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I would like to do two things:

(1) Obtain a list of all NCBI (Entrez) gene ID's.

(2) Obtain the "Official Symbol", "Official Full Name", and "Also known as" fields from the NCBI gene pages for each of those genes.

This information, since it is displayed on the NCBI website, must be located in some databases, but I have not had luck finding a tool that will allow me to extract this information.

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All of these data are in the gene_info.gz file on the NCBI FTP site: https://ftp.ncbi.nlm.nih.gov/gene/DATA/ Specifically, you may want to look at the gene_info.gz file. It has the following fields (shown for an example gene below):

                              #tax_id [  1]: 9606
                               GeneID [  2]: 5768
                               Symbol [  3]: QSOX1
                             LocusTag [  4]: -
                             Synonyms [  5]: Q6|QSCN6
                              dbXrefs [  6]: MIM:603120|HGNC:HGNC:9756|Ensembl:ENSG00000116260
                           chromosome [  7]: 1
                         map_location [  8]: 1q25.2
                          description [  9]: quiescin sulfhydryl oxidase 1
                         type_of_gene [ 10]: protein-coding
   Symbol_from_nomenclature_authority [ 11]: QSOX1
Full_name_from_nomenclature_authority [ 12]: quiescin sulfhydryl oxidase 1
                  Nomenclature_status [ 13]: O
                   Other_designations [ 14]: sulfhydryl oxidase 1|quiescin Q6 sulfhydryl oxidase 1|testis tissue sperm-binding protein Li 62n|thiol oxidase 1
                    Modification_date [ 15]: 20200604
                         Feature_type [ 16]: -

If you are starting with a set of NCBI GeneIDs and want this sort of information for just those, you can use Entrez Direct for that. If you are starting with RefSeq transcript or protein accessions, be sure to check out the other files in the FTP path mentioned above.

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  • $\begingroup$ I had tried using this file, but a bug in my code made me think it didn't have what I wanted. Your answer made me look into it again, and I found the bug. It's exactly what I needed. $\endgroup$
    – BioBroo
    Jun 29 '20 at 17:09
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Go to Ensembl (https://www.ensembl.org/index.html), click BioMart on the menu at the top of the page. Select the dataset you want to use, then go to Attributes, select the feature of each gene you want to get. Then click "Results" button to make sure that the table looks like what you want. Then output the results to a file.

enter image description here

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  • $\begingroup$ This is almost exactly what I'm looking for. The only thing it is missing is as comprehensive a "Also known as" list. For example, NCBI lists the PPP4C gene has having a total of 7 symbols, while this data set has 2. $\endgroup$
    – BioBroo
    Jun 29 '20 at 14:00

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