What should uniprot.geneIDfield be for NCBI Gene identifiers

[PkiwiBird]

What should go in the model adapter in the field obj.params.uniprot.geneIDfield if the genes in the yaml model are NCBI genes and there are no gene names? Only NCBI gene ids are in the - genes and in the genes in the gene_reaction_rule.
The gecko3 article says to look under Names and Taxonomy - Gene Names of one of the proteins of the proteome, but I cannot find the NCBI gene ids there, e.g. https://www.uniprot.org/uniprotkb/A0JNW5/entry
The ecModelGEMAdapter.m contains the following fields:

obj.params.kegg.ID = 'hsa';
obj.params.kegg.geneID = 'NCBI-GeneID';
obj.params.uniprot.type = 'proteome';
obj.params.uniprot.ID = 'UP000005640';

Genes in yaml file:

...
- gene_reaction_rule: "1591"
...
- genes:
    - !!omap
      - id: "100"
    - !!omap
      - id: "10005"

[edkerk]

The UniProt page seems to show the NCBI Gene identifiers under the Genome annotation databases heading, as GeneID (in your example, it is "23074"). And then here is indicated that these annotations will be returned when specifying 'xref_geneid'. So this should do the trick:

obj.params.uniprot.geneIDfield = 'xref_geneid';

[edkerk]

The problem is maybe the trailing ; that is behind the GeneID in uniprot.tsv? 7923 will not match with 7923;.

GECKO/src/geckomat/get_enzyme_data/loadDatabases.m

Line 75 in afa2334

databases.uniprot.genes = fileContent{2};

should then be changed to:

databases.uniprot.genes = regexprep(fileContent{2},';$','');

to automatically remove all trailing ';' behind any gene identifier.

[PkiwiBird]

In write yaml stage 1 is giving another error with developer and main branch of RAVEN:

writeYAMLmodel(ecModel, fullfile(BaseDir,'models', 'ecYeastGEM_stage1.yml'));
Error using fprintf
Invalid file identifier. Use fopen to generate a valid file identifier.

Error in writeYAMLmodel (line 62)
fprintf(fid,'---\n!!omap\n');

[edkerk]

Does the fullfile(BaseDir,'models') path exist?

[mihai-sysbio]

I'm wondering, might there be an issue with relative paths?
edit: or with path aliases such as ~?

[PkiwiBird]

I made a mistake with path. it's working now.

[mihai-sysbio]

Thanks @PkiwiBird for confirming that this discussion may be closed.