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I have a document in .bib format, namelad by savedrecs1.bib, obtained from Web of Science. The document have a set of reference, of the type:

@article{ WOS:000315745900009,
Author = {Bini, Daniel and dos Santos, Cristiane Alcantara and Bouillet,
   Jean-Pierre and de Morais Goncalves, Jose Leonardo and Bran Nogueira
   Cardoso, Elke Jurandy},
Title = {Eucalyptus grandis and Acacia mangium in monoculture and intercropped
   plantations: Evolution of soil and litter microbial and chemical
   attributes during early stages of plant development},
Journal = {APPLIED SOIL ECOLOGY},
Year = {2013},
Volume = {63},
Pages = {57-66},
Month = {JAN},
Abstract = {Soil microorganisms and microbial processes are influenced by the
   quality and quantity of plant waste entering the soil, by its seasonal
   and spatial distribution, by the ratio of above- to below-ground inputs,
   and by changes in nutrient inputs. Soil management strategies sometimes
   promote mixed-species plantations to mitigate the loss of soil nutrients
   and improve biogeochemical cycling. The objective of this study was to
   explore changes in microbiological and chemical attributes of soils and
   litter in the early stages of the second rotation of mixed and pure
   plantations of Eucalyptus grandis and Acacia mangium, and to look for
   correlations between attributes. Soil samples at 0-10 cm depth were
   collected two, seven, 14, and 20 months after planting in the following
   treatments: monocultures of A. mangium and E. grandis, a monoculture of
   E. grandis with N-fertilizer, and an intercropped plantation with E.
   grandis and A. mangium. Microbial soil attributes varied dramatically
   between treatments 20 months after planting. Total C, N and P contents
   in litter showed the strongest correlations with microbial biomass C and
   N (C-mic and N-mic), microbial respiration, and dehydrogenase activity
   in all sampling periods. Lower C/N and C/P ratios in litter and lower
   C/N and C-mic/tC ratios in soils after 20 months in the intercropped
   plantation illustrated the system's capacity for supplying inputs of
   high-quality organic matter rich in N and P, but this did not result in
   higher contents of these elements or greater microbial activity in
   soils. An implication of this finding is that, at least in the initial
   growth phase of these plantations, chemical attributes of the litter and
   variation in those attributes govern microbial processes and,
   consequently, are mostly responsible for plant development. Canonical
   discriminant analysis revealed changes in the microbiological and
   chemical attributes of soil in the intercropped plantation due to the
   plants growth and the leaf litter accumulation. Twenty months after
   planting, the different plantations could be discriminated by
   differences in litter chemistry (C, N, and P), total soil C, N-mic, and
   dehydrogenase activity, which were very similar in intercropped
   plantations and E. grandis with N-fertilizer. These results from the
   early stages of plantation development are important for understanding
   the dynamics of soil attributes in these systems, and especially in
   intercropped plantations. In intercropped areas the cumulative effect of
   microbial attributes reflects a more sustainable system. Long-term
   studies are needed to identify patterns that develop after 20 months,
   during the growth period of these plantations. (C) 2012 Elsevier B.V.
   All rights reserved.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Bini, D (Corresponding Author), Univ Sao Paulo, Luiz de Queiroz Coll Agr, Ave Padua Dias,11,Cx Postal 9, BR-13418900 Piracicaba, SP, Brazil.
   Bini, Daniel; dos Santos, Cristiane Alcantara; Bran Nogueira Cardoso, Elke Jurandy, Univ Sao Paulo, ESALQ, Dept Ciencia Solo, BR-13418900 Piracicaba, SP, Brazil.
   Bouillet, Jean-Pierre; de Morais Goncalves, Jose Leonardo, Univ Sao Paulo, ESALQ, Dept Ciencias Florestais, BR-13418900 Piracicaba, SP, Brazil.
   Bouillet, Jean-Pierre, SupAgro CIRAD INRA IRD, CIRAD, UMR Ecol Fonct \& Biogeochim Sols \& Agroecosyst, F-34060 Montpellier, France.},
DOI = {10.1016/j.apsoil.2012.09.012},
ISSN = {0929-1393},
EISSN = {1873-0272},
Keywords = {Microbial biomass; Forestry; Mixed-species; Legumes; Litter},
Keywords-Plus = {MIXED-SPECIES PLANTATIONS; ENZYME-ACTIVITIES; GROWTH DYNAMICS; BIOMASS
   CARBON; ORGANIC-CARBON; NITROGEN; DECOMPOSITION; FOREST; GLOBULUS;
   FERTILIZATION},
Research-Areas = {Agriculture},
Web-of-Science-Categories  = {Soil Science},
Author-Email = {dani\[email protected]},
Affiliations = {Universidade de Sao Paulo; Universidade de Sao Paulo; CIRAD; INRAE;
   Institut Agro; Montpellier SupAgro},
ResearcherID-Numbers = {Bini, Daniel/E-8231-2013
   Bouillet, Jean-Pierre/E-6929-2014
   Cardoso, Elke JBN/E-5039-2013
   Moraes Goncalves, Jose Leonardo/G-4979-2013},
ORCID-Numbers = {Bini, Daniel/0000-0002-0127-0788
   Moraes Goncalves, Jose Leonardo/0000-0003-1068-5448},
Funding-Acknowledgement = {FAPESP {[}2009/17525-6, 2010/16623-9]; ANR (Agence Nationale de la
   Recherche) {[}2010-STRA-004]; USP/COFECUB project {[}22193PA]; CNPq;
   Cardoso {[}307563/2009-0, 140893/2011-3]},
Funding-Text = {We thank to FAPESP (Project no 2009/17525-6 and no 2010/16623-9), to ANR
   (Agence Nationale de la Recherche - 2010-STRA-004), to ATP Neucapalm
   (CIRAD) and to the USP/COFECUB project (no 22193PA) for funding this
   project. Thanks are also due to the staff of the Itatinga Forest
   Sciences Experimental Station and of the Laboratory of Soil Microbiology
   at the Luiz de Queiroz College of Agriculture for their assistance in
   conducting the experiments. We thank CNPq for providing research a
   productivity fellowship to E.J.B.N. Cardoso (No. 307563/2009-0) and for
   granting a doctoral scholarship to D.Bini (No. 140893/2011-3).},
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Number-of-Cited-References = {59},
Times-Cited = {58},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {90},
Journal-ISO = {Appl. Soil Ecol.},
Doc-Delivery-Number = {100ZZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000315745900009},
DA = {2023-05-11},
}

@article{ WOS:000468188300047,
Author = {Congio, Guilhermo F. S. and Chiavegato, Marilia B. and Batalha, Camila
   D. A. and Oliveira, Patricia P. A. and Maxwell, Thomas M. R. and
   Gregorini, Pablo and Da Silva, Sila C.},
Title = {Strategic grazing management and nitrous oxide fluxes from pasture soils
   in tropical dairy systems},
Journal = {SCIENCE OF THE TOTAL ENVIRONMENT},
Year = {2019},
Volume = {676},
Pages = {493-500},
Month = {AUG 1},
Abstract = {Greenhouse gases emissions are considered one of the most important
   environmental issues of dairy farming systems. Nitrous oxide (N2O) has
   particular importance owing to its global warming potential and
   stratospheric ozone depletion. The objective of this study was to
   investigate the influence of two rotational grazing strategies
   characterized by two pre-grazing targets (95\% and maximum canopy light
   interception: LI95\% and LIMax, respectively) on milk production
   efficiency and N2O fluxes from soil in a tropical dairy farming system
   based on elephant grass (Pennisetum purpureum Schum. cv. Cameroon).
   Results indicated that LI95\% pre-grazing target provided more frequent
   defoliations than LIMax.Water-filled pore space, soil and chamber
   temperatures were affected by sampling periods (P-1 and P-2). There was
   a significant pre-grazing target treatment x sampling period interaction
   effect on soil NH4+ concentration, which was most likely associated with
   urinary-N discharge. During P-1, there was a greater urinary-N discharge
   for LI95\% than LIMax (26.3 vs. 20.9 kg of urinary-N/paddock) caused by
   higher stocking rate, which resulted in greater N2O fluxes for LI95\%.
   Inversely, during P-2, the soil NH4+ and N2O fluxes were greater for
   LIMax than LI95\%. During this period, the greater urinary-N discharge
   (46.8 vs. 44.8 kg of urinary-N/paddock) was likely associated with
   longer stocking period for LIMax relative to LI95\%, since both
   treatments had similar stocking rate. Converting hourly N2O fluxes to
   daily basis and relating to milk production efficiency, LI95\% was 40\%
   more efficient than LIMax (0.34 vs. 0.57 g N-N2O/kg milk .ha). In
   addition, LI(95\% )pre-grazing target decreased urea-N loading per milk
   production by 34\%. Strategic grazing management represented by the
   LI95\% pre-grazing target allows for intensification of tropical
   pasture-based dairy systems, enhanced milk production efficiency and
   decreased N-N2O emission intensity. (C) 2019 Elsevier B.V. All rights
   reserved.},
Publisher = {ELSEVIER SCIENCE BV},
Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Congio, GFS (Corresponding Author), Univ Sao Paulo, Anim Sci Dept, Luiz de Queiroz Coll Agr USP ESALQ, Piracicaba, SP, Brazil.
   Congio, Guilhermo F. S.; Chiavegato, Marilia B.; Batalha, Camila D. A.; Da Silva, Sila C., Univ Sao Paulo, Anim Sci Dept, Luiz de Queiroz Coll Agr USP ESALQ, Piracicaba, SP, Brazil.
   Oliveira, Patricia P. A., Embrapa Pecuaria Sudeste, Sao Carlos, SP, Brazil.
   Maxwell, Thomas M. R.; Gregorini, Pablo, Lincoln Univ, Fac Agr \& Life Sci, Christchurch, New Zealand.},
DOI = {10.1016/j.scitotenv.2019.04.186},
ISSN = {0048-9697},
EISSN = {1879-1026},
Keywords = {Canopy light interception; Nitrous oxide fluxes; Grazed soils; Soil
   nitrogen; Sustainable intensification; Elephant grass},
Keywords-Plus = {MAXIMUM CV-MOMBACA; CATTLE URINE; HERBAGE ACCUMULATION; ROTATIONAL
   STOCKING; ELEPHANT GRASS; ENVIRONMENTAL-IMPACT; MILK-PRODUCTION; N2O
   EMISSIONS; BOVINE URINE; INTENSITY},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Environmental Sciences},
Author-Email = {[email protected]
   [email protected]
   [email protected]
   [email protected]
   [email protected]
   [email protected]
   [email protected]},
Affiliations = {Universidade de Sao Paulo; Empresa Brasileira de Pesquisa Agropecuaria
   (EMBRAPA); Lincoln University - New Zealand},
ResearcherID-Numbers = {Congio, Guilhermo F. S./D-8307-2015
   Oliveira, Patrícia/L-1909-2017
   Da Silva, Sila C/B-8158-2012
   Batalha, Camila Delveaux Araujo/AAG-5927-2020
   Maxwell, Thomas/V-2036-2018
   },
ORCID-Numbers = {Congio, Guilhermo F. S./0000-0002-7659-594X
   Oliveira, Patrícia/0000-0003-4665-3755
   Da Silva, Sila C/0000-0001-9104-3353
   Batalha, Camila Delveaux Araujo/0000-0002-0303-3962
   Maxwell, Thomas/0000-0001-9204-1667},
Funding-Acknowledgement = {Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)
   {[}2014/20182-9, 2016/22040-2]; Conselho Nacional de Desenvolvimento
   Cientifico e Tecnologico (CNPq) {[}140074/2017-1]; Coordenacao de
   Aperfeicoamento de Pessoal de Nivel Superior, Brazil (CAPES) {[}001]},
Funding-Text = {The authors are grateful to Fundacao de Amparo a Pesquisa do Estado de
   Sao Paulo (FAPESP; grants 2014/20182-9 and 2016/22040-2) for financial
   support and scholarship, to Conselho Nacional de Desenvolvimento
   Cientifico e Tecnologico (CNPq, grant 140074/2017-1) and Coordenacao de
   Aperfeicoamento de Pessoal de Nivel Superior, Brazil (CAPES, finance
   code 001) for scholarships, and Carlos Eduardo Jordao for his help with
   gas chromatograph analysis. We also acknowledge the valuable suggestions
   from reviewers.},
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   2010, SCIENCE, V327, P812, DOI DOI 10.1126/SCIENCE.1185383.},
Number-of-Cited-References = {74},
Times-Cited = {13},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {29},
Journal-ISO = {Sci. Total Environ.},
Doc-Delivery-Number = {HY5SP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000468188300047},
DA = {2023-05-11},
}

My objective is to import the document to then export the same document in csv format. To import the document, I used

Import["C:\\Users\\User\\Downloads\\savedrecs1.bib"]

However, the following message appear

enter image description here

Please, anybody help me to import .bib and export it in .csv?

Thank you in advance.

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1
  • 1
    $\begingroup$ You might be able to use the code from this answer $\endgroup$
    – Jason B.
    May 11, 2023 at 18:58

2 Answers 2

2
$\begingroup$

It seems that there is no built-in parser of bib. But it can be easily done by string patterns.

Here is an example code dealing with article entries.

bibEntryDivide[bib_]:=
    StringCases["\n\n"~~bib~~"\n\n","\n@article{"~~Shortest[key__]~~",\n"~~Shortest[entry__]~~",\n}\n":><|StringTrim[key]->StringTrim[entry]|>]//Association;

bibEntryToAssoc[entry_]:=
    StringCases[entry,",\n"~~fieldHead_?UpperCaseQ~~Shortest[field__]~~" = {"~~Shortest[value__]~~"},\n":><|fieldHead~~field->value|>]//Association;
    
bibToAssoc[bib_]:=
    bib//bibEntryDivide//Map[bibEntryToAssoc]//Dataset;

bibEntryDivide divides the string of bib file into entries, and bibEntryToAssoc extracts the fields of an entry.

For the OP's example we have

enter image description here

then

Export["example.csv",bibToAssoc@bib]

gives the csv file

enter image description here

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3
  • $\begingroup$ Certainly we can using Import to read the bib file. Or do you know if there are some built-in method of analysing the structure of bib file, since OP tends to solving this problem within MMA instead of other tools. $\endgroup$
    – Lacia
    May 15, 2023 at 22:44
  • $\begingroup$ I come from a different backgrount (linux and regular rexpressions, yacc and lex or ANTLR). I misunderstood what you were trying to do. This may be of use: A complete guide to the BibTeX format. My issues with the question is the presumption that Mathematica is a proper tool for this task and a lack of description of what is goiing to be done with the data once it is in a spreadsheet. $\endgroup$
    – anon
    May 16, 2023 at 17:51
  • $\begingroup$ I myself use e.g. bibdesk to deal with bib files. Maybe the OP is developing some other tools in MMA, and bib-to-csv is just an intermediate step. I don't know. But I think it's a good exercise of string pattern in MMA. BTW I didn't vote down to your answer since I agree that if not necessary we should not reinvent something. $\endgroup$
    – Lacia
    May 17, 2023 at 5:52
-4
$\begingroup$
  1. XY problem

  2. If Your Only Tool Is a Hammer Then Every Problem Looks Like a Nail

  3. Open, Edit, and Convert BIB and BIBTEX Files

  4. BIB BIBTEX Converter

  5. Working with Bib files in Word/LibreOffice

  6. By the way, what is the actual problem that you are trying to solve? Spreadsheets basically assume that your data is vectors, matrices, or tensors, bibliographic data are not all well structured as that.

  7. Are you sure that this is in fact a Mathematica class problem? I would use gawk in Linux for such jobs. For more complex grammars, I would consider yacc and lex or ANTLR to write a toy compiler for the conversion. Then, you can make the conversion as you like it (hat tip to William Shakespeare).

  8. You showed us the input. Now, show us the desired output. I, for one, have no idea what kind of output you want except spreadsheet.

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