Polished model read with errors in cobrapy

[EnuhBlaise]

Hello, I am developed an draft model reconstruction with Carveme and used ModelPolisher with docker for the annotations. I got the model output but on opening with CobraPy I got errors as below.

"MNXR98569 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98641 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98003 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98012 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98643 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98639 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98014 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98700 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98047 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98061 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR97540 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98062 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98256 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98349 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98180 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98086 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98278 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id", "MNXR98058 does not conform to 'http(s)://identifiers.org/collection/id' or'http(s)://identifiers.org/COLLECTION:id",

There are several more lines. Using the SBML validator in cobrapy these are the errors that appear as well under 'COBRA_WARNING', other tests look fine Is it something wrong I am doing or is there another step to do in order to get rid of the errors.

Thank you for considering

Enuh

[mephenor]

Could you provide one of the respective annotations from the ModelPolisher Output?

[EnuhBlaise]

Gene identifier | fig_29330_40_peg_3551 -- | -- Name | G_fig_29330_40_peg_3551 Memory address | 0x07ff361790650 Functional | True In 1 reaction(s) | ACCOAC

This is what the gene annotation from a random gene in the output model shows.

[mephenor]

Sorry, I meant the annotation in the SBML file

[EnuhBlaise]

ohh Sorry for that.

[mephenor]

What I need from that is the URI it produces, e.g. I have https://identifiers.org/metanetx.reaction/MNXR98569 in one my output models. This should be present in the SBML XML file and the surrounding parts should look something like this:

 135497           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
 135498             <rdf:Description rdf:about="#EX_glc__D_e">
 135499               <bqbiol:is>
 135500                 <rdf:Bag>
 135501                   <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR98569" />
 135502                   <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/EX_glc__D_e" />
 135503                   <rdf:li rdf:resource="https://identifiers.org/sbo/SBO:0000627" />
 135504                   <rdf:li rdf:resource="https://identifiers.org/biocyc/META:TRANS-RXN0-574" />
 135505                   <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR100188" />
 135506                   <rdf:li rdf:resource="https://identifiers.org/seed.reaction/rxn08617" />
 135507                   <rdf:li rdf:resource="https://identifiers.org/seed.reaction/rxn09679" />
 135508                   <rdf:li rdf:resource="https://identifiers.org/seed.reaction/rxn09875" />
 135509                 </rdf:Bag>
 135510               </bqbiol:is>
 135511             </rdf:Description>
 135512           </rdf:RDF>
 135513         </annotation>

[EnuhBlaise]

Sorry for the mix up. I hope I got it right this time.

[mephenor]

I don't see an issue with this annotation. <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR100381" /> -> is this one of the identifiers you get the errors/warnings for? If so, this might rather be an issue with CobraPy

[EnuhBlaise]

Yes it was and this is still another. In that case, I will try opening the model in matlab as well to see if anything comes up

[Midnighter]

Hi, from what you posted above, I think the issue is with

<rdf:li rdf:resource="MNXR99051" />

The other annotations look fine.

[EnuhBlaise]

Hello @Midnighter, What are you recommendations about the fields with same issue?

[Midnighter]

I don't know how they are created, i.e., whether it was carveme, you, or model polisher who created that annotation. They should look like this field:

<rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR105270" />

[mephenor]

ModelPolisher should not add such annotations, as there is some code to check with the identifiers.org registry to validate that identifiers match the collection pattern, i.e. you would get a warning message that there is a mismatch and the annotation was not added. However, annotations that are already present are not removed if they can't be fixed.

[EnuhBlaise]

Ok I understand now. I had not put in any annotations manually myself. I will go over the reconstruction process again and verify closely.

Thank you @mephenor and @Midnighter for your help.

[EnuhBlaise]

Hello @mephenor and @Midnighter I succeeded to resolve the issue. I had to restart the building process and manually handle the annotations.

Thank you

[GwennyGit]

The same problem occurs with my model. I used CarveMe version 1.5.1 to build the draft model. Then I applied the not yet published refineGEMs python package from the Dräger lab GitHub using the modules polish, KEGG pathways as groups, charge correction and SBO annotation. Each module creates a new model which is checked by the function cobra.io.sbml.validate_sbml_model from COBRApy version 0.22.0 which gave me for each of the steps neither errors nor warnings. After using ModelPolisher with docker as described in the README, I get the following warnings with cobra.io.sbml.validate_sbml_model for 165 entries. Example warning: MNXR98014 does not conform to 'http(s):[//identifiers.org/collection/id](https://compsysbio-group.slack.com//identifiers.org/collection/id)' or'http(s):[//identifiers.org/COLLECTION:id](https://compsysbio-group.slack.com//identifiers.org/COLLECTION:id) Additionally, I compared the models before and after ModelPolisher. Before ModelPolisher the reaction looked like this:

      </reaction>
      <reaction metaid="R_EX_2hxmp_e" sboTerm="SBO:0000627" id="R_EX_2hxmp_e" name="R_EX_2hxmp_e" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
        <notes>
          <html xmlns="http://www.w3.org/1999/xhtml">
            <p>SBOTerm: SBO:0000627</p>
          </html>
        </notes>
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#R_EX_2hxmp_e">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/EX_2hxmp_e"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference species="M_2hxmp_e" stoichiometry="1" constant="true"/>
        </listOfReactants>
      </reaction>

And after ModelPolisher the same reaction looks like this:

      <reaction compartment="e" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub" id="R_EX_2hxmp_e" metaid="R_EX_2hxmp_e" name="2  Hydroxymethyl phenol exchange" reversible="true" sboTerm="SBO:0000627">
        <notes>
          <body xmlns="http://www.w3.org/1999/xhtml">
            <p>SBOTerm: SBO:0000627</p>
          </body>
        </notes>
        <annotation>
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
            <rdf:Description rdf:about="#R_EX_2hxmp_e">
              <bqbiol:is>
                <rdf:Bag>
                  <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/EX_2hxmp_e" />
                  <rdf:li rdf:resource="MNXR98014" />
                  <rdf:li rdf:resource="https://identifiers.org/biocyc/META:TRANS-RXN0-528" />
                  <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR124044" />
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </annotation>
        <listOfReactants>
          <speciesReference constant="true" sboTerm="SBO:0000010" species="M_2hxmp_e" stoichiometry="1" />
        </listOfReactants>
      </reaction>

I realised that two metanetx.reaction identifiers were added, namely MNXR98014 and MNXR124044. From both of these only one was added correctly: <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR124044" /> while the other one was added like this: <rdf:li rdf:resource="MNXR98014" />. I looked at three different warnings randomly and each looked similar to the reaction mentioned before. Hence, I think the warnings come from the wrongly added metanetx.reaction identifiers. Though, I do not know why two are added and one is added correctly while the other one is not.

[GwennyGit]

I just realised that this problem was also discussed in issue #106, hence I will close this issue again.

[draeger]

It looks like the prefix (i.e., https://identifiers.org...) for the annotation resource <rdf:li rdf:resource="MNXR98014" /> is missing or anything else? If so, this could be fixed using a simple search and replace because the identifiers from MetaNetX start with MNXR. If this is a general problem of ModelPolisher, an issue should be raised there as well.