on smaller screens (<800px)
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Merging with Unstable and resolving conflicts
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- Do a more in-depth mapping of INDRA datasource to MIRIAM registered…
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… collection, if exists

- Show the data source in the interaction-level display
@jvwong
Swallow any INDRA errors on initial submit (issue 985)
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@jvwong
- tag the INDRA data source as a given type (nlp, db)
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- add some extra fields from INDRA to the interaction/source
@jvwong
Abstract out a RelatedInteraction component
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Abstract an Evidence component for reuse
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Abstract an Evidence component for reuse
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s
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- RelatedInterations just extends component
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- link styling and naming
@jvwong
Resolving conflicts in related-papers component
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@jvwong
Merge origin/iss937_interaction-info into iss937_interaction-info
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@jvwong
Addressing misc conflicts in merge
caca6ea
@jvwong jvwong changed the title Exploring at the network-leve: Related Interactions Exploring at the network-level: Related Interactions Jun 16, 2021
@maxkfranz
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@jvwong, would you merge this in and link to a live example of the results on the unstable instance?

The code looks OK, and I'd like to have a live example to point to in order to comment on the UI.

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jvwong commented Jun 22, 2021

OKey, I'll put in on master.factoid.baderlab.org - ping you when its done

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jvwong commented Jun 22, 2021

@maxkfranz I updated the site, and kicked off an example: https://master.factoid.baderlab.org/document/e5dc3eef-6af0-4c61-8a42-ddeb4a4285b5

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Looks good. Minor feedback:

  • It would be nice if there were just a bit of spacing between the title, author list, and journal name. It's close, making it a bit harder to make things out.
  • The journal name wouldn't blend in so much with the author list if it were italicised.

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jvwong commented Dec 7, 2021 •
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We've try to mitigate failures and provide fall-backs upon

Another existing issue is that when semantic-search returns an error, for whatever reason (PathwayCommons/semantic-search#98) there is no reasonable fallback herein, which ultimately leads to no related papers - its 'all or none'.

All of these points of failure should be considered in this PR since the relevant code is being updated.

@jvwong jvwong mentioned this pull request Dec 8, 2021
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@jvwong jvwong closed this Apr 13, 2022
@jvwong jvwong deleted the iss937_interaction-info branch March 2, 2023 17:59
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