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 |