Java or Pathon?

autism4j

1. A generic package for loading/parsing/inmorting/exporting ontology to neo4j.
2. A module which deal with annotation data, specifically autism patient data.
3. A statistic module for analysis such as enrichment analysis and semantic similarity.
4. may contain possible wrapping of existing C++/R/Python code

resources

loading of ontologies files (a) in topOnto and

• pheno4j
• SciGraph
• ont4j

semantic similarities

• https://arxiv.org/pdf/cmp-lg/9511007.pdf
• https://www.biorxiv.org/content/biorxiv/early/2017/02/16/108977.full.pdf
• https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115692

network clusting

• graph-tool

Page rank

• (wiki)[https://en.wikipedia.org/wiki/PageRank]

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• Colin has python code to export/import obo file to/from the server. NRG is running a neo4j server. (account created:xin)
• Colin: C++ code to contruct a network/vetice/edge object.
• Colin: C++ hypergeometric test for enrichment test. Accept the two comparing gene list as input.
• R code for entrypy calculation on igraph network. Example in PPI network. Code is currently workong with undirect graph, needs to be implement to work with directional graph.

NRG server ip:

129.215.164.31

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Meeting note 5th Oct 2018

Neo4j

• Graph structure:

Nodes, Edges, Graph...neo4j.jar

• Communication with server

driver

Loading ontology into python/java

Owl

Java api:

https://github.com/owlcs/owlapi/

• An API for OWL 2 and an in-memory reference implementation
• RDF/XML parser and writer
• OWL/XML parser and writer
• OWL Functional Syntax parser and writer
• Turtle parser and writer
• KRSS parser
• OBO format parser
• Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet, Racer, JFact and Chainsaw.*

python api:

• rdflib

git update-index --assume-unchanged ddp2neo4j/settings.py