Batch import definition files for ontologies
Please see Owl2Neo4J for details about how batch imports work.
The general procedure is the following:
-
Download or clone this repo:
git clone https://github.com/refinery-platform/ontology-imports cd ontology-imports -
Download ontologies using the helper methods:
./download-stemcellcommons.sh -
Go to Refinery and import ontologies.
./manage.py import_ontology -b ./import-stemcellcommons.json
Pro-Tip: If you are developing Refinery, step 1 and 2 should ideally be executed in your transfer directory on your host VM and step 3 should be triggered from within the VM. Make sure to adjust the path to the JSON file accordingly.
Stem Cell Commons
Date: March 1, 2016
| Ontology | Downloadable | Importable | Memory (*) |
|---|---|---|---|
| BTO | ✓ | ✓ | |
| CHEBI | ✓ | ✓ | |
| CL | ✓ | ✓ | |
| EFO | ✓ | ✓ | |
| FMA | ✓ | ✓ | |
| GO | ✓ | ✓ | |
| MA | ✓ | ✓ | |
| NCBITAXON | ✓ | ||
| NCIT | ✓ | ✓ | |
| OBI | ✓ | ✓ | |
| PATO | ✓ | ✓ | |
| UO | ✓ | ✓ |
*) The number of coffee mugs directly correlates with the import time and amount of memory your system needs. As an indicator: ontologies marked as importable were imported on a MacBook Pro with 16 GB Ram.
Note: Importing on the development VM might require even more memory. (And might make your drink even more coffee, so please watch your heart rate.)
MetaboLights
Last tested: April 28, 2017
Note: Ontologies that are not available in OWL ignored.
| Ontology | Downloadable | No OWL | Importable | Memory (*) | Issues |
|---|---|---|---|---|---|
| AURA | ✓ | ||||
| BAO | ✓ | ✓ | |||
| BP | ✓ | ✓ | |||
| BTO | ✓ | ✓ | |||
| CADSRVS | ✗ | ||||
| CCON | ✓ | ✓ | |||
| CHEBI | ✓ | ✓ | |||
| CHMO | ✓ | ✓ | |||
| CLO | ✓ | ||||
| CNO | ✓ | ✗ | Could not load http://www.obofoundry.org/ro/ro.owl | ||
| CO-WHEAT | ✗ | ||||
| CSEO | ✓ | ✓ | |||
| DOID | ✓ | ✓ | |||
| DRON | ✓ | ✓ | |||
| EDAM | ✓ | ✓ | |||
| EFO | ✓ | ✓ | |||
| ENVO | ✓ | ✓ | |||
| FIX | ✓ | ✓ | |||
| GO | ✓ | ✓ | |||
| HP | ✓ | ✓ | |||
| ICF | ✓ | ✓ | |||
| IDO | ✓ | ✓ | |||
| MEDDRA | ✗ | ||||
| MESH | ✓ | ✓ | |||
| MI | ✓ | ✓ | |||
| MS | ✓ | ✓ | |||
| NCBITAXON | ✓ | ? | Java heap space issue | ||
| NCIT | ✓ | ✓ | |||
| NEMO | ✓ | ✓ | |||
| NIFSTD | ✓ | ✗ | Non-simple property | ||
| NMR | ✓ | ✓ | |||
| OBI | ✓ | ✓ | |||
| PATO | ✓ | ✓ | |||
| PO | ✓ | ✓ | |||
| PW | ✓ | ✓ | |||
| ROLEO | ✓ | ✓ | |||
| SIO | ✓ | ✓ | |||
| SNOMEDCT | ✗ | ||||
| SOY | ✗ | ||||
| SWEET | ✓ | ✓ | |||
| UNITSONT | ✓ | ✓ | |||
| UO | ✓ | ✓ | |||
| XCO | ✓ | ✓ | |||
| Total: | |||||
| 43 | 38 | 5 | 34 | 3 |