ontox-hu / ontox-phymdos

Phymdos - the ONTOX Physiological maps documentation software

Phymdos
The ONTOX Physiological Maps documentation software

This application was created to serve as a bridge between sysrev.com and Celldesigner. Its core functionality is to allow the user to easily create SBML style physiological maps from literature by filling out easy to use data tables and converting them to the desired format by the click of a button. The format used to create these data tables is SBtab, which is essentially a .tsv file containing several tables that together define a system. These tables can be filled out on sysrev.com and in this app and can then be converted to SBML files which can be used by Celldesigner to build physiological maps. This workflow has been illustrated below.

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1. Upon opening the app, users will first be guided to the home screen where they are presented with 3 choices.





1. Create new SBtab:
   Creating a new SBtab will allow users to create their own SBtab from scratch. (Continues from point 3)
2. Upload an SBtab object:
   Uploading an SBtab object will allow users to upload a .tsv containing an SBtab document. The tabs within the .tsv will be opened in the app.
3. Upload an SBML object:
   Uploading an SBML object will allow users to upload a .xml containing an SBML document. The SBML will be converted to SBtab and the tabs within the SBtab will be opened in the app.


2. Upon clicking one of the uploading options, users will be presented an uploading screen in which they can upload either a .tsv file for SBtab or a .xml file for SBML.





3. Once the upload is complete and the continue button is clicked the app will open the tables corresponding to the upload file, and users will be redirected to the first setup where they can enter a name for the document and choose a SBtab version (change only if needed, the newest version is standard).





4. Clicking 'save input' will redirect users to the 'select tables' tab which can also be accessed from the menu on the left side of the screen. Here users can add or remove tables from the menu. The app currently only features the three most important table types. Please also note that removing a table from the menu does NOT delete any data that is inside the table.





5. Once all the correct tables are selected users can start filling the new tables or start adding to the uploaded tables however they see fit.





For empty tables the first step is to start adding columns to the table. This can also be done on existing tables to add information.




To find out what columns, users can view the description of table elements found at the bottom of the page.




6. When users are done filling out the tables they can go to the download screen by clicking the button underneath the table or they can click Setup on the menu on the left. Here they can export the file to SBtab- and SBML format.

ontox-phymdos's Issues

pmdep - Write R functions to upgrade the SBtab - SBML converter to the Celldesigner formatting

Upgrade the converter to a Celldesigner formatted converter

pmdep - review sysrev -> sbml code

Review and test Tom's code for converting data from sysrev to sbml

pmdep - test Cytoscape SBGN visualization on node.js

Test if the Cytoscape SBGN stylesheet will work on node.js.

Modules:
https://github.com/PathwayCommons/sbgnml-to-cytoscape
https://github.com/PathwayCommons/cytoscape-sbgn-stylesheet

pmdep - Create ability to opt-in and opt-out data-table columns

When users fill in the data-table they need to be able to easily add and remove different columns based on the available data

pmdep - Add a legend of the available data-table column choices

Add a easily accessible (pop-up) legend with the available columns and their descriptions.

pmdep - Create definitions file containing minimal amount of tables and columns

The app needs more simplicity in its tables so the amount of tables and columns need to be trimmed with the options from Celldesigner as a baseline

pmdep - Get familiar with Celldesigner SBML and raw SBML formats.

Have a thorough look at the structures in the file to get a general idea of how a conversion between SBtab and SBML would work.

Python error in RsConnect publishing

Trying to publish Phymdos to RsConnect yielded the error:

[Connect] 2022/04/14 10:03:15.700411447 /usr/bin/python3.8: No module named virtualenv
[Connect] 2022/04/14 10:03:15.703449512 virtualenv failed with exit code 1
[Connect] Build error: exit status 1
Application deployment failed with error: exit status 1

pmdep - add examples in the tables - pre filled

When users open empty tables, show examples in the columns.

pmdep - Study persistence of data in app

see link: https://shiny.rstudio.com/articles/persistent-data-storage.html

pmdep - Create validator for SBtab files

The converter needs a validator so wrong SBtab files do not crash the app but instead tell a user what they need to change.

pmdep - download data to .tsv

Create ability to download the data locally in the form of a .tsv file

• Need refinement @DanielRoodzantHU

pmdep - implement persistent data storage for the app.

Each user should be able to see existing maps, add data and store that in the persistent storage. How to handle duplicates?

pmdep - add documentation tab that shows and explains how to use the app

pmdep - look into a way to externally launch Cytoscape visualization

Get Cytoscape to launch externally and then source that location from the app.

pmdep - Add small example graph in dashboard

Add small graph in table screen displaying made connections to user as they are written.

Create minimal example workflow article-data -> celldesinger

Add phymdos as SRVC flow

pmdep - Create home screen to start a map by choosing (a) data-table(s)

The portal needs a home screen where a user is able to easily select the desired data-table type or types to work with.

pmdep - Add list of chemicals (for chemical selection) to a new Postgres database

Create knowledge graph from literature ONTOX chemicals

pmdep - deploy app so that people can test it

pmdep - clear table upon button click

When a user clicks a button at the table, empty it

pmdep - integrate SBOterms for SBtab -> sbml and for sysrev -> sbml

After reviewing Tom's code, add the possibility to use SBO terms for the visualization of the sbml

pmdep - download data to .xml

Create ability to download the data locally in the form of a .tsv file

pmdep - Polish app dashboard

Give the app a new look using CSS and premade styling

pmdep - Create ability to upload TSV files

After choosing a data-table in the home screen, give users the option to upload existing TSV files to the portal and automatically render a data-table based on the file.

pmdep - Write R functions for converting SBML to SBtab.

Get into creating the converter from SBML to SBtab.

Create R-package?

pmdep - Create Google form for entering compound information

To establish a database with compound information, design a form in Google forms that can connect to the Shiny app or other tools.

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!! This is done right? If yes, close issue. If no, email Daniël and move to 'In progress'.!!

pmdep - definitions.tsv sourcen van SBtab github ipv lokaal

pmdep - Create ability to upload xml files

In the home screen, give users the option to upload an xml file that automatically creates data-tables in the portal based on the data within.

PMDEP - Add status bar for MINERVA

Have the app display upload status for MINERVA maps and open map on 100%

pmdep - Refine conversion to .tsv

pmdep - create clean home screen

Create a nice inviting home screen

pmdep - Add app title and emailaddress and more details in the top header

Perform clustering knowledge graph, based on chemical simularity

Run literature mining pipeline on ONTOX compound list

pmdep - Recreate tables to include minimal nnumber of columns

pmdep - Integrate RSysrev in app

Give users the option to pull Sysrev SBtab tables into PMDEP by entering the Sysrev project ID.

pmdep - Add error handlers to the app to prevent crashing

The app needs error handlers for things like file uploading so it does not crash on a wrong move.

pmdep - Get familiar with the python code from the SBtab - SBML converters.

Look into the existing python code for the conversion to draw inspiration from it.

pmdep - render live map during build

Have the app render a live (celldesigner) map based on the data tables (needs .xml conversion in app)

pmdep - Create prefab systems to select upon entering the app

Premade systems like liver and brain for the users to select and adjust

pmdep - make use of python scripts available in online version of app

pmdep - Write R functions for converting SBtab to SBML.

Get into creating the converter from SBtab to SBML.

Create R-package?