How to parse PubMed Medline records using biopython in 2022

#SuvethaSuresh #PubMed #biopython #medline #parser #metadata
In this video we learn, how to extract meta data from PubMed Medline format using biopython #python module.

For example in this video i will extract 3 meta datas
PMID
Title
Abstract
#medlineparser #research #researchpaper #abstract #article #literature #bibliography

Biopython:
The Biopython project is an open-source collection of non-commercial Python tools for computational biology and bioinformatics, created by an international association of developers.

Code editor:
#VSCode

module:
#Pandas - Save output in csv format

PubMed Medline format:
AB - Abstract
CI - Copyright Information
AD - Affiliation
IRAD - Investigator Affiliation
AID - Article Identifier
AU - Author
FAU - Full Author
CN - Corporate Author
DCOM - Date Completed
DA - Date Created
LR - Date Last Revised
DEP - Date of Electronic Publication
DP - Date of Publication
EDAT - Entrez Date
GS - Gene Symbol
GN - General Note
GR - Grant Number
IR - Investigator Name
FIR - Full Investigator Name
IS - ISSN
IP - Issue
TA - Journal Title Abbreviation
JT - Journal Title
LA - Language
LID - Location Identifier
MID - Manuscript Identifier
MHDA - MeSH Date
MH - MeSH Terms
JID - NLM Unique ID
RF - Number of References
OAB - Other Abstract
OCI - Other Copyright Information
OID - Other ID
OT - Other Term
OTO - Other Term Owner
OWN - Owner
PG - Pagination
PS - Personal Name as Subject
FPS - Full Personal Name as Subject
PL - Place of Publication
PHST - Publication History Status
PST - Publication Status
PT - Publication Type
PUBM - Publishing Model
PMC - PubMed Central Identifier
PMID - PubMed Unique Identifier
RN - Registry Number/EC Number
NM - Substance Name
SI - Secondary Source ID
SO - Source
SFM - Space Flight Mission
STAT - Status
SB - Subset
TI - Title
TT - Transliterated Title
VI - Volume
CON - Comment on
CIN - Comment in
EIN - Erratum in
EFR - Erratum for
CRI - Corrected and Republished in
CRF - Corrected and Republished from
PRIN - Partial retraction in
PROF - Partial retraction of
RPI - Republished in
RPF - Republished from
RIN - Retraction in
ROF - Retraction of
UIN - Update in
UOF - Update of
SPIN - Summary for patients in
ORI - Original report in

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[vitorlima]

Helpful vídeo. Thank you from Brazil!

[criticalnodecapital]

Hi suvetha, can you help me on how to use this with chatgpt and infuse it into my articles?

[felixmeier]

Thanks for the video, do you know how to parse more than one file ? If I have a medline.txt with a lot of articles, not just one, how do I create a new row in the df to add the files to there ?

[mariliaignaciodeespindola]

Hi, thank you very much for your video. How can I implement this in a Jupyter notebook? If possible? Because I didn't create a parse file.

[es_t]

Hi, thanks for this! Really helpful. Do you know which identifier that gives how many citation within the article? or we have to scrape it by ourselves? Again, thanks!

[mouriyanithin]

Thank u but i have a doubt what is the advantage of doing this? Already there is an option to download into CSV format in pubmed website which can be done in a single click

[ANIMESHPANDA-tvzm]

Is it possible to do it without using the pubmed-egfrmutati-set.txt file?

[mosesmekala]

Bro how to explode the author names from single string to next row