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'])
...
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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'])
...
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