Krusty

Krusty is a library to synchronize the NGLY1 Deficiency Knowledge Graph in the Knowledge Navigation (Neo4j) and Knowledge Contribution (Wikibase) components.

Prerequisites

• Set up a Wikibase instance
• Set up a Neo4j server

Data

We used the NGLY1 Deficiency Knowledge Graph v3.2: csv neo4j format network

Wikibase Setup

• Follow instructions here: https://github.com/wmde/wikibase-docker/blob/master/README-compose.md
• Create a bot account in your wikibase (do it manually, or see this)
• Change settings in config.cfg
• Run this to create an 'equivalent property' and 'equivalent class' property in the Wikibase, or make sure these properties have the appropriate URIs (http://www.w3.org/2002/07/owl#equivalentProperty and http://www.w3.org/2002/07/owl#equivalentClass).
• Increase label, description, alias string length limit (see Wikibase Setup Notes below)

Neo4j Setup

We setup a Neo4j Community Server 3.5: Neo4j Server Download

Usage

Neo4j to Wikidata Bot: neo4j_to_wd.py

For usage: neo4j_to_wd.py --help

File Formats

Expects nodes and edges csv with the following format

nodes

Expects the following column names: id:ID,:LABEL,preflabel,synonyms:IGNORE,name,description

• "id:ID" is used as the canonical identifier and should be unique
• ":LABEL" is a string that is used as the "instance of" statement
• "prefLabel" is used as the item label
• "synonyms:IGNORE" and "name" are merged and used as the aliases. Pipe separated
• "description" is the description

edges

Expects the following column names: :START_ID,:TYPE,:END_ID,reference_uri,reference_supporting_text,reference_date,property_label,property_description:IGNORE,property_uri

• ":START_ID" and ":END_ID": subj and obj of the edge. These should match an "id:ID" in the nodes file
• ":TYPE": property canonical ID
• "reference_uri": a pipe-separated ("|") string of reference URLs
• "reference_supporting_text": string
• "reference_date": ignored
• "property_label": used as the label for the property item in wikibase
• "property_description:IGNORE": used as the description for the property item in wikibase
• "property_uri": property uri. added as equivalent property statement

Notes

• Multiple rows in the edges file that consist of identical (start_id, property, end_id) will be used to generate multiple references on the same statement.
• Multiple reference_uris within the same row will result in multiple reference urls on one reference.
• If a reference url is longer than 400 characters, it will truncated, unless it is a pubmed reference (i.e., it starts with "https://www.ncbi.nlm.nih.gov/pubmed/"). In that case, the pmids in the url will be split among multiple reference url statements within the same reference.
• Reference urls starting with "ISBN-13" or "ISBN-10" are handled specially. If the reference url is not a URL (besides those isbns), it will fail.

Wikibase Setup Notes

To increase label, description, alias string length limit

ID=$(docker-compose ps -q wikibase)
docker exec -it $ID /bin/bash
nano /var/www/html/extensions/Wikibase/repo/config/Wikibase.default.php
# change the following line from 250 to whatever you want
# 'multilang-limits' => ['length' => 250],

Wikidata to Neo4j Bot: wd_to_neo4j.py

Write out all item and statements in the Wikibase to a nodes and edges file in the format described above

The only thing that will be lossy is if a reference url was truncated.

For usage: wd_to_neo4j.py --help

Cron

Use cron jobs in bash to synchronize Neo4j-Wikibase graphs. We deployed each component distributed in different servers.

Example of use

We showcase the workflow to setup a wikibase, populate it and synchronize it with Neo4j.