Closed cannin closed 4 years ago
Hi, I looked at number of Pathway database which provided biological pathways. I also looked http://www.pathwaycommons.org/pc2/datasources and http://cpdb.molgen.mpg.de/ where user can find all integrated pathways.
My questions is about Example Input Dataset which provided above. Is that input from all pathways database are similar to example input dataset? If no, then why we should to consider to this example input file?
Regards, Jinal
Hi @cannin ,
I'm a senior Computer Science university student from Spain, and I feel interested on this project for GSoC'17.
I have been looking and understanding the code at [1], as well as the given references, but I have still some questions:
With the "Example Input Dataset" stated on the project description, what should be the output?
If I'm correctly understanding, the main idea to make this a Generic converter is the 3rd point idea: "Working on the refactoring the code such that hard coded BioPAX concepts are extracted from the input data.", so the blk of work will be here, am I right?
Thank you!
Background
Pathway Commons is an aggregated database of molecular interactions with a web service that receives millions of hits per year. Data stored in the Pathway Commons is in the BioPAX XML-based format. Currently, the data is aggregated from a collection of approximately 20 databases, and we would like to continue to expand this. Currently, this process involves the creating a custom converter for each database in Java; a process that may be difficult for data providers that may not be working with Java.
The converters make use of the the Java Paxtools library to create BioPAX output.
Goal
The goal of this project is to make it easier to aggregate additional databases into Pathway Commons by building a generic converter that may be more widely used. The project is to generalize an existing converter that was made in a previous GSOC to support a format that is easier to understand. Below is an example of the data format that would be the input to the converter.
Example Input Dataset
Data from this file: http://www.pathwaycommons.org/archives/PC2/current/PathwayCommons.8.transfac.EXTENDED_BINARY_SIF.hgnc.txt.gz NOTE: Not all columns have data.
Interaction Information
Entity Information
Description
Skills
Java, XML
Difficulty level 2
This project makes use of pre-exisiting code, so the participant would not be starting from scratch.
Public Repository
Project Code for Work on the Pathway Database Converters for the Expansion of Pathway Commons
Potential mentors
Augustin Luna (aluna@jimmy.harvard.edu)
References