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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