I want to create a database that contains information about several research papers so that I can vectorize phrases or paragraphs to be used by an AI. I am using Python to get text from a PDF and I am getting a string that I do not know how to parse. This is an example of the first page of a paper (I am an author of the paper so there is no problem with the data copyright).
An aditional problem is that not every papers have the same style/organization

I’m sorry if the problem is too complex. Any ideas or thoughts would be welcome.

I know you can request papers from their original website but this limits my database to free research and it does not work for me

The first page of the paper looks like this

What I’m trying:

from PyPDF2 import PdfReader

reader = PdfReader("paper1.pdf")
number_of_pages = len(reader.pages)
page = reader.pages[0]
text = page.extract_text()

fname = "paper1.txt"
with open(fname, "w", encoding="utf-8") as f:
    f.write(text)

the file paper1.txt looks like this:

A matter of hierarchy: activation of orfamide
production by the post-transcriptional Gac-Rsmcascade of Pseudomonas protegens CHA0 through
expression upregulation of the two dedicatedtranscriptional regulators
Patricio Martı ´n Sobrero,1†Andr /C19es Muzlera,1†
Julieta Frescura,1Edgardo Jofr /C19e2and
Claudio Valverde1*
1CONICET, Departamento de Ciencia y Tecnologı ´a,
Laboratorio de Bioquı ´mica, Microbiologı ´ae
Interacciones Biol /C19ogicas en el Suelo. Roque S /C19aenz
Pe~na 352, Bernal B1876BXD, Universidad Nacional de
Quilmes, Buenos Aires, Argentina.
2CONICET, Facultad de Ciencias Exactas Fı ´sico-
Quı´micas y Naturales, Departmento de Ciencias
Naturales. Ruta Nacional 36 Km 601, Universidad
Nacional de Rı ´o Cuarto, 5800 Rı ´o Cuarto, C /C19ordoba,
Argentina.
Summary
In this work, we surveyed the genome of P. protegens
CHA0 in order to identify novel mRNAs possibly
under the control of the Gac-Rsm cascade that might,for their part, serve to elucidate as-yet-unknown func-
tions involved in the biocontrol of plant pathogens
and/or in cellular processes required for fitness innatural environments. In view of the experimental evi-
dence from former studies on the Gac-Rsm cascade,
we developed a computational screen supported by acombination of sequence, structural and evolutionary
constraints that led to a dataset of 43 potential novel
mRNA targets. We then confirmed several mRNA tar-gets experimentally and next focused on two of the
respective genes that are physically linked to the
orfamide biosynthetic gene cluster and whose pre-dicted open-reading frames resembled cognate
LuxR-type transcriptional regulators of cyclic lipo-
peptide clusters in related pseudomonads. In thisreport, we demonstrate that in strain CHA0, orfamide
production is stringently dependent on a functionalGac-Rsm cascade and that both mRNAs encoding
transcriptional regulatory proteins are under direct
translational control of the RsmA/E proteins. Ourresults have thus revealed a hierarchical control overthe expression of orfamide biosynthetic genes withthe final transcriptional control subordinated to theglobal Gac-Rsm post-transcriptional regulatorysystem.
Introduction
InPseudomonas spp., the ubiquitous and global regula-
tory two-component system GacS-GacA controls sensi-
tive traits like cell–cell communication, secondary
metabolite production and motility (Lapouge et al .,
2008). In Pseudomonas protegens Pf-5, the global regu-
lation by GacA extends to more than 10% of the anno-tated genes, whereas in P . aeruginosa M18 that system
influences the expression of some 15% of the encodedgenes (Hassan et al ., 2010; Wei et al ., 2013). Such a
striking impact on global gene expression operatesmainly at the post-transcriptional level through the actionof GacA-responsive small, noncoding and trans -acting
regulatory RNAs (sRNAs) of the Csr/Rsm family
(Lapouge et al ., 2008). The entire global regulatory
pathway, known as the Gac-Rsm cascade in the genusPseudomonas , is also present in other members of the
g-proteobacteria, thus tracing the ancestral and pivotal
role of that cascade in gene regulatory networks(Lapouge et al., 2007).
In the biocontrol strain P . protegens CHA0 the Gac-
Rsm cascade upregulates the expression of genes
required for production of all secondary metabolites that
have been identified as relevant to the biocontrol of fun-gal and oomycete plant pathogens and to insect toxicity,as well as to escaping predation by bacterivorous proto-zoa and nematodes, for example, 2,4-diacetylphorogluci-nol (DAPG), pyoluteorin, HCN and exoprotease A (Haasand Defago, 2005; Jousset et al ., 2006; Romanowski
et al ., 2011; Flury et al ., 2017). The histidine kinase
Received 24 March, 2017; accepted 21 June, 2017. *For corre-
spondence. E-mail cvalver@unq.edu.ar; Tel. 154-11-4365-7100
ext. 5638; Fax 154-11-4365-7132.
†These authors contributed equally to this work.
VC2017 Society for Applied Microbiology and John Wiley & Sons LtdEnvironmental Microbiology Reports (2017) 00(00), 00–00 doi:10.1111/1758-2229.12566