https://github.com/evancarroll/mumine
Work pertaining to import and analytics of unknown data source (mass spec), example of Chado integration
https://github.com/evancarroll/mumine
chado flybase postgresql
Last synced: 3 months ago
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Work pertaining to import and analytics of unknown data source (mass spec), example of Chado integration
- Host: GitHub
- URL: https://github.com/evancarroll/mumine
- Owner: EvanCarroll
- Created: 2018-01-03T17:07:16.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2018-01-03T17:13:29.000Z (over 7 years ago)
- Last Synced: 2025-02-25T02:05:48.296Z (3 months ago)
- Topics: chado, flybase, postgresql
- Language: PLpgSQL
- Homepage:
- Size: 1.95 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.markdown
Awesome Lists containing this project
README
NAME
====
Chado FDW and data loaders.
DESCRIPTION
====
No idea what generates this data, but essentially I got a bunch of stuff like
```
B5X552,SD13785p (Fragment) (CG11873-RA) [] - [B5X552_DROME],,,1,5.678E5
Q4V5Z4,IP11818p (CG11360) [MEX3A;MEX3B;MEX3C;MEX3D] - [Q4V5Z4_DROME],,,1,1.168E5
```
The fields are described in [the sql column names](./sql/24_mumine_tables.sql).
The compound name, second field in the above example gets parsed into the
constituent parts,
* name_uniprotkb
* name_human_ortholog
* name_orf_gene
* name_protein
Then a normalized name gets produced which is ideally the `orf_gene`, unless
that's wrong otherwise it is the `name_protein` unless that's also wrong
(search `EG:`) in which case we fall back and use the `orf_gene`.
We further link with Chado using PostgreSQL's
[`postgres_fdw`](https://www.postgresql.org/docs/current/static/postgres-fdw.html)
so we can run cross-db queries.
**EVERYTHING INSTALLS INTO `mumine` SCHEMA**
LICENSE
====
CC-BY-SA 4.0