Bio.Medline package
Module contents
Code to work with Medline from the NCBI.
- Classes:
Record A dictionary holding Medline data.
- Functions:
read Reads one Medline record
parse Allows you to iterate over a bunch of Medline records
- class Bio.Medline.Record
Bases:
dict
A dictionary holding information from a Medline record.
All data are stored under the mnemonic appearing in the Medline file. These mnemonics have the following interpretations:
Mnemonic
Description
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
- Bio.Medline.parse(handle)
Read Medline records one by one from the handle.
The handle is either is a Medline file, a file-like object, or a list of lines describing one or more Medline records.
Typical usage:
>>> from Bio import Medline >>> with open("Medline/pubmed_result2.txt") as handle: ... records = Medline.parse(handle) ... for record in records: ... print(record['TI']) ... A high level interface to SCOP and ASTRAL ... GenomeDiagram: a python package for the visualization of ... Open source clustering software. PDB file parser and structure class implemented in Python.
- Bio.Medline.read(handle)
Read a single Medline record from the handle.
The handle is either is a Medline file, a file-like object, or a list of lines describing a Medline record.
Typical usage:
>>> from Bio import Medline >>> with open("Medline/pubmed_result1.txt") as handle: ... record = Medline.read(handle) ... print(record['TI']) ... The Bio* toolkits--a brief overview.