johardi

Loading OWL Axioms Into Neo4j

Date: January 15, 2021

Make sure you have the OWL2LPG-Translator library installed in your local system.

$ pwd
owl2lpg-translator
$ ls
LICENSE				neo4j-plugin-text-analyzer/	owl2lpg-translation-cli/	owl2lpg-translation-exporter/
README.md			owl2lpg-client-api/		owl2lpg-translation-core/	pom.xml

johardi

CALL {
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(axiom:AssertionAxiom)
   MATCH (entity:NamedIndividual { iri: $subjectIri })-[:IS_SUBJECT_OF]->(axiom)
   WHERE project.projectId = $projectId
   AND branch.branchId = $branchId
   AND document.ontologyDocumentId = $ontoDocId
   RETURN entity
   UNION
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(annotation)
   MATCH (entity)-[:ENTITY_IRI]->(:IRI { iri: $subjectIri })-[:IS_SUBJECT_OF]->(annotation)

johardi

CALL {
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(axiom:AnnotationAxiom)
   MATCH (entity:AnnotationProperty { iri: $subjectIri })-[:IS_SUBJECT_OF]->(axiom)
   WHERE project.projectId = $projectId
   AND branch.branchId = $branchId
   AND document.ontologyDocumentId = $ontoDocId
   RETURN entity
   UNION
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(annotation:AnnotationAssertion)
   MATCH (entity)-[:ENTITY_IRI]->(:IRI { iri: $subjectIri })-[:IS_SUBJECT_OF]->(annotation)

johardi

CALL {
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(axiom:DataPropertyAxiom)
   MATCH (entity:DataProperty { iri: $subjectIri })-[:IS_SUBJECT_OF]->(axiom)
   WHERE project.projectId = $projectId
   AND branch.branchId = $branchId
   AND document.ontologyDocumentId = $ontoDocId
   RETURN entity
   UNION
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(annotation:AnnotationAssertion)
   MATCH (entity)-[:ENTITY_IRI]->(:IRI { iri: $subjectIri })-[:IS_SUBJECT_OF]->(annotation)

johardi

CALL {
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(axiom:ObjectPropertyAxiom)
   MATCH (entity:ObjectProperty { iri: $subjectIri })-[:IS_SUBJECT_OF]->(axiom)
   WHERE project.projectId = $projectId
   AND branch.branchId = $branchId
   AND document.ontologyDocumentId = $ontoDocId
   RETURN entity
   UNION
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(annotation:AnnotationAssertion)
   MATCH (entity)-[:ENTITY_IRI]->(:IRI { iri: $subjectIri })-[:IS_SUBJECT_OF]->(annotation)

johardi

// Get Class Frame
CALL {
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(axiom:ClassAxiom)
   MATCH (entity:Class { iri: $subjectIri })-[:IS_SUBJECT_OF]->(axiom)
   WHERE project.projectId = $projectId
   AND branch.branchId = $branchId
   AND document.ontologyDocumentId = $ontoDocId
   RETURN entity
   UNION
   MATCH (project)-[:BRANCH]->(branch)-[:ONTOLOGY_DOCUMENT]->(document)-[:AXIOM]->(annotation:AnnotationAssertion)

johardi

Running the Frame Query

STEP 1

In a Terminal:

Run the SSH Tunneling command:

ssh -L 7474:localhost:7474 -L 7687:localhost:7687 <username>@13.79.232.10

johardi

Import CIDO ontology to Neo4j Workflow

STEP 0

Download the CIDO ontology from the BioPortal: https://bioportal.bioontology.org/ontologies/CIDO

STEP 1

In a terminal, after unpacking the owl2lpg-translation-cli package:

./run.sh translate -f csv /path/to/ontology/cido.owl > cido.csv

johardi

import os
import csv
import numpy as np

data = {}
with open(os.path.expanduser('~/Downloads/people_wiki.csv')) as csvfile:
    reader = csv.DictReader(csvfile)
    for row in reader:
        for column, value in row.items():
            data.setdefault(column, []).append(value)

johardi

# Cellfie 2.1.0 Release Note

## Summary
This release contains new features, UI improvements and fixes various bugs and this is the official release package.

## New Features

* Implemented user mouse movement tracking for an interactive cell range selection
* Implemented check box selection for selecting transformation rules to use when generating the axioms (#55)
* Implemented the new MappingMaster feature `mm:EntityIRI` to extract the IRI from an existing entity (#70)