INCATools / INCATools/biosample-analysis
provide NER output from SQLlite/basex tables
- Dominant language
- Jupyter Notebook
- Stars
- 3
- Forks
- 1
- PR merge metrics
- No merged PRs in 30d
Description
NER methods were run on an earlier version of the Biosample data, specifically for the Title and Description fields. This process used a simple TSV file with these fields source from the Biosample table:
biosample id
title
description
For the next iteration, it should be possible to have an additional piece of code as part of the NER pipeline to execute a basex query and output the results in the TSV format above for NER input.
@hrshdhgd @turbomam
Contributor guide
No contributing guide indexed for this repository
Research direction
No file or test is named. Start by locating the existing NER pipeline and the Biosample table/query entry point, then inspect how the current TSV input is produced and consumed. Done means an added pipeline step can query the tables and emit TSV containing biosample id, title, and description for NER input.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, sqlite
- Domain
- data, databases
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100