INCATools/dosdp-tools

Name: dosdp-tools

Owner: INCATools

Description: Utility for working with DOSDP design patterns and OWL ontologies

Created: 2016-08-30 14:58:21.0

Updated: 2017-11-09 17:20:14.0

Pushed: 2017-12-02 04:31:40.0

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Size: 80

Language: Scala

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README

dosdp-tools

dosdp-tools is a command-line utility for working with DOSDP design patterns and OWL ontologies. Given a YAML design pattern following the DOSDP spec, it can either generate ontology axioms from an input table of terms, or instead generate a SPARQL query that can be used to query an ontology for terms matching the pattern.

Releases

Pre-packaged releases can be downloaded from here.

Building

Install sbt on your system. For Mac OS X, it is easily done using Homebrew: brew install sbt

To compile and build the executable package, run:

sbt stage

You will find executables for Unix and Windows in target/universal/stage/bin/. These depend on the libraries in target/universal/stage/lib.

Usage

e

dp-tools [options] command [command options]

ons

-obo-prefixes : Assume prefixes are OBO ontologies; predefine rdf, rdfs, and owl
-ontology     : OWL ontology (provide labels, query axioms)
-outfile      : Output file (OWL or TSV)
-prefixes     : CURIE prefixes (YAML)
-template     : DOSDP file (YAML)

ands

enerate [command options] : generate ontology axioms for TSV input to a Dead Simple OWL Design Pattern
  --infile : Input file (TSV)

uery [command options] : query an ontology for terms matching a Dead Simple OWL Design Pattern
  --print-query : Print generated query without running against ontology
  --reasoner    : Reasoner to use for expanding variable constraints (currently only valid option is `elk`)

dosdp-tools has two modes: generate and query:

Generate

The generate command creates an ontology from a DOSDP pattern file and an input file of tab-separated filler values. Column names in the TSV file need to match variables defined in the DOSDP. A special defined_class column should provide the IRI for the newly created class instantiating the pattern. A provided ontology is used to find labels for terms, needed to generate annotation values. Example:

p-tools generate --obo-prefixes=true --template=exposure_to_chemical.yaml --infile=exposure_to_chemical.tsv --outfile=exposure_to_chemical.ofn --ontology=chebi_import.owl

Query

The query command queries an ontology for terms that meet the logical patterns defined in a DOSDP pattern file. Instead of performing the query, you can also simply print the generated SPARQL. Example:

p-tools query --template=entity_attribute_location.yaml --prefixes=prefixes.yaml --print-query

Output:

IX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
IX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
IX owl: <http://www.w3.org/2002/07/owl#>

CT DISTINCT ?defined_class (STR(?defined_class__label) AS ?defined_class_label) ?attribute (STR(?attribute__label) AS ?attribute_label) ?entity (STR(?entity__label) AS ?entity_label) ?location (STR(?location__label) AS ?location_label)
E {
ined_class owl:equivalentClass ?ba95b4a7b13f4a86af50c3e0e1182838 .
5b4a7b13f4a86af50c3e0e1182838 owl:intersectionOf/rdf:rest*/rdf:first ?c90d72646ac64cc19318ca3273f11cd6 .
5b4a7b13f4a86af50c3e0e1182838 owl:intersectionOf/rdf:rest*/rdf:first ?attribute .
5b4a7b13f4a86af50c3e0e1182838 owl:intersectionOf/rdf:rest/rdf:rest rdf:nil .
d72646ac64cc19318ca3273f11cd6 owl:onProperty <http://purl.obolibrary.org/obo/RO_0000052> .
d72646ac64cc19318ca3273f11cd6 owl:someValuesFrom ?7f7e348c174d42f0a76663cc59f21e37 .
e348c174d42f0a76663cc59f21e37 owl:intersectionOf/rdf:rest*/rdf:first ?75f4eb2eae374a77878c36acda870206 .
e348c174d42f0a76663cc59f21e37 owl:intersectionOf/rdf:rest*/rdf:first ?entity .
e348c174d42f0a76663cc59f21e37 owl:intersectionOf/rdf:rest/rdf:rest rdf:nil .
4eb2eae374a77878c36acda870206 owl:onProperty <http://purl.obolibrary.org/obo/BFO_0000050> .
4eb2eae374a77878c36acda870206 owl:someValuesFrom ?location .
ER(?entity != ?75f4eb2eae374a77878c36acda870206)
ER(?c90d72646ac64cc19318ca3273f11cd6 != ?attribute)
ONAL { ?defined_class rdfs:label ?defined_class__label . }
ONAL { ?attribute rdfs:label ?attribute__label . }
ONAL { ?entity rdfs:label ?entity__label . }
ONAL { ?location rdfs:label ?location__label . }