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Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) Database #62

Closed MoHelmy closed 7 years ago

MoHelmy commented 7 years ago

Adding support for PSIMI-TAB format to the Disease Variant Impact (DV-IMPACT) Database

Background

DV-IMPACT is an online resource for the disease variants impact assessment on domain-peptide PPI networks. DV-IMPACT stores the PPI interaction networks mediated by wildtype and disease variants and visualizes the overlay of the two networks to understand the effects of mutations on the network and consequently their cellular and biological impact. Furthermore, DV-IMPACT provides the full sequences of the wildtype and disease variant proteins with a comprehensive search and download interface to easily build customized protein databases for genomic and proteomic analysis. The Proteomics Standards Initiative (PSI) of the Human Proteomics Organization (HUPO) defines community standards for data representation in proteomics to facilitate data comparison, exchange, and verification. PSI provides the PSIMI (PSI-Molecular Interactions) format as a tab-delimited data exchange format for molecular interactions. PSIMI format describes binary interactions, one pair of interactors per row. Columns are separated by tabulations. Tools allowing to manipulate this data format are available.

Focus

The data deposition into DV-IMPACT is passed on uploading multiple TAB delimited files through the website backend. Each TAB delimited file corresponds to one of the database tables. Thus, the files need to have the same format, number of columns and data types of the tables. This process is highly manual and a source of human error. Furthermore, the data upload needs to be done through the database admin. In this project, we want to add support for PSIMI-TAB format to DV-IMPACT in both data upload and data download. Goals 1- Add support for PSIMI-TAB format to the admin tools of the DV-IMPACT database. 2- Add download PPI networks in PSIMI-TAB format to the frontend of DV-IMPACT database. 3- Create registration and user profile system that allows users to register and upload their own data independently (without the need of the DB admin to be involved in the upload process).

Inputs

The student will be provided with access to the database, its design and data as well as an introduction to the topic and the details of the needed features. The student will have the freedom to choose among several tools and technologies to work with as long as they are compatible with the current setup of the DV-IMPACT server.

Technology and Skills

JSON, PHP, JQuery, HTML5, CSS3, Javascript, Cytoscape.js

Potential Mentors

Mohamed Helmy, Gary Bader

Contact

Interested students should contact: Mohamed Helmy, Gary Bader

jajodiaraghav commented 7 years ago

Hello everyone Although i haven't used cytoscape.js before, i have been working on web technologies for quite sometime. I have a sound knowledge of HTML, JS , jQuery, PHP, SQL etc. I have also contributed to several Open Source project and has an experience on working with various web technologies. I do have have a few queries in mind

  1. Do i have to mail alex.pico@gladstone.ucsf.edu or the mentors, in order to get in touch?
  2. What steps should i take in order to be a strong candidate?

I have also read another idea Developing a web interface for DoMo-Pred. I found it to be interesting as well. Is it too late to ponder over that idea, as 'ankanch' has already submitted a prototype? Thank you

MoHelmy commented 7 years ago

Hi Rajhav,

Thanks for being interested in our ideas. The DoMo-Pred idea is almost occupied as we have two very good candidates. However, you are welcome to the DV-IMPACT project. Cytoscape is not a very big deal, all our previous students learnt it during the projects.

We select students based on a small evaluation task, like the one done by ankanch for the other idea. If you are interested, I can send you a description of the task.

Thanks, Mohamed

Sent from my iPad

On Jan 22, 2017, at 7:04 AM, Raghav Jajodia notifications@github.com wrote:

Hello everyone Although i haven't used cytoscape.js before, i have been working on web technologies for quite sometime. I have a sound knowledge of HTML, JS , jQuery, PHP, SQL etc. I have also contributed to several Open Source project and has an experience on working with various web technologies. I do have have a few queries in mind

Do i have to mail alex.pico@gladstone.ucsf.edu or the mentors, in order to get in touch? What steps should i take in order to be a strong candidate? I have also read another idea Developing a web interface for DoMo-Pred. I found it to be interesting as well. Is it too late to ponder over that idea, as 'ankanch' has already submitted a prototype? Thank you

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jajodiaraghav commented 7 years ago

That sounds good to me. Please send the task description. Will my time start as soon as you post the task description?

MoHelmy commented 7 years ago

Hi, Will send you the task soon, sorry a bit busy with something here. Yes, your time will start after you receive the task.

On Mon, Jan 23, 2017 at 9:53 AM Raghav Jajodia notifications@github.com wrote:

That sounds good to me. Please send the task description. Will my time start as soon as you post the task description?

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jajodiaraghav commented 7 years ago

No issues. Will be waiting for your response.

MoHelmy commented 7 years ago

Hi, Sorry again for the delay. Please find the task description below. Let me know of you need any further details. Best of luck, Mohamed

Task Description: Developing a simple web interface for DV-IMPACT database admin. The interface should perform the following functions: 1- Uploads a PSI-MI-TAB file. 2- Process the uploaded file and insert the contents into the corresponding fields of the database. 3- Display the uploaded data in tabular format. 4- Bonus: instead of displaying the uploaded data as table, implement a simple and display the results as table or network (using Cytoscape.JS).

Tools and technologies: DV-IMPACT is developed using PHP, MySQL, HTML5, CSS3, JS and JQuery and hosted on Apache webserver. These are the tools/technologies to be used in the project.

Timeline: The time for this task is 1~3.

Expected Deliverables: The developed prototype is expected to be hosted online so that we can access and evaluate the work. In case it is difficult to host the system online, you can send the work in one comprised file include all files required to run the system together with a detailed deployment guide.

Evaluation:

Resources: -The DV-IMPACT website http://dvimpact.baderlab.org -The database design (for simplicity, create a DB of the required table and fields). http://dvimpact.baderlab.org/deposit/

Note: The PSI-MI-TAB files at HuRI portal do not contain mutation information. Just use the available information and map them to the corresponding fields in the databases.

jajodiaraghav commented 7 years ago

Hi @MoHelmy I am a little confused regarding whether i have to just process the uploaded file and display the table, or do i have to map the dataset with the corresponding database design provided in http://dvimpact.baderlab.org/deposit/?

Also, Are my column headings going to be the same as the headings in the PSI-MI-TAB file? Thanks in advance

jajodiaraghav commented 7 years ago

Hi @MoHelmy I have almost completed the task. All i need is the answer to the queries i posted before, so that i can submit it by today. Will be waiting for your response. Thanks

MoHelmy commented 7 years ago

@jajodiaraghav 1- You need to map the columns in the file to the corresponding columns in the DB. 2- The table headings in the DB columns have to be the same as the diagram @ http://dvimpact.baderlab.org/deposit/

jajodiaraghav commented 7 years ago

@MoHelmy The site is hosted at Heroku. Here is the link: http://dvimpact.herokuapp.com. Since i have been working with web technologies for a long time, it didn't took me long to code the interface. Although i really struggled a lot while mapping the format within the TAB file to the DV-IMPACT Database schema and I am not very sure whether the mapping is correct. It would be great if you could elucidate the mapping part. Thanks

MoHelmy commented 7 years ago

This is a very good start, we can work together to improve it. 1- Remove the domain tab, it is not in the PSI data of HuRI. 2- Add search option where the user can search for one protein and get all its interactions. 3- Remove the word "uniprotkb" and the header line of the PSI files. 4- In the search results, add an option for visualizing the results in Cytoscape.JS (this is important as some of the work will reflect in the network visualization so we will modify the current version).

The task will be used for evaluation by other mentors from NRNB, so it needs to be as good as possible and demonstrates your suitability to the project. Best wishes.

jajodiaraghav commented 7 years ago

@MoHelmy

Link to the site : http://dvimpact.herokuapp.com/ The repository: https://github.com/jajodiaraghav/DV-IMPACT

BTW, CytoscapeJS is an amazing tool. I can even use it for some of my university projects for data visualization. This would make my task easier.

MoHelmy commented 7 years ago

Cool, happy that you liked Cytoscape. Let's do a couple of things before freezing and writing the proposal. 1- Cytoscape has several network layouts, the best for the purpose of this DB is Circle layout. 2- In the network, the searched protein should be in different color. 3- As a matter of good practice, whenever you implement a search form, add an example (or examples) that the users can use to run the search function and see the result. Please add one or more examples of proteins that have enough interactions to show a good network. Remember, the evaluation will be done by other mentors who are not always aware of the details of the project, so we need to help them see the effort you did as well as your potential as GSoC student. Thanks.

jajodiaraghav commented 7 years ago

Is there anything else that i should work on? Thanks

MoHelmy commented 7 years ago

Looks good. you can start drafting your proposal. THAKNS FOR THE NICE WORK

jajodiaraghav commented 7 years ago

Thanks a lot for helping me with the evaluation task. Should i be posting the link to my draft proposal here or will i be mailing it to you directly? Thanks again

MoHelmy commented 7 years ago

Please send it by mail. M

Sent from my iPhone

On Feb 5, 2017, at 9:30 AM, Raghav Jajodia notifications@github.com wrote:

Thanks a lot for helping me with the evaluation task. Should i be posting the link to my draft proposal here or will i be mailing it to you directly? Thanks again

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

MoHelmy commented 7 years ago

Are you done with your proposal drafting?

jajodiaraghav commented 7 years ago

I am extremely sorry, i couldn't send you the draft proposal due to some inevitable medical emergency in my family followed by my university exams. I request you to grant me a few more hours to sent you the draft.

MoHelmy commented 7 years ago

Ok, I hope everything is fine now, please send me the draft in your nearest convenience.

jajodiaraghav commented 7 years ago

I had emailed the draft proposal yesterday at helmy.sfc@gmail.com.

MoHelmy commented 7 years ago

Got it, thanks. Looks good. We can freeze now and wait until GSoC officially starts is the next few weeks. Then we revisit the draft and improve more.

MoHelmy commented 7 years ago

Hi, Google announced the accepted orgs yesterday. We were accepted. Next step is to improve your proposal and be ready for students application (I think this will be the last week of March).

jajodiaraghav commented 7 years ago

Yes, I too saw it yesterday. Really excited to work on the proposal further. The student application starts from March 25th. Where should we begin?

jajodiaraghav commented 7 years ago

I think i should start by improving the "Timeline" part.

jajodiaraghav commented 7 years ago

@MoHelmy Made a few changes to the doc. Thinking of further additions that can be made. Waiting for your feedback.

MoHelmy commented 7 years ago

Great, will check and come back to you.

Sent from my iPhone

On Mar 2, 2017, at 4:01 AM, Raghav Jajodia notifications@github.com wrote:

@MoHelmy Made a few changes to the doc. Thinking of further additions that can be made. Waiting for your feedback.

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jajodiaraghav commented 7 years ago

Here are a few of the additions that might be a good addition to the timeline and milestones:

  1. Providing a documentation section which describes i) DV-IMPACT ii) Protein interactions iii) Workflow of our website

  2. A gallery section to display some commonly searched PPI interaction networks

  3. Some "Bookmarking" mechanism where user can save specific networks for future reference.

Which of these would make the proposal look more promising? Waiting for your feedback

Thanks

MoHelmy commented 7 years ago

Documentation is a good option to add. The other 2 need a user profile, which can also be added.

On Mar 6, 2017, at 4:27 AM, Raghav Jajodia notifications@github.com wrote:

Here are a few of the additions that might be a good addition to the timeline and milestones:

Providing a documentation section which describes i) DV-IMPACT ii) Protein interactions iii) Workflow of our website

A gallery section to display some commonly searched PPI interaction networks

Some "Bookmarking" mechanism where user can save specific networks for future reference.

Which of these would make the proposal look more promising? Waiting for your feedback

Thanks

― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

jajodiaraghav commented 7 years ago

Modified the draft. Will add more in the coming days. Waiting for the start of Student Application period. :)

Thanks

MoHelmy commented 7 years ago

Great, we are days ahead the application date.

On Mar 15, 2017, at 8:23 AM, Raghav Jajodia notifications@github.com wrote:

Modified the draft. Will add more in the coming days. Waiting for the start of Student Application period. :)

Thanks

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MoHelmy commented 7 years ago

@jajodiaraghav: The submission started today, please submit and update me.

jajodiaraghav commented 7 years ago

MoHelmy I have shared the draft link already at GSoC website. Do you also want me to submit the PDF now?

Or should we submit a day or two before the deadline?

jajodiaraghav commented 7 years ago

@MoHelmy Anything else that you think could be added as an improvement?

MoHelmy commented 7 years ago

The proposal looks good so far, I left you a comment on the CSoC website, please response to it. Best wishes.

On Mar 23, 2017, at 12:22 PM, Raghav Jajodia notifications@github.com wrote:

@MoHelmy https://github.com/MoHelmy Anything else that you think could be added as an improvement?

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jajodiaraghav commented 7 years ago

Sir, I have couldn't find any comment on my GSoC dashboard or on my shared draft.

MoHelmy commented 7 years ago

Ya, I realized you can’t see it now. Here it is "Please add link to your prototype here to make it easier for mentors to check.”

On Mar 23, 2017, at 1:03 PM, Raghav Jajodia notifications@github.com wrote:

Sir, I have couldn't find any comment on my GSoC dashboard or on my shared draft.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nrnb/GoogleSummerOfCode/issues/62#issuecomment-288789294, or mute the thread https://github.com/notifications/unsubscribe-auth/AHQkzJusW3-XbuMtd1zsjHyefXaLlCagks5roqXtgaJpZM4LBw1y.

jajodiaraghav commented 7 years ago

Hi Submission date is approaching. Will submit the proposal to the GSoC website in a few hours.

Thanks

MoHelmy commented 7 years ago

Please proceed. Good luck

On Apr 1, 2017, at 6:48 AM, Raghav Jajodia notifications@github.com wrote:

Hi Submission date is approaching. Will submit the proposal to the GSoC website in a few hours.

Thanks

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khanspers commented 7 years ago

GSoC 2017 selected project