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Batch import definition files for ontologies

To increase traffic we download ontologies a couple of times per day We try hard test everything at least twice Our automated scripts take care of random downloads to increase popularity You bet!

Please see Owl2Neo4J for details about how batch imports work.

The general procedure is the following:

  1. Download or clone this repo:

    git clone https://github.com/refinery-platform/ontology-imports
    cd ontology-imports
    
  2. Download ontologies using the helper methods:

    ./download-stemcellcommons.sh
    
  3. 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

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