The ensembl_gene_id is postfix with random number like ENSG00000000003.14 which is not the standard format of ENSEMBL. Can you clarify that you mean ENSG00000000003, not ENSG00000000003.14?
Hello Joe,
The postfix is the gene version number. You can trim it and just use ENSG00000000003.
The standard format for an ENSEMBL gene ID is ENSG00000000003 and the additional number after the dot, as in ENSG00000000003.14, usually represents a specific version of the gene annotation.
Gene annotations in ENSEMBL database can be updated as new information becomes available. These updates can include changes in the gene’s structure, its transcripts, or even the genomic coordinates it occupies. To keep track of these changes, each updated version of a gene’s annotation is given a new version number. So, in your example, ENSG00000000003.14 would refer to the 14th version of the annotation for the gene ENSG00000000003.
We also provided gene metadata here that can be useful for gene name mapping.