Question: Automatically Abbreviating Journal Names
8
gravatar for David D
8.2 years ago by
David D90
David D90 wrote:

Hello, I have a list of journal names:

Acta Veterinaria Scandinavica
Algorithms for Molecular Biology
Allergy, Asthma & Clinical Immunology
Alzheimer's Research & Therapy
Annals of Clinical Microbiology and Antimicrobials
Annals of General Psychiatry
Annals of Surgical Innovation and Research
Arthritis Research & Therapy
Asia Pacific Family Medicine
Automated Experimentation
BMC Anesthesiology
......

I try to construct PubMed queries for automatic retrieval. The queries are of the form of

"Allergy, Asthma & Clinical Immunology"[Journal] AND "2006"[Publication Date] AND <more_terms_come_here>

Unfortunately, searching for the full journal name with the [journal] tag leads to zero results. I figured out that one needs to specified the abbreviated, rather than full, name of the journal. Is there any way to automatically abbreviate journal name? Alternatively, is there any dictionary that couples between the full and the abbreviated names? Thank you

pubmed library retrieval • 1.8k views
ADD COMMENTlink written 8.2 years ago by David D90
7
gravatar for Bio_X2Y
8.2 years ago by
Bio_X2Y3.6k
Ireland
Bio_X2Y3.6k wrote:

I'm not sure about the abbreviations, but you can download a full list of the formal journal names from here (in various formats): http://www.ncbi.nlm.nih.gov/books/NBK3827/?rendertype=table&id=pubmedhelp.pubmedhelptable45.

If you go for the 'Uncompressed' option at the top-left, you'll get a 5MB file that contains a few lines for each journal. One of the lines will be the "JournalTitle" line, which will give the full name of the journal as recognised by NCBI. You can use this file to search for the formal names of your target journals (either manually, or perhaps write a script to automate the search using some rules-of-thumb).

For example, if you grep the file for "allergy, asthma", you can see that the full name of the journal you're interested in is: "Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology". You can use this with the [journal] tag, and it returns results.

ADD COMMENTlink written 8.2 years ago by Bio_X2Y3.6k
4
gravatar for Alex
8.2 years ago by
Alex1.4k
Theodosius Dobzhansky Center for Genome Bioinformatics
Alex1.4k wrote:

As Bio_X2Y said, you need to download this file ftp://ftp.ncbi.nih.gov/pubmed/J_Medline.txt.

Data format:

JrId: 34
JournalTitle: Acta biotheoretica
MedAbbr: Acta Biotheor
ISSN: 0001-5342
ESSN: 1572-8358
IsoAbbr: Acta Biotheor.
NlmId: 0421520

Journal field description from NCBI:

The journal title abbreviation, full journal title, or ISSN number (e.g., J Biol Chem, Journal of Biological Chemistry, 0021-9258). If a journal title contains special characters, e.g., parentheses, > brackets, enter the name without these characters, e.g., enter J Hand Surg [Am] as J Hand Surg Am.

I think that the best way is to choose one Journal identificator (full name or title abbreviation or ISSN). And then translate all other to choosen. ISSN will be good as numeric identificator.

ADD COMMENTlink written 8.2 years ago by Alex1.4k
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