Hello again,

I am very happy to announce that bio models have been integrated into the sbml plugin. This enables the user to search the bio models from the bio models database and import them into the pathvisio editor.

There is a very good web service which is provided by the biomodels website. I used this web service to integrate the bio models into the plugin. In the start, I was hit by many road blocks, but eventually I was successful in completing the feature enhancement.

Now we can search the bio models based upon different terms such as “Bio model Name“, “Person name i.e., the Encoder /Author Name“,”Publication Title/Id“, “CHEBIId” and finally “Uniprot Id“.

Refer: BioModelPanel.java

The following screen shots depicts the functionality of the bio models integration feature:



Figure 1: Bio models Import Button[Highlighted part ].


Figure 2: Bio model Panel.


Figure 3: Tool tips for every search field.


Figure 4: Search by Bio model Name. Here: “Tyson1991 – Cell Cycle 6 var“.



Figure 5: Search result displayed in the table bottom.


Figure 6 : Opening the selected bio model. Here : http://www.ebi.ac.uk/biomodels-main/BIOMD0000000005



Figure 7 : Imported SBML Model.



 Figure 8: Searching by Publication Name/Id . Here: ‘sbml‘.



Figure 9 : Search by CHEBI Id. Here: “24996“.


Figure 10: Search by Person/Encoder/Author name. Here : ‘Rainer‘.


Figure 11 : Search by Uniprot ID. Here :”P04637 “.


Figure 12: Searching with empty strings gives you an error.


Figure 13: Searching with invalid strings will give you a message.

Note: If you search with two search terms i.e., for example Publication Name and Biomodel Name and press search, the two results will be added up and showed in the results table.


Sri Harsha.P

4 thoughts on “Bio Models Integration

  1. Good Job SriHarsha!

    But the search by publication ID should search using a pubmed id, for example

    searching using the pubmed id 8983160 should display the biomodel – BIOMD0000000001 .

    Is that the case?

    • Here You can search with both publication id and publication name too.So if you search with the pubmed id 8983160 it will display the biomodel BIOMD0000000001 in the search results 🙂

  2. And it would also be nice to have a browsing biomodels for all models (client.getAllModelsId), all curated models client.getAllCuratedModelsId, and all non-curated models (client.getAllNonCuratedModelsId).

    As well as more options for searching such as, search by reactome id, taxon etc


Leave a reply

<a href="" title=""> <abbr title=""> <acronym title=""> <b> <blockquote cite=""> <cite> <code> <del datetime=""> <em> <i> <q cite=""> <s> <strike> <strong>