Skip to content
Branch: master
Find file History
Latest commit 75d19d1 Sep 11, 2019
Permalink
Type Name Latest commit message Commit time
..
Failed to load latest commit information.
Makefile Remove obsolete terms from GENO import Feb 7, 2019
README.md Add RO to import list Jul 6, 2018
annotations.txt Add FOODON import for 'has allergic trigger' axioms, update import te… May 31, 2018
catalog-v001.xml Simplify imports for easier local development Nov 28, 2016
chebi_import.owl Fix removed equivalent classes Jun 13, 2018
chebi_terms.txt Add new IEDB classes Jun 7, 2018
cl_import.owl added Cell Ontology terms Feb 15, 2019
cl_terms.txt added Cell Ontology terms Feb 15, 2019
eco_import.owl First pass at adding some reference types Sep 1, 2019
foodon_import.owl Fix FOODON import Aug 20, 2018
foodon_terms.txt Add missing allergy/material basis mappings Aug 18, 2018
geno_full.owl Add GENO import Aug 3, 2018
geno_import.owl Remove obsolete terms from GENO import Feb 7, 2019
geno_terms.txt Add GENO inheritance terms Feb 6, 2019
go_import.owl import fix Mar 20, 2017
hp_import.owl Update imports, sort IDs Jun 6, 2018
hp_terms.txt Update imports, sort IDs Jun 6, 2018
ncbitaxon_import.owl Add new IEDB classes Jun 7, 2018
ncbitaxon_terms.txt Add new IEDB classes Jun 7, 2018
omim_susc_import.owl Fix test errors Sep 11, 2019
ro_import.owl Add RO to import list Jul 6, 2018
ro_terms.txt Add RO to import list Jul 6, 2018
so_import.owl June 2019 DO release files Jun 28, 2019
symp_import.owl updated ischemia due to name conflicts Apr 18, 2019
trans_import.owl June 2019 DO release files Jun 28, 2019
uberon_import.owl Remove deprecated entities from imports Apr 19, 2019
uberon_terms.txt Remove deprecated entities from imports Apr 19, 2019

README.md

DO Imports

Each import consists of two files: a *_terms.txt file and a *_import.owl file. The .txt file is used to generate the .owl import module using ROBOT extract.

To add a new import term

Open the corresponding .txt file and do a text search to ensure the ID has not yet been added. Append a new line with the ID, followed by a comment with the class label, e.g.:

UBERON:0000955	# brain

Save the file, and then in terminal, run the desired make command (see below). This can be run from the ontology directory OR the imports directory. You can make one at a time with the command make <import name>, e.g.:

make uberon

Or you can make all the import modules at once:

make imports

Keep in mind that NCBITaxon is very large and will take some time to extract the terms.

To remove an import term

Open the corresponding .txt file and do a text search to find the line with the ID to remove. Delete the whole line, and then follow the steps above to make the import module.

Current 'makeable' imports

  • chebi - Chemical Entities of Biological Interest
  • cl - Cell Ontology
  • foodon - Food Ontology
  • hp - Human Phenotype Ontology
  • ncbitaxon - NCBI organismal classification
  • uberon - Uberon multi-species anatomy ontology
  • ro - Relations Ontology (object properties)
You can’t perform that action at this time.