Is there a programmatic way to extract the Gene Description of a gene given the Gene Symbol?
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4 months ago
dustyl259 ▴ 10

Is there software out there that extracts Gene Description (aka, the full gene name) given a gene symbol? For instance, an example using NCBI for gene symbol "TNFSF13B" as input would give output: "TNF superfamily member 13b". I have a list of over 200 gene symbols that I would like to do this for and was wondering if this is possible.

For NCBI TNFSF13B, click here

genes bioinformatics NCBI • 262 views
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4 months ago
GenoMax 102k

Using EntrezDirect:

$ esearch -db gene -query "TNFSF13B [GENE] AND human [ORGN]" | efetch -format ft

1. TNFSF13B
Official Symbol: TNFSF13B and Name: TNF superfamily member 13b [Homo sapiens (human)]
Other Aliases: BAFF, BLYS, CD257, DTL, TALL-1, TALL1, THANK, TNFSF20, TNLG7A, ZTNF4
Other Designations: tumor necrosis factor ligand superfamily member 13B; ApoL related ligand TALL-1; B-cell-activating factor; B-lymphocyte stimulator; Delta4 BAFF; TNF and ApoL-related leukocyte expressed ligand 1; TNF homolog that activates apoptosis; delta BAFF; dendritic cell-derived TNF-like molecule; epididymis secretory sperm binding protein; tumor necrosis factor (ligand) superfamily, member 13b; tumor necrosis factor (ligand) superfamily, member 20; tumor necrosis factor ligand 7A; tumor necrosis factor superfamily member 13b; tumor necrosis factor-like protein ZTNF4
Chromosome: 13; Location: 13q33.3
Annotation: Chromosome 13 NC_000013.11 (108268240..108308484)
MIM: 603969
ID: 10673

If you want to get them all (remove head -20 and re-direct to a file to save) :

$ esearch -db gene -query "human [ORGN]" | efetch -format ft | grep -B 1 "Official Symbol" | head -20
1. TP53
Official Symbol: TP53 and Name: tumor protein p53 [Homo sapiens (human)]
--
2. EGFR
Official Symbol: EGFR and Name: epidermal growth factor receptor [Homo sapiens (human)]
--
3. TNF
Official Symbol: TNF and Name: tumor necrosis factor [Homo sapiens (human)]
--
4. APOE
Official Symbol: APOE and Name: apolipoprotein E [Homo sapiens (human)]
--
5. VEGFA
Official Symbol: VEGFA and Name: vascular endothelial growth factor A [Homo sapiens (human)]
--
6. IL6
Official Symbol: IL6 and Name: interleukin 6 [Homo sapiens (human)]
--
7. TGFB1
Official Symbol: TGFB1 and Name: transforming growth factor beta 1 [Homo sapiens (human)]
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