semantic-sql

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See https://github.com/obophenotype/uberon/issues/3267

cmungall

Duckdb has a lot of advantages over sqlite - speed - extended syntax - built in support for arrays and other datatypes In theory there is no particular reason for...

cmungall

Include PyOBO products

6

See https://github.com/biopragmatics/obo-db-ingest It would be quite easy to add these as builds, and distribute the sqlite on s3. Advantages: - easy to query in OAK (though some methods and commands...

cmungall

Left over intermediate artefacts

5

## Overview I ran: `semsql make doid.db`, and these files remained afterwards: 1. `.template.db`: Appears the CWD (current working directory) from where I'm running the command. It _might_ be that...

joeflack4

Make semsql prefix maps configurable

4

matentzn

Make everything installable via PyPI

11

- [ ] rewrite relation-graph in rust and use PyO3 bindings - [ ] use PyO3 to wrap rdftab As an alternative to wrapping rdftab is to directly load the...

cmungall

Improve speed of converting SQLite to FHIR

2

## Overview I tried to convert HPO to FHIR using `semsql` as an intermediary. However, after about 40 minutes, I decided to give up and switch to Obographs for speed....

joeflack4

Create a demo of querying OBO in SQL in the browser using sql.js

4

h/t @kltm https://sql.js.org/#/

cmungall

I cant figure out how to tell semsql how to generate prefixes during the owl->db conversion process..

matentzn

SQLite console opens (0.1.7)

4

## Overview When using `semsql`, the SQLite console opens. I need to exit it manually in order for the command to continue. Since this is running in a pipeline that...

joeflack4