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pubmedToGarganText

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# pubmedCorpusToTSV
## About The project
pubmedCorpusToTSV transform a text file from PubMed into TSV file usable in GarganText
## Usage
```shell
python3 pubmedCorpusToTSV.py corpus.txt
```
corpus.txt -> Text file from PubMed
Output a TSV legacy file next to the text file : corpus.csv
## Date
This script have been last updated the 2023/07/25.
It can be outdated if the futur.
## Note
Every nbib file also work with this script
\ No newline at end of file
Conversion/ToTSV/pubmedCorpusToTSV/pubmedCorpusToTsv.py 0 → 100644
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#######
# pubmedCorpusToCsv.py
# description : turn a pubmed file (nbib) into a gargantext csv corpus
# licence : AGPL + CECILL v3
# author : quentin lobbé - qlobbe@iscpif.fr
#######
import sys
import csv
import nbib
import re
import calendar
# python3 pubmedCorpusToCsv.py corpus.txt
path = ""
try :
path = sys.argv[1]
except :
print ("! args error\n")
sys.exit(0)
def normalizePath(path) :
splited = path.split('/')
name = (splited[-1]).split('.')[0]
root = '/'.join(splited[:-1])
return (root,name)
root,name = normalizePath(path)
if root != '':
root += '/'
output = open(root + name + ".csv", "w")
header = "title\tsource\tpublication_year\tpublication_month\tpublication_day\tabstract\tauthors\tweight\n"
output.write(header)
docs = nbib.read_file(path)
for doc in docs :
keys = doc.keys()
if len(list(set(['title','publication_date','authors']) & set(keys))) < 3 :
continue
if 'journal' in keys :
source = doc['journal']
else :
source = ""
if 'abstract' in keys :
abstract = doc['abstract']
else :
abstract = ""
title = doc['title']
date = doc['publication_date'].split(' ')
year = date[0]
if len(date) > 1:
try:
month = list(calendar.month_abbr).index(date[1])
except Exception as e:
month = '1'
else:
month = '1'
if len(date) > 2:
day = date[2]
else:
day = '1'
abstract = re.sub('\"', "", abstract).replace("\t", "")
title = re.sub('\"', "", title).replace("\t", "")
authors_lst = []
for author in doc['authors'] :
authors_lst.append((author['author']).replace(',',''))
authors = ','.join(authors_lst)
row = str(title) + "\t" + "scopus" + "\t" + year + "\t" + str(month) + "\t" + str(day) + "\t" + abstract + "\t" + authors + "\t" + str(1) + "\n"
output.write(row)
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Conversion/ToTSV/pubmedCorpusToTSV/sample/pubmed-Biologie-set.txt 0 → 100644
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PMID- 22137193
OWN - NLM
STAT- MEDLINE
DCOM- 20120501
LR - 20111205
IS - 1768-3114 (Electronic)
IS - 0369-8114 (Linking)
VI - 59
IP - 6
DP - 2011 Dec
TI - [Pathologie Biologie: an evolution].
PG - 293
LID - 10.1016/j.patbio.2011.11.002 [doi]
FAU - Farge, D
AU - Farge D
FAU - Robert, L
AU - Robert L
FAU - Verecchia, F
AU - Verecchia F
LA - fre
PT - Editorial
TT - Pathologie Biologie: une évolution.
PL - France
TA - Pathol Biol (Paris)
JT - Pathologie-biologie
JID - 0265365
SB - IM
MH - Biology/education/*methods/*trends
MH - Education, Medical, Continuing
MH - Humans
MH - Interdisciplinary Communication
MH - Pathology, Clinical/education/methods/*trends
MH - Periodicals as Topic/*trends
MH - Publishing/organization & administration/*trends
EDAT- 2011/12/06 06:00
MHDA- 2012/05/02 06:00
CRDT- 2011/12/06 06:00
PHST- 2011/12/06 06:00 [entrez]
PHST- 2011/12/06 06:00 [pubmed]
PHST- 2012/05/02 06:00 [medline]
AID - S0369-8114(11)00151-9 [pii]
AID - 10.1016/j.patbio.2011.11.002 [doi]
PST - ppublish
SO - Pathol Biol (Paris). 2011 Dec;59(6):293. doi: 10.1016/j.patbio.2011.11.002.
PMID- 24674657
OWN - NLM
STAT- MEDLINE
DCOM- 20141211
LR - 20140415
IS - 1768-3114 (Electronic)
IS - 0369-8114 (Linking)
VI - 62
IP - 2
DP - 2014 Apr
TI - [Pathologie Biologie, 60 years already!].
PG - 58
LID - S0369-8114(14)00026-1 [pii]
LID - 10.1016/j.patbio.2014.02.005 [doi]
FAU - Boiron, M
AU - Boiron M
AD - Pathologie Biologie, Elsevier Masson, 62, rue Camille-Desmoulins, 92442
Issy-les-Moulineaux cedex, France. Electronic address: patho-bio@elsevier.com.
LA - fre
PT - Editorial
PT - Historical Article
TT - Pathologie Biologie, 60 ans déjà !
DEP - 20140325
PL - France
TA - Pathol Biol (Paris)
JT - Pathologie-biologie
JID - 0265365
SB - IM
MH - France
MH - History, 20th Century
MH - History, 21st Century
MH - Pathology/*history
MH - Periodicals as Topic/*history
EDAT- 2014/03/29 06:00
MHDA- 2014/12/17 06:00
CRDT- 2014/03/29 06:00
PHST- 2013/11/15 00:00 [received]
PHST- 2014/02/17 00:00 [accepted]
PHST- 2014/03/29 06:00 [entrez]
PHST- 2014/03/29 06:00 [pubmed]
PHST- 2014/12/17 06:00 [medline]
AID - S0369-8114(14)00026-1 [pii]
AID - 10.1016/j.patbio.2014.02.005 [doi]
PST - ppublish
SO - Pathol Biol (Paris). 2014 Apr;62(2):58. doi: 10.1016/j.patbio.2014.02.005. Epub
2014 Mar 25.
PMID- 29981800
OWN - NLM
STAT- MEDLINE
DCOM- 20200729
LR - 20200729
IS - 1872-8294 (Electronic)
IS - 0169-409X (Linking)
VI - 146
DP - 2019 Jun
TI - Re-epithelialization of adult skin wounds: Cellular mechanisms and therapeutic
strategies.
PG - 344-365
LID - S0169-409X(18)30158-3 [pii]
LID - 10.1016/j.addr.2018.06.019 [doi]
AB - Cutaneous wound healing in adult mammals is a complex multi-step process
involving overlapping stages of blood clot formation, inflammation,
re-epithelialization, granulation tissue formation, neovascularization, and
remodelling. Re-epithelialization describes the resurfacing of a wound with new
epithelium. The cellular and molecular processes involved in the initiation,
maintenance, and completion of epithelialization are essential for successful
wound closure. A variety of modulators are involved, including growth factors,
cytokines, matrix metalloproteinases, cellular receptors, and extracellular
matrix components. Here, we focus on cellular mechanisms underlying keratinocyte
migration and proliferation during epidermal closure. Inability to
re-epithelialize is a clear indicator of chronic non-healing wounds, which fail
to proceed through the normal phases of wound healing in an orderly and timely
manner. This review summarizes the current knowledge regarding the management and
treatment of acute and chronic wounds, with a focus on re-epithelialization,
offering some insights into novel future therapies.
CI - Copyright © 2018 Elsevier B.V. All rights reserved.
FAU - Rousselle, Patricia
AU - Rousselle P
AD - Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS -
Université Lyon 1, Institut de Biologie et Chimie des Protéines, SFR BioSciences
Gerland-Lyon Sud, 7 passage du Vercors, F-69367, France. Electronic address:
patricia.rousselle@ibcp.fr.
FAU - Braye, Fabienne
AU - Braye F
AD - Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS -
Université Lyon 1, Institut de Biologie et Chimie des Protéines, SFR BioSciences
Gerland-Lyon Sud, 7 passage du Vercors, F-69367, France; Plastic, reconstructive
and aesthetic surgery department, Croix-Rousse hospital, hospices civils de Lyon,
103, grande rue de la Croix-Rousse, 69004 Lyon, France.
FAU - Dayan, Guila
AU - Dayan G
AD - Laboratoire de Biologie Tissulaire et Ingénierie Thérapeutique, UMR 5305, CNRS -
Université Lyon 1, Institut de Biologie et Chimie des Protéines, SFR BioSciences
Gerland-Lyon Sud, 7 passage du Vercors, F-69367, France.
LA - eng
PT - Journal Article
PT - Research Support, Non-U.S. Gov't
PT - Review
DEP - 20180705
PL - Netherlands
TA - Adv Drug Deliv Rev
JT - Advanced drug delivery reviews
JID - 8710523
RN - 0 (Cytokines)
RN - 0 (Hormones)
RN - 0 (Intercellular Signaling Peptides and Proteins)
RN - 0 (RNA, Small Interfering)
SB - IM
MH - Adult
MH - Animals
MH - Cytokines/*metabolism
MH - Hormones/*metabolism
MH - Humans
MH - Intercellular Signaling Peptides and Proteins/*metabolism
MH - RNA, Small Interfering/*pharmacology
MH - Skin Diseases/metabolism/pathology/*therapy
MH - Tissue Engineering
MH - Wound Healing/*drug effects
OTO - NOTNLM
OT - Chronic wounds
OT - Epidermal regeneration
OT - Extracellular matrix
OT - Keratinocyte
OT - Re-epithelialization
OT - Therapeutic strategies
OT - Wound healing
EDAT- 2018/07/10 06:00
MHDA- 2020/07/30 06:00
CRDT- 2018/07/09 06:00
PHST- 2018/01/30 00:00 [received]
PHST- 2018/04/28 00:00 [revised]
PHST- 2018/06/25 00:00 [accepted]
PHST- 2018/07/10 06:00 [pubmed]
PHST- 2020/07/30 06:00 [medline]
PHST- 2018/07/09 06:00 [entrez]
AID - S0169-409X(18)30158-3 [pii]
AID - 10.1016/j.addr.2018.06.019 [doi]
PST - ppublish
SO - Adv Drug Deliv Rev. 2019 Jun;146:344-365. doi: 10.1016/j.addr.2018.06.019. Epub
2018 Jul 5.
PMID- 34463289
OWN - NLM
STAT- MEDLINE
DCOM- 20211025
LR - 20211025
IS - 1950-6112 (Electronic)
IS - 0003-3898 (Linking)
VI - 79
IP - 4
DP - 2021 Aug 1
TI - [The missions of Biologie Sans Frontières (BSF)].
PG - 387-393
LID - 10.1684/abc.2021.1665 [doi]
AB - « Biologie sans Frontières » (BSF) is a non-governmental organisation whose
mission is to develop medical biology where it is most needed, particularly in
French-speaking Africa. In Guinea Conakry, with Fondation Mérieux and the Guinean
Ministry of Health, BSF is in charge of training "trainers/teachers" of
technicians. This training will take place at the National Health School of
Kindia, a school that has been completely rehabilitated and re-equipped thanks to
the support of Fondation Mérieux. This project is supported by the French
Development Agency. BSF has an in-depth knowledge of the local needs in medical
biology training. After an audit carried out by two BSF members, the findings
were alarming: these trainers had no experience in medical biology and their
theoretical knowledge was still of low level. Three training courses were then
provided by BSF, the first in biochemistry, sero-immunology and
immuno-hematology, the second in cyto-hematology and the last one in
bacteriology-parasitology. The basic techniques have been acquired, the "student
trainers" have shown great assiduity, but the level remains fragile and will
require new training, which is essential to help these future teachers to provide
structured, functional and above all useful practical work adapted to local
practices and needs.
FAU - Massoubre, Bernard
AU - Massoubre B
AD - Hôpital d'Instruction des Armées Desgenettes, Lyon, France, Biologie Sans
Frontière, Lyon, France.
FAU - Terry, Odette
AU - Terry O
AD - Biologie Sans Frontière, Lyon, France.
FAU - Chabin, Evelyne
AU - Chabin E
AD - Biologie Sans Frontière, Lyon, France.
FAU - Brisbourg, Catherine
AU - Brisbourg C
AD - Biologie Sans Frontière, Lyon, France.
FAU - Emeraud, Cécile
AU - Emeraud C
AD - Biologie Sans Frontière, Lyon, France.
FAU - Moreno, Nabila
AU - Moreno N
AD - Biologie Sans Frontière, Lyon, France.
FAU - Boulliat, Caroline
AU - Boulliat C
AD - Hôpital d'Instruction des Armées Desgenettes, Lyon, France.
FAU - Flori, Pierre
AU - Flori P
AD - Biologie Sans Frontière, Lyon, France.
LA - fre
PT - Journal Article
TT - Les missions de Biologie Sans Frontières (BSF).
PL - France
TA - Ann Biol Clin (Paris)
JT - Annales de biologie clinique
JID - 2984690R
SB - IM
MH - Africa
MH - Guinea/epidemiology
MH - Humans
OTO - NOTNLM
OT - BSF
OT - Guinea Conakry
OT - West Africa
OT - education
EDAT- 2021/09/01 06:00
MHDA- 2021/10/26 06:00
CRDT- 2021/08/31 09:01
PHST- 2021/09/01 06:00 [pubmed]
PHST- 2021/10/26 06:00 [medline]
PHST- 2021/08/31 09:01 [entrez]
AID - abc.2021.1665 [pii]
AID - 10.1684/abc.2021.1665 [doi]
PST - ppublish
SO - Ann Biol Clin (Paris). 2021 Aug 1;79(4):387-393. doi: 10.1684/abc.2021.1665.
PMID- 17848117
OWN - NLM
STAT- MEDLINE
DCOM- 20080110
LR - 20181201
IS - 1434-6621 (Print)
IS - 1434-6621 (Linking)
VI - 45
IP - 9
DP - 2007
TI - Third "Biologie Prospective" Santorini Conference.
PG - 1107-8
FAU - Kazmierczak, Steven
AU - Kazmierczak S
LA - eng
PT - Congress
PT - Editorial
PL - Germany
TA - Clin Chem Lab Med
JT - Clinical chemistry and laboratory medicine
JID - 9806306
RN - 0 (Biomarkers)
SB - IM
MH - Animals
MH - Biochemistry/methods
MH - Biomarkers
MH - Genetic Predisposition to Disease
MH - Genetic Variation
MH - Genomics/*trends
MH - Greece
MH - Humans
MH - Medical Oncology/*trends
MH - Pharmacogenetics/trends
MH - Systems Biology/*trends
EDAT- 2007/09/13 09:00
MHDA- 2008/01/11 09:00
CRDT- 2007/09/13 09:00
PHST- 2007/09/13 09:00 [pubmed]
PHST- 2008/01/11 09:00 [medline]
PHST- 2007/09/13 09:00 [entrez]
AID - 10.1515/CCLM.2007.329 [doi]
PST - ppublish
SO - Clin Chem Lab Med. 2007;45(9):1107-8. doi: 10.1515/CCLM.2007.329.
PMID- 36803694
OWN - NLM
STAT- MEDLINE
DCOM- 20230223
LR - 20230223
IS - 1638-6183 (Electronic)
IS - 0300-9084 (Linking)
VI - 205
DP - 2023 Feb
TI - Membrane proteins.
PG - 1-2
LID - S0300-9084(23)00027-5 [pii]
LID - 10.1016/j.biochi.2023.01.018 [doi]
FAU - Picard, Martin
AU - Picard M
AD - CNRS UMR 7099, Laboratoire de Biologie Physico-Chimique des Protéines
Membranaires, Institut de Biologie Physico-Chimique (IBPC), 13, rue Pierre et
Marie Curie 75005, Paris, France. Electronic address: martin.picard@ibpc.fr.
LA - eng
PT - Editorial
PL - France
TA - Biochimie
JT - Biochimie
JID - 1264604
RN - 0 (Membrane Proteins)
SB - IM
MH - *Membrane Proteins/metabolism
MH - Protein Conformation
MH - Cell Membrane/metabolism
EDAT- 2023/02/22 06:00
MHDA- 2023/02/25 06:00
CRDT- 2023/02/21 18:17
PHST- 2023/02/21 18:17 [entrez]
PHST- 2023/02/22 06:00 [pubmed]
PHST- 2023/02/25 06:00 [medline]
AID - S0300-9084(23)00027-5 [pii]
AID - 10.1016/j.biochi.2023.01.018 [doi]
PST - ppublish
SO - Biochimie. 2023 Feb;205:1-2. doi: 10.1016/j.biochi.2023.01.018.
PMID- 33815586
OWN - NLM
STAT- PubMed-not-MEDLINE
LR - 20210405
IS - 1773-035X (Print)
IS - 1773-0368 (Electronic)
IS - 1773-035X (Linking)
VI - 2021
IP - 531
DP - 2021 Apr
TI - [Not Available].
PG - 27
LID - 10.1016/S1773-035X(21)00103-9 [doi]
FAU - Beauvillain, Céline
AU - Beauvillain C
AD - Laboratoire d'immunologie et allergologie, CHU Angers, 4, rue Larrey; 49933
Angers cedex 09, France.
AD - Équipe Immunité innée et immunothérapie, Inserm U1232, Centre de recherche en
cancérologie et immunologie Université d'Angers, Institut de Biologie en Santé
CHU Angers, 4, rue Larrey; 49933 Angers cedex 09, France.
AD - Université d'Angers, Institut de Biologie en Santé, CHU Angers, 4, rue Larrey;
49933 Angers cedex 09, France.
FAU - Kolopp Sarda, Marie-Nathalie
AU - Kolopp Sarda MN
AD - Laboratoire d'Immunologie, Centre de biologie, CH Lyon Sud, 165 chemin du
Grand-Revoyet, 69495 Pierre-Bénite cedex, France.
AD - EA4130 Immunogénomique et Inflammation, Université Lyon 1, Lyon, France, hôpital
Édouard-Herriot, 69437 Lyon cedex 03, France.
LA - fre
PT - Editorial
TT - Les immunoglobulines.
DEP - 20210330
PL - France
TA - Rev Francoph Lab
JT - Revue francophone des laboratoires : RFL
JID - 101264920
PMC - PMC8008874
EDAT- 2021/04/06 06:00
MHDA- 2021/04/06 06:01
CRDT- 2021/04/05 05:59
PHST- 2021/04/05 05:59 [entrez]
PHST- 2021/04/06 06:00 [pubmed]
PHST- 2021/04/06 06:01 [medline]
AID - S1773-035X(21)00103-9 [pii]
AID - 10.1016/S1773-035X(21)00103-9 [doi]
PST - ppublish
SO - Rev Francoph Lab. 2021 Apr;2021(531):27. doi: 10.1016/S1773-035X(21)00103-9. Epub
2021 Mar 30.
PMID- 29386147
OWN - NLM
STAT- MEDLINE
DCOM- 20181024
LR - 20181202
IS - 1950-6112 (Electronic)
IS - 0003-3898 (Linking)
VI - 76
IP - 1
DP - 2018 Jan 1
TI - Editor-in-chief of the Annales de Biologie Clinique (Paris) for 10 years: thanks
for your confidence!
PG - 7-8
LID - 10.1684/abc.2017.1315 [doi]
FAU - Beaudeux, Jean-Louis
AU - Beaudeux JL
AD - Rédacteur en chef.
LA - eng
PT - Editorial
TT - Dix ans de rédaction en chef des Annales de biologie clinique… Merci de votre
confiance !
PL - France
TA - Ann Biol Clin (Paris)
JT - Annales de biologie clinique
JID - 2984690R
SB - IM
MH - Biology/*organization & administration/standards/trends
MH - Humans
MH - Medical Laboratory Personnel/organization & administration/standards/trends
MH - *Medical Laboratory Science/organization & administration/standards/trends
MH - Paris
MH - Professional Practice/standards/trends
MH - Publishing/standards/*trends
MH - Workforce
EDAT- 2018/02/02 06:00
MHDA- 2018/10/26 06:00
CRDT- 2018/02/02 06:00
PHST- 2018/02/02 06:00 [entrez]
PHST- 2018/02/02 06:00 [pubmed]
PHST- 2018/10/26 06:00 [medline]
AID - abc.2017.1315 [pii]
AID - 10.1684/abc.2017.1315 [doi]
PST - ppublish
SO - Ann Biol Clin (Paris). 2018 Jan 1;76(1):7-8. doi: 10.1684/abc.2017.1315.
PMID- 31864527
OWN - NLM
STAT- MEDLINE
DCOM- 20200707
LR - 20200707
IS - 1879-0402 (Electronic)
IS - 1367-5931 (Linking)
VI - 53
DP - 2019 Dec
TI - A measure of force.
PG - A4-A6
LID - S1367-5931(19)30132-2 [pii]
LID - 10.1016/j.cbpa.2019.11.011 [doi]
FAU - Strick, Terence R
AU - Strick TR
AD - Ecole normale supérieure, Institut de Biologie de l'Ecole normale supérieure
(IBENS), CNRS, INSERM, PSL Research University, 75005, Paris, France; Programme
Equipe Labellisées, Ligue Contre le Cancer, 75013, Paris, France. Electronic
address: strick@biologie.ens.fr.
FAU - Yan, Jie
AU - Yan J
AD - Department of Physics, National University of Singapore, 117546, Singapore;
Mechanobiology Institute, National University of Singapore, 117411, Singapore.
Electronic address: phyyj@nus.edu.sg.
LA - eng
PT - Editorial
PT - Introductory Journal Article
PL - England
TA - Curr Opin Chem Biol
JT - Current opinion in chemical biology
JID - 9811312
SB - IM
MH - *Microscopy, Atomic Force
MH - *Single Molecule Imaging
EDAT- 2019/12/23 06:00
MHDA- 2020/07/08 06:00
CRDT- 2019/12/23 06:00
PHST- 2019/12/23 06:00 [entrez]
PHST- 2019/12/23 06:00 [pubmed]
PHST- 2020/07/08 06:00 [medline]
AID - S1367-5931(19)30132-2 [pii]
AID - 10.1016/j.cbpa.2019.11.011 [doi]
PST - ppublish
SO - Curr Opin Chem Biol. 2019 Dec;53:A4-A6. doi: 10.1016/j.cbpa.2019.11.011.
PMID- 26405094
OWN - NLM
STAT- MEDLINE
DCOM- 20160113
LR - 20181202
IS - 1460-2105 (Electronic)
IS - 0027-8874 (Linking)
VI - 107
IP - 12
DP - 2015 Dec
TI - Response.
PG - djv277
LID - djv277 [pii]
LID - 10.1093/jnci/djv277 [doi]
FAU - Delhem, Nadira
AU - Delhem N
AD - Immunoregulation of Virus-Induced Cancer, Institut de Biologie de Lille, Pasteur
Institute of Lille, Lille Cedex, France. nadira.delhem@ibl.cnrs.fr.
FAU - Mustapha, Rami
AU - Mustapha R
AD - Immunoregulation of Virus-Induced Cancer, Institut de Biologie de Lille, Pasteur
Institute of Lille, Lille Cedex, France.
LA - eng
PT - Comment
PT - Letter
DEP - 20150923
PL - United States
TA - J Natl Cancer Inst
JT - Journal of the National Cancer Institute
JID - 7503089
SB - IM
CON - J Natl Cancer Inst. 2015 Jan;107(1):363. PMID: 25505237
CON - J Natl Cancer Inst. 2015 Dec;107(12):djv276. PMID: 26405093
MH - Animals
MH - Carcinoma/*metabolism
MH - Exosomes/*metabolism
MH - Humans
MH - Nasopharyngeal Neoplasms/*metabolism
MH - T-Lymphocytes, Regulatory/*immunology/*metabolism
EDAT- 2015/09/26 06:00
MHDA- 2016/01/14 06:00
CRDT- 2015/09/26 06:00
PHST- 2015/09/26 06:00 [entrez]
PHST- 2015/09/26 06:00 [pubmed]
PHST- 2016/01/14 06:00 [medline]
AID - djv277 [pii]
AID - 10.1093/jnci/djv277 [doi]
PST - epublish
SO - J Natl Cancer Inst. 2015 Sep 23;107(12):djv277. doi: 10.1093/jnci/djv277. Print
2015 Dec.
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