Story #7296

Document Sprite Annotation Server

Added by Sarah Guthrie almost 4 years ago. Updated about 1 year ago.

Status:
Closed
Priority:
Normal
Assigned To:
Sarah Guthrie
Start date:
05/10/2017
Due date:
% Done:

100%

Estimated time:
(Total: 0.50 h)
Story points:
1.0

Description

Should include CAVA, ExAC, and ClinVar annotations and be able to respond to basic API requests

Lightning.pdf (225 KB) Lightning.pdf Sarah Guthrie, 10/20/2015 04:13 PM

Subtasks

Task #7612: Review Story 7296ClosedAbram Connelly

History

#1 Updated by Sarah Guthrie over 3 years ago

  • Subject changed from Document common annotation queries to Document Sprite Annotation Server
  • Description updated (diff)

#2 Updated by Sarah Guthrie over 3 years ago

  • Parent task deleted (#7269)
  • Story points set to 1.0

#3 Updated by Sarah Guthrie over 3 years ago

  • Tracker changed from Task to Story
  • Target version changed from 2015-10-02 sprint to 2015-10-23 Lightning sprint

#4 Updated by Sarah Guthrie over 3 years ago

  • Project changed from Curoverse Science to Lightning

#5 Updated by Sarah Guthrie over 3 years ago

  • Target version changed from 2015-10-23 Lightning sprint to 2015-11-13 Lightning sprint

#6 Updated by Sarah Guthrie over 3 years ago

  • Target version changed from 2015-11-13 Lightning sprint to 2015-10-23 Lightning sprint

#7 Updated by Sarah Guthrie over 3 years ago

  • Status changed from New to In Progress

#8 Updated by Sarah Guthrie over 3 years ago

Check OpenCB, possibly focusing on biodata:
https://github.com/opencb/biodata/tree/6adba1a95fb71bcdc9ec0f92cf38a869ec5075e3/biodata-models/src/main/java/org/opencb/biodata/models/variant/annotation

ClinVar:
opencb/biodata -> biodata-models/src/main/java/org/opencb/biodata/models/variant/annotation/Clinvar.java
  • acc (string)
  • clinicalSignificance (string)
  • traits (list of strings)
  • geneName (list of strings)
  • reviewStatus (string)

#9 Updated by Sarah Guthrie over 3 years ago

  • Description updated (diff)

Take out requirement on ExAC - highly complicated and vastly less useful than ClinVar and CAVA.

#10 Updated by Sarah Guthrie over 3 years ago

Altered the sprite/annotations.txt file, so focus there for review. I uploaded the latex pdf document required, but it has some problems with text wrapping. If you want a dynamic visualization that looks a lot better, follow this recipe using the curoverse/lightning github repository:

git pull origin master
sudo apt-get install python-pip
sudo pip install Sphinx
sudo pip install sphinx_rtd_theme
cd docs
make html

Open lighting/docs/_build/html/index.html in your browser. Enjoy!

#11 Updated by Sarah Guthrie over 3 years ago

  • Target version changed from 2015-10-23 Lightning sprint to 2015-11-13 Lightning sprint

#12 Updated by Sarah Zaranek about 1 year ago

  • Status changed from In Progress to Closed

Closing this out for now.

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