add google doc edits to manubot

[jaybee84]

Purpose

1. Port back google doc edits to manubot for further work
2. closes #124

Directions for reviewers

Which areas should receive a particularly close look?

1. Please double check if the right references for each section were ported

Is there anything that you want to discuss further?

No. All further edits will be added as new PRs

Is the pull request ready for review?

yes

Manuscript checklist

Unless otherwise noted above, this PR will be considered ready for review when all four items have been checked.

• [x] All changes to text follow "one sentence per line" [Manubot instructions]
• [x] All citations follow the Manubot citation instructions
• [x] All changes or additions to tables follow the Manubot table instructions
• [x] All figures follow the Manubot figure instructions
• [x] All terms that need to be added to glossary have been added to #50
• [x] There are no new spelling errors identified by the Manubot spellchecker

[AppVeyorBot]

AppVeyor build 1.0.262 for commit 478d102aa689a84378e91e6b08d80793c3176701 failed.

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AppVeyor build 1.0.263 for commit c433184912e8dce5701c4dcd00db35f5f7081520 failed.

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AppVeyor build 1.0.264 for commit 76aad55a3eb8a5f617ca7c7f1e35229dbb19fa6c failed.

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AppVeyor build 1.0.265 for commit 07feb772e78588e958077b4a899154b39adf6b8b failed.

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AppVeyor build 1.0.266 for commit ddd39ded940c18dbf9fa292dd2025d93bdbea565 failed.

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AppVeyor build 1.0.267 for commit 3fa61ba02ec33c8aa06cb41b85796de127432edb failed.

[AppVeyorBot]

AppVeyor build 1.0.270 for commit 56999847b2514570af0a17dce012d4cc6494ace1 is now complete.

Found 12 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:13:hyperparameters content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:5:KGs content/05.prior-knowledge.md:5:Orphanet content/05.prior-knowledge.md:7:KGs content/05.prior-knowledge.md:9:comorbidities content/05.prior-knowledge.md:26:Chemogenomic content/05.prior-knowledge.md:26:CTD content/05.prior-knowledge.md:26:TO...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.270-5699984.html
  • manuscript-1.0.270-5699984.pdf
  • spelling-errors-1.0.270-5699984.txt
  • spelling-error-locations-1.0.270-5699984.txt

[allaway]

content/03.heterogeneity.md:23:TODO

Manubot calling out TODOs is an awesome unexpected (by me, anyway) feature.

[jaybee84]

I think the TODOs are being called out as spelling errors :)

[allaway]

Oh, for sure, but I guess it's a nice way to keep track of them!

[AppVeyorBot]

AppVeyor build 1.0.271 for commit a891e40a82d08df90c5230d64609a69f3e2a8fef is now complete.

Found 0 potential spelling error(s). Preview:

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The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.271-a891e40.html
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[jaybee84]

Actually, seeing the spelling error callout, I had added "TODO" to the custom dictionary so that it wouldn't get called out... but your comment makes me think that calling it out is actually a good thing...So removed TODO from the custom dictionary :)

[AppVeyorBot]

AppVeyor build 1.0.272 for commit 4b623a35dbd452c293b91f4ec122b80410339920 is now complete.

Found 5 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:26:TODO content/06.multiple-approaches-required.md:5:TODO...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.272-4b623a3.html
  • manuscript-1.0.272-4b623a3.pdf
  • spelling-errors-1.0.272-4b623a3.txt
  • spelling-error-locations-1.0.272-4b623a3.txt

[AppVeyorBot]

AppVeyor build 1.0.273 for commit f19b27ac70b46cabe8cc5fb0c0519ef519d2a52d is now complete.

Found 5 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:26:TODO content/06.multiple-approaches-required.md:5:TODO...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.273-f19b27a.html
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[AppVeyorBot]

AppVeyor build 1.0.274 for commit 6831fae159b5a3c58125348f82efb29748531ce4 is now complete.

Found 11 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:26:TODO content/06.multiple-approaches-required.md:5:TODO content/07.conclusions.md:4:TODO content/07.conclusions.md:4:tSNE content/07.conclusions.md:11:Autoencoders content/07.conclusions.md:11:VAEs content/07.conclusions.md:12:autoencoders content/07.conclusions.md:12:VAEs...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.274-6831fae.html
  • manuscript-1.0.274-6831fae.pdf
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[AppVeyorBot]

AppVeyor build 1.0.275 for commit 124c88002d21b520f3579254ea2014817e1b0895 is now complete.

Found 11 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:26:TODO content/06.multiple-approaches-required.md:5:TODO content/07.definitions.md:4:TODO content/07.definitions.md:4:tSNE content/07.definitions.md:11:Autoencoders content/07.definitions.md:11:VAEs content/07.definitions.md:12:autoencoders content/07.definitions.md:12:VAEs...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.275-124c880.html
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[AppVeyorBot]

AppVeyor build 1.0.276 for commit 7c87a2b6d8800fdf0352db93743a848d1a64a8b0 is now complete.

Found 6 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:26:TODO content/06.multiple-approaches-required.md:5:TODO content/07.definitions.md:4:TODO...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.276-7c87a2b.html
  • manuscript-1.0.276-7c87a2b.pdf
  • spelling-errors-1.0.276-7c87a2b.txt
  • spelling-error-locations-1.0.276-7c87a2b.txt

[AppVeyorBot]

AppVeyor build 1.0.277 for commit 40fcfadfc6417122a8f856712a644b4d07f255d6 is now complete.

Found 6 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:26:TODO content/06.multiple-approaches-required.md:5:TODO content/07.definitions.md:4:TODO...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.277-40fcfad.html
  • manuscript-1.0.277-40fcfad.pdf
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[AppVeyorBot]

AppVeyor build 1.0.280 for commit 4a4914dfb0e3b2d11fc89355cb352f48b191fce9 is now complete.

Found 5 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:23:TODO content/05.prior-knowledge.md:26:TODO content/07.definitions.md:4:TODO...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.280-4a4914d.html
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[AppVeyorBot]

AppVeyor build 1.0.281 for commit cb53373bc6ea1958b3603c6a8f95df27e20cbcfb failed.

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AppVeyor build 1.0.282 for commit 71b2e5bcf61ba2af4df6fd046af91a4398cb350b failed.

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AppVeyor build 1.0.283 for commit 3bdbf7a362125c349e585d31d345a01b34b7e6ee failed.

[allaway]

It looks like my suggestion of a dash is breaking the build....my bad.

[AppVeyorBot]

AppVeyor build 1.0.284 ... for commit 42adb583e0ea2e6681011601b8d6f17a5b64ad0e is now complete.

Found 5 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:22:TODO content/05.prior-knowledge.md:26:TODO content/07.definitions.md:4:TODO The rendered manuscript from this build is temporarily available for download at:

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[AppVeyorBot]

AppVeyor build 1.0.285

Found 5 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:22:TODO content/05.prior-knowledge.md:26:TODO content/07.definitions.md:4:TODO for commit d62cc971007374609a96ee991d2d41f141cc8fb4 is now complete....

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.285-d62cc97.html
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[AppVeyorBot]

AppVeyor build 1.0.286 for commit e98b339d617184e4744675bbcbb15c793224ca01 is now complete.

Found 5 potential spelling error(s). Preview:

content/01.synopsis.md:6:TODO content/03.heterogeneity.md:4:TODO content/03.heterogeneity.md:22:TODO content/05.prior-knowledge.md:25:TODO content/07.definitions.md:4:TODO...

The rendered manuscript from this build is temporarily available for download at:

• manuscript-1.0.286-e98b339.html
  • manuscript-1.0.286-e98b339.pdf
  • spelling-errors-1.0.286-e98b339.txt
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