In [1]:
import bibtexparser
In [4]:
with open('articles.bib') as f:
articles = bibtexparser.load(f)
articles
Out[4]:
<bibtexparser.bibdatabase.BibDatabase at 0x10d4ce320>
In [5]:
for entry in articles.entries:
print(entry)
{'volume': '133', 'number': '7', 'title': 'Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences', 'ENTRYTYPE': 'article', 'ID': 'berger2008variation', 'publisher': 'Elsevier', 'year': '2008', 'author': 'Berger, Michael F and Badis, Gwenael and Gehrke, Andrew R and Talukder, Shaheynoor and Philippakis, Anthony A and Pena-Castillo, Lourdes and Alleyne, Trevis M and Mnaimneh, Sanie and Botvinnik, Olga B and Chan, Esther T and others', 'pages': '1266--1276', 'journal': 'Cell'}
{'volume': '5', 'number': '224', 'title': 'MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma', 'ENTRYTYPE': 'article', 'ID': 'wood2012microscale', 'publisher': 'NIH Public Access', 'year': '2012', 'author': 'Wood, Kris C and Konieczkowski, David J and Johannessen, Cory M and Boehm, Jesse S and Tamayo, Pablo and Botvinnik, Olga B and Mesirov, Jill P and Hahn, William C and Root, David E and Garraway, Levi A and others', 'pages': 'rs4', 'journal': 'Science Signaling'}
{'volume': '5', 'number': '1', 'title': 'Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome', 'ENTRYTYPE': 'article', 'ID': 'galili2012prediction', 'publisher': 'BioMed Central', 'year': '2012', 'author': 'Galili, Naomi and Tamayo, Pablo and Botvinnik, Olga B and Mesirov, Jill P and Brooks, Margarita R and Brown, Gail and Raza, Azra', 'pages': '1', 'journal': 'Journal of Hematology \\& Oncology'}
{'volume': '118', 'number': '21', 'title': 'Gene Expression Studies May Identify Lower Risk Myelodysplastic Syndrome Patients Likely to Respond to Therapy with Ezatiostat Hydrochloride (TLK199)', 'ENTRYTYPE': 'article', 'ID': 'galili2011gene', 'publisher': 'American Society of Hematology', 'year': '2011', 'author': 'Galili, Naomi and Tamayo, Pablo and Botvinnik, Olga B and Mesirov, Jill P and Zikria, Jennifer and Brown, Gail and Raza, Azra', 'pages': '2779--2779', 'journal': 'Blood'}
{'journal': 'Nature Biotechnology', 'title': 'Characterizing genomic alterations in cancer by complementary functional associations', 'ENTRYTYPE': 'article', 'ID': 'kim2016characterizing', 'year': '2016', 'author': 'Kim*, Jong Wook and Botvinnik*, Olga B and Abudayyeh, Omar and Birger, Chet and Rosenbluh, Joseph and Shrestha, Yashaswi and Abazeed, Mohamed E and Hammerman, Peter S and DiCara, Daniel and Konieczkowski, David J and others', 'publisher': 'Nature Publishing Group'}
{'volume': '15', 'file': 'Cell Reports 2016 Nutter.pdf:/Users/olga/Documents/Library.papers3/Articles/2016/Nutter/Cell Reports 2016 Nutter.pdf:application/pdf;Cell Reports 2016 Nutter.pdf:/Users/olga/Documents/Library.papers3/Articles/2016/Nutter/Cell Reports 2016 Nutter.pdf:application/pdf', 'rating': '0', 'doi': '10.1016/j.celrep.2016.05.002', 'link': 'http://linkinghub.elsevier.com/retrieve/pii/S2211124716305551', 'author': 'Nutter, Curtis A and Jaworski, Elizabeth A and Verma, Sunil K and Deshmukh, Vaibhav and Wang, Qiongling and Botvinnik, Olga B and Lozano, Mario J and Abass, Ismail J and Ijaz, Talha and Brasier, Allan R and Garg, Nisha J and Wehrens, Xander H T and Yeo, Gene W and Kuyumcu-Martinez, Muge N', 'pages': '2200--2213', 'number': '10', 'date-modified': '2016-12-26T22:43:33GMT', 'title': 'Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes', 'ENTRYTYPE': 'article', 'ID': 'Nutter:2016fd', 'language': 'English', 'year': '2016', 'uri': '\\url{papers3://publication/doi/10.1016/j.celrep.2016.05.002}', 'local-url': 'file://localhost/Users/olga/Documents/Library.papers3/Articles/2016/Nutter/Cell%20Reports%202016%20Nutter.pdf', 'date-added': '2016-12-26T22:41:36GMT', 'journal': 'Cell Reports'}
{'file': '2012 Goncearenco.pdf:/Users/olga/Documents/Library.papers3/Articles/2012/Goncearenco/2012 Goncearenco.pdf:application/pdf', 'rating': '0', 'journal': 'BMC Bioinformatics', 'link': 'http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S18-A1', 'read': 'Yes', 'uri': '\\url{papers3://publication/doi/10.1186/1471-2105-13-S18-A1}', 'abstract': '... BMC Bioinformatics201213(Suppl 18):A1. DOI: 10.1186 / 1471 - 2105 - 13 - S18 - A1 . {\\textcopyright} Goncearenco et al; licensee BioMed Central Ltd. 2012. Published: 14 December 2012. Abstract. The report summarizes the scientific content of ...', 'date-modified': '2016-12-26T22:45:51GMT', 'title': 'Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012', 'ENTRYTYPE': 'article', 'ID': 'Goncearenco:2012eha', 'author': 'Goncearenco, A and Grynberg, P and Botvinnik, Olga B and Macintyre, Geoff and Abeel, Thomas', 'year': '2012', 'local-url': 'file://localhost/Users/olga/Documents/Library.papers3/Articles/2012/Goncearenco/2012%20Goncearenco.pdf', 'date-added': '2016-12-26T22:41:19GMT', 'doi': '10.1186/1471-2105-13-S18-A1'}
In [14]:
def reverse_last_first(name):
try:
last, first = name.split(', ')
return '{first} {last}'.format(first=first, last=last)
except ValueError:
return 'et al'
lines = []
for entry in articles.entries:
authors = entry['author'].split(' and ')
print(entry['title'])
for last_first in authors:
first_last = reverse_last_first(last_first)
print('\t', first_last)
Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
Michael F Berger
Gwenael Badis
Andrew R Gehrke
Shaheynoor Talukder
Anthony A Philippakis
Lourdes Pena-Castillo
Trevis M Alleyne
Sanie Mnaimneh
Olga B Botvinnik
Esther T Chan
et al
MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma
Kris C Wood
David J Konieczkowski
Cory M Johannessen
Jesse S Boehm
Pablo Tamayo
Olga B Botvinnik
Jill P Mesirov
William C Hahn
David E Root
Levi A Garraway
et al
Prediction of response to therapy with ezatiostat in lower risk myelodysplastic syndrome
Naomi Galili
Pablo Tamayo
Olga B Botvinnik
Jill P Mesirov
Margarita R Brooks
Gail Brown
Azra Raza
Gene Expression Studies May Identify Lower Risk Myelodysplastic Syndrome Patients Likely to Respond to Therapy with Ezatiostat Hydrochloride (TLK199)
Naomi Galili
Pablo Tamayo
Olga B Botvinnik
Jill P Mesirov
Jennifer Zikria
Gail Brown
Azra Raza
Characterizing genomic alterations in cancer by complementary functional associations
Jong Wook Kim*
Olga B Botvinnik*
Omar Abudayyeh
Chet Birger
Joseph Rosenbluh
Yashaswi Shrestha
Mohamed E Abazeed
Peter S Hammerman
Daniel DiCara
David J Konieczkowski
et al
Dysregulation of RBFOX2 Is an Early Event in Cardiac Pathogenesis of Diabetes
Curtis A Nutter
Elizabeth A Jaworski
Sunil K Verma
Vaibhav Deshmukh
Qiongling Wang
Olga B Botvinnik
Mario J Lozano
Ismail J Abass
Talha Ijaz
Allan R Brasier
Nisha J Garg
Xander H T Wehrens
Gene W Yeo
Muge N Kuyumcu-Martinez
Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012
A Goncearenco
P Grynberg
Olga B Botvinnik
Geoff Macintyre
Thomas Abeel
In [ ]:
Content source: olgabot/permission-letters
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