Week 11

-
Greetings!

I hope you are in great health. As my previous week had been very busy due to online tests and interviews during an internship drive in my college, I wanted to complete the next task for this project, that was to produce `glossary` files in `rdf` format takin inspiration from this file.

To get an idea, please look at this model and its respective glossary file in this folder for non-standardised SBML for BIOMD0000000176. 
Here you can observe that all the annotations from the model are extracted and are put in as children of a single XMLNode. The glossary can be linked to the model by `rdf:about` tag which basically contains the `metaid` for various elements from the model.

 This glossary file becomes important and purposeful when you consider models which are hard to annotate. Biological models of the same thing can be present in various formats and it can be hard to annotate models in some formats whereas others (like SBML) can be easily annotated (with present tools like ModelPolisher). Both models contain the same elements, and thus if a model is annotated in one format, the same annotations can be used for another format with help of mapping through `metaid`s.
Also, a Combine Archive can be used to save models in different formats together in a single zip file. When such an archive is used, it can be convenient in the future to have a single glossary file for all the models which basically contains annotations for each element mapped using `metaid`s.

So, my target for this week was to strip out all the annotations from a polished model and save them separately in a single glossary file (format: rdf). Initially, I tried to find different rdf parsers (like Apache Jena) and go through their documentation to find a suited one, but the output format that was required for the glossary could be easily produced using an existing class in jsbml repository: SBMLRDFAnnotationParser.

I was able to figure out the usage of this particular class but had some problems in passing the inputs as the input was an XMLNode which was confusing for me. I took help from Nicolas Rodriguez regarding the issue via some meetings and was finally able to produce the output rdf by iterating through all the elements in the model, get the annotations using the first child of produced XMLNode(s), and putting them as children of a parent XMLNode. This was further written to a file: model_glossary.rdf.

After successful production of the glossary rdf, just one problem persisted: the produced glossary was not in a tidy format.
To produce the glossary in a tidier format, I took inspiration from TidySBMLWriter and successfully produced the glossary rdf in a tidy format using repository jtidy.

Some minor bug fixes and comments were added along the way, which concluded in the successful completion of this task.

Thank You!

Comments

Post a Comment

Popular posts from this blog

Final Report: GSoC 2019

-
This is the final report for project  Extending ModelPolisher to a universal model annotation tool  under Google Summer of Code 2019, organization: NRNB . ModelPolisher is a model annotation tool originally developed for the BiGG Models Knowledgebase. Annotations enhance the reusability and interoperability of biological models. During this project, I extended the model annotation capabilities of ModelPolisher, updated the MatlabParser (reading models in the COBRA matlab format), containerized ModelPolisher using Docker, added functionality to use AnnotateDB for model annotation, and added a feature to produce a model annotation glossary and CombineArchives as outputs. As part of this work, the SQLite version of the ModelPolisher database backend could be removed. Link to G ithub Project:  https://github.com/draeger-lab/ModelPolisher The project proceeded according to the goals and timeline of the project  proposal ,  except for one major change: I completed my goal of contain
Read more

Week 9, 10

-
Greetings! The following blog contains my progress in Week 9, 10. In the last days of the previous week, I had already integrated AnnotateDB in ModelPolisher but it was not yet properly checked. So, this week my major goal was to completely check the integration of AnnotateDB and solve bugs (if any). Also, I had to update the README file to provide proper instructions for users to add annotations from AnnotateDB. Testing AnnotateDB Integration:   I had already tested the to query to get the annotations from ADB using BiGG Id of species and reactions, so here only ModelPolisher was tested for successful extraction of annotations from ADB. Issue Observed : After I had added support for ADB in ModelPolisher, I tried to polish some random models (after temporarily removing code to extract annotations from BiGG DB). I observed that ModelPolisher is not making queries to ADB while the extracting annotations from ADB in class `AnnotateDB`, but rather the queries are being made to BiGG D
Read more

Week 12

-
Greetings! After completing the code for the production of the glossary file, my next task for this project was to give the user an option to produce the output in form of a Combine Archive which contains the polished model and the glossary file. This feature may look redundant now, but it is very helpful to keep biological models in differents formats in one Combine Archive which also contains a single glossary file which has all the annotations from the polished model. So, for this task, I first added an option `--output-combine` for users in which they can provide a boolean to produce output as a single Combine Archive. After addition of this option, if the user provides value `true` for this option, I use binfalse/CombineArchive  repository to put in the output polished model and the glossary file in a Combine Archive zip. Note that, in this case, any annotated model or glossary rdf file will not be produced. There were multiple issues during the implementation of this fe
Read more