Idea #7296
closed
Document Sprite Annotation Server
Added by Sarah Guthrie over 8 years ago. Updated about 6 years ago.
Description
Should include CAVA, ExAC, and ClinVar annotations and be able to respond to basic API requests
Files
| Lightning.pdf (225 KB) Lightning.pdf | Sarah Guthrie, 10/20/2015 04:13 PM |
Updated by Sarah Guthrie over 8 years ago
- Subject changed from Document common annotation queries to Document Sprite Annotation Server
- Description updated (diff)
Updated by Sarah Guthrie over 8 years ago
- Parent task deleted (
#7269) - Story points set to 1.0
Updated by Sarah Guthrie over 8 years ago
- Tracker changed from Task to Idea
- Target version changed from 2015-10-02 sprint to 2015-10-23 Lightning sprint
Updated by Sarah Guthrie over 8 years ago
- Target version changed from 2015-10-23 Lightning sprint to 2015-11-13 Lightning sprint
Updated by Sarah Guthrie over 8 years ago
- Target version changed from 2015-11-13 Lightning sprint to 2015-10-23 Lightning sprint
Updated by Sarah Guthrie over 8 years ago
- Status changed from New to In Progress
Updated by Sarah Guthrie over 8 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
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)
Updated by Sarah Guthrie over 8 years ago
- Description updated (diff)
Take out requirement on ExAC - highly complicated and vastly less useful than ClinVar and CAVA.
Updated by Sarah Guthrie over 8 years ago
- File Lightning.pdf Lightning.pdf added
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!
Updated by Sarah Guthrie over 8 years ago
- Target version changed from 2015-10-23 Lightning sprint to 2015-11-13 Lightning sprint
Updated by Sarah Zaranek about 6 years ago
- Status changed from In Progress to Closed
Closing this out for now.