Re: [sbml-multi] [sbml-discuss] A question on SBML multi

[Zhang, F. (NIH/N. [E] <zha...@ni...>]

Hi Robert,

Thank you for working to support the multi package! Thank you for the question. I include this reply to the multi list. I think we could also continue to discuss here as multi is part of sbml.

Specific to your question, you could first define mult:speciesTypes in the following way:
<multi:listOfSpeciesTypes>
    <multi:speciesType multi:id="st_SMAD1" multi:name=" SMAD1" …/>
    <multi:speciesType multi:id="st_SMAD5" multi:name=" SMAD5" …/>
    <multi:speciesType multi:id="st_SMAD8" multi:name=" SMAD8" …/>
<multi:speciesType multi:id="st_SMAD1_5_8" multi:name=" SMAD1_5_8" …>
    <multi:listOfSpecieTypeInstances>
        <multi:speciesTypeInstance multi:id=”sti_SMAD1” multi:speciesType=”st_SMAD1” … />
        <multi:speciesTypeInstance multi:id=”sti_SMAD5” multi:speciesType=”st_SMAD5” … />
        <multi:speciesTypeInstance multi:id=”sti_SMAD8” multi:speciesType=”st_SMAD8” … />
    </ multi:listOfSpecieTypeInstances >
</multi:speciesType >
…
</multi:listOfSpeciesTypes >

And in speces to reference the speciesTypes, you may have:
<listOfSpeces>
    <species id=”species_SMAD1_5_8” multi:speciesType=”st_SMAD1_5_8”… />
    <species id=”species_SMAD1” multi:speciesType=”st_SMAD1”… />
    <species id=”species_SMAD5” multi:speciesType=”st_SMAD5”… />
<species id=”species_SMAD8” multi:speciesType=”st_SMAD8”… />
…
</listOfSpeces>

Depending the purpose, annotation can be added to species, speciesType, and/or speciesTypeInstance. I consider species should be a good place to be annotated with a uniprot id.

I would be happy to answer any further questions and clarify my reply if needed.

Best,

Fengkai

====================
Fengkai Zhang, MD, MMath
Staff Scientist
Laboratory of Immune System Biology, DIR, NIAID
9000 Rockville Pike
Building 4, Room 137
MSC 0421
Bethesda MD 20892
Phone: 301.761.5442
Fax: 301.480.1660
NIAID, National Institutes of Health, DHHS

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From: Robert Phair <rd...@gm...>
Reply-To: "sbm...@go..." <sbm...@go...>
Date: Thursday, March 4, 2021 at 8:54 PM
To: sbml-discuss <sbm...@go...>
Subject: [sbml-discuss] A question on SBML multi

We want to support import of at least some of the information encoded in SBML multi, but UML is not my first language and I'm having trouble discerning which multi: constructs are used for which biological scenarios. I have spent a good deal of time reading the spec.

Let me start with a basic scenario. The formation of protein complexes, by which I mean non-covalent binding of two or more proteins, is a simple and very common scenario.

When I import an SBML file, in this case, produced by the software tool, MINERVA, there is a species with a multi:speciesType="minerva_species_type_Complex". The line of SBML is:

<species boundaryCondition="false" compartment="comp_1" constant="false" hasOnlySubstanceUnits="false" id="species_45" initialAmount="0" multi:speciesType="minerva_species_type_Complex" name="SMAD1/5/8" sboTerm="SBO:0000253">

This complex is made up of three proteins, SMAD1, SMAD5, and SMAD8.

The question is: which multi: constructs should be used to specify the component proteins of this complex so that each can be annotated with an rdf:resource such as a uniprot id?

I'm not asking how MINERVA does this (I've already raised this question with them). What I'm asking is how the designers of multi: would code this information.

If this is not the correct discussion group for this question, please point me to the right place to ask it. Thanks.
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