Java or Pathon?
autism4j
- A generic package for loading/parsing/inmorting/exporting ontology to neo4j.
- A module which deal with annotation data, specifically autism patient data.
- A statistic module for analysis such as enrichment analysis and semantic similarity.
- may contain possible wrapping of existing C++/R/Python code
resources
loading of ontologies files (a) in topOnto and
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
Page rank
- 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
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