Week 4: Markdown-based Semantic Annotation of Workflow Scripts – Project 1

Week 4 – Update

Hello everyone, I am Xiaoliang Jiang from project 1. This is the fourth week for my internship. For this week, I did a lot of interesting things on the “prototype” function I made last week. I modified the structure of the output RDF file, added a User domain option, and created another important function which could generate a RDF diagram in Rstudio by using “igraph” package.

First of all, after I posted my working blog and discussed some problems I had with my mentors, I started to revise my R scripts to let the output file in a more formal format. In detail, I added prefix header into the output file by using a function which could automatically generate the headers by the keywords in the content. I also modified the format of entities and the structure of whole RDF files follows the TTL format.

Secondly, I added several arguments into my function to provide an editable user domain. This may be useful in the future, especially when users connect their codings to their working domain.

Thirdly, I added an important function into the package, which could generate an RDF diagram in nodes and lines in Rstudio by using “igraph” package. In general, the “igraph” package is a really good tool to generate a network in R, which is very easy to learn and understand. I modified the “key-value pairs” functions in original “strcode” to make it work properly, and could serve as a relationship holder for my function. After that, I added several variables into my functions to save the information of entity names, and the relationships between entities. At last, by using an input called “graph”, users could decide to generate an RDF diagram in Rstudio or not by themselves.

Although I think I made a lot of interesting changes this week, I should say some of them are just in prototype. I need to revise and modified them in the future. So, in the following weeks, I think I need to learn how to modify the UI to add more functions and create a better interface for existing functions. In addition, I need to learn more about JSON-LD which may be a better format for my output file.


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