Making imports

PCO uses the Robot functions extract to make OWL files that import selected terms other ontologies. The plan is to move all this to the makefile, but for now, it is documented here.

Robot takes as input a text file listing the terms to be imported and the source ontology (stored locally at src/ontology/imports/files, but not committed to the github repo) and generates an OWL import file in that same directory. Note that to update the import, you must first download the latest copy of the source ontology file. The `--annotate-with-source true' option should be included.

During editing, import files are stored in /src/ontology/imports. In order to edit the ontology, you must import from this working directory, rather than from the release file PURLs (see below). If you import from a local file in Protege, that should work.

For releases, all import text files and extracted OWL files are stored in the imports directory in the root directory. Using partial redirect, these can be referenced using PURLs such as http://purl.obolibrary.org/obo/pco/imports/go_import.owl.

There are multiple extraction methods that can be used. The table below describes PCO imports and the extraction methods used to create them. Some ontologies are imported whole.

Source Ontology	extraction method	term file	import file
OBO Metadata Ontology (OMO)	full import
RO core	full import	http://purl.obolibrary.org/obo/ro/core.owl
BFO	BOT	/src/ontology/imports/bfo_terms.txt	/src/ontology/imports/bfo_import.owl
ECOCORE	MIREOT	/src/ontology/imports/ecocore_terms.txt	/src/ontology/imports/ecocore_import.owl
ENVO	MIREOT	/src/ontology/imports/envo_terms.txt	/src/ontology/imports/envo_import.owl
GO	BOT	/src/ontology/imports/go_terms.txt	/src/ontology/imports/go_import.owl
IAO	MIREOT	/src/ontology/imports/iao_terms.txt	/src/ontology/imports/iao_import.owl
NCBITaxon	STAR	/src/ontology/imports/ncbitaxon_terms.txt	/src/ontology/imports/ncbitaxon_import.owl
PATO	BOT	/src/ontology/imports/pato_terms.txt	/src/ontology/imports/pato_import.owl
RO	MIREOT	/src/ontology/imports/ro_terms.txt	/src/ontology/imports/ro_import.owl
STATO	MIREOT	/src/ontology/imports/stato_terms.txt	/src/ontology/imports/stato_import.owl
CARO	manual import	n/a	CARO terms were added to the ontology file manually. Soon these will be replaced by a proper import from COB

Robot by default gives the import files the IRIs for their source ontologies. These need to be changed to the pco import directory. For example, the IRI for the GO imports file should be http://purl.obolibrary.org/obo/pco/imports/go_import.owl. This can be done using the robot annotate command with the --ontology-iri option.

The robot command used with each term file should be appended to the file as a comment.

Below is an example robot command to create the GO import module:

robot extract --method BOT
--input files/go.owl
--term-file go_terms.txt
--annotate-with-source true
annotate --ontology-iri "http://purl.obolibrary.org/obo/pco/imports/go_import.owl"
--output go_import.owl

Note that ENVO imports a lot of terms from PCO, so using an SMLE method to extract imports leads to import cycles. The current ENVO extract command (based on /src/ontology/imports/envo_terms.txt) is:

robot extract --method MIREOT
--input files/envo.owl
--upper-term "http://purl.obolibrary.org/obo/BFO_0000040"
--lower-term "http://purl.obolibrary.org/obo/ENVO_01000744"
--lower-term "http://purl.obolibrary.org/obo/ENVO_01001369"
--intermediates minimal
--annotate-with-source true
--copy-ontology-annotations true
annotate --ontology-iri "http://purl.obolibrary.org/obo/pco/imports/envo_import.owl"
--output envo_import.owl