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Here is the file:

@article {1,
    author = {Morreel, Kris and Saeys, Yvan and Dima, Oana and Lu, Fachuang and Van de Peer, Yves and Vanholme, Ruben and Ralph, John and Vanholme, Bartel and Boerjan, Wout},
    title = {Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks},
    volume = {26},
    number = {3},
    pages = {929--945},
    year = {2014},
    doi = {10.1105/tpc.113.122242},
    publisher = {American Society of Plant Biologists},
    issn = {1040-4651},
    journal = {The Plant Cell}
}
@article {2,
    author = {Chandrasekaran, Sriram and Price, Nathan D.},
    title = {Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis},
    volume = {107},
    number = {41},
    pages = {17845--17850},
    year = {2010},
    doi = {10.1073/pnas.1005139107},
    publisher = {National Academy of Sciences},
    issn = {0027-8424},
    journal = {Proceedings of the National Academy of Sciences}
}


@article{3,
    author = {Fernie, Alisdair R.},
    title = {The future of metabolic phytochemistry: Larger numbers of metabolites, higher resolution, greater understanding},
    volume = {68},
    number = {22-24},
    pages = {2861--2880},
    year = {2007},
    doi = {10.1016/j.phytochem.2007.07.010},
    isbn = {0031-9422 (Print)},
    issn = {00319422},
    journal = {Phytochemistry}
}

and in a tex file I write command \cite{3}. However I ended up like this:

circumstances [1]

instead of [3]. and it didn't print the third article in my references.

\documentclass[12pt]{article}
\usepackage[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage{biblatex}
\addbibresource{references.bib}



\begin{document}

\begin{abstract}
bla bla
\end{abstract}
\title{data \thanks{F}}
\maketitle
\begin{abstract}
    blah blah
    \end{abstract}
\section{Introduction}
blah blah \cite{3}
\printbibliography
\end{document}
SaRa
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    it's a really bad idea to use numbers for the cite keys, they should just be internal strings they have no relation to any printed number. the whole point is that latex/bibtex number as needed, either alphabetically or in order of citation, according to the style you specify – David Carlisle Dec 24 '18 at 12:21
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    The keys in the bib file (and the order of the entries) is completly unrelated to the numbering in the tex file. It depends on the bibliography style how the entries are numbered and sorted. – Ulrike Fischer Dec 24 '18 at 12:21
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    With the shown code biblatex will (i) only print those entries that were explicitly \cited (or \nocited), which means that only the entry called 3 will be printed in the bibliography, and will (ii) sort entries by author name, title and year. That usually means that the number you used as entry key 3 will not coincide with the number printed in the document (in this case "[1]"). That's why it is usually seen as a very bad idea to use numeric entry keys: They don't coincide with the numbers in the output. – moewe Dec 24 '18 at 12:39
  • Did the comments from above help you? Can you clarify what exactly you are asking for? – moewe Dec 26 '18 at 07:47

1 Answers1

1

With the code as shown biblatex will

  1. only print those references that were explicitly \cited (or \nocited either with \nocite{<key>} or the blanket \nocite{*}, see Using BibTeX to make a list of references without having citations in the body of the document?) in the bibliography and
  2. sort entries in the bibliography by (author) name, title and year (simply because the default setting for biblatex's sorting option is sorting=nty).

That means that in the MWE only one entry will be printed in the bibliography, namely the one called 3 that was cited. The other two entries 1 and 2 will not be shown. Naturally that one entry that is printed is going to get the number "1" (citations usually start at 1 and count up).

In general the (label) number that appears in the citations and bibliographies is context-dependent and not predictable unless you also know which other entries are cited. That's why it is seen as a bad idea to use numeric entry keys. The keys have no relation to the printed labels. Instead you should consider choosing an entry key that is memorable and has a connection to the paper (for example author names, a few words from the title, ...)

@article{morreel,
  author  = {Morreel, Kris and Saeys, Yvan and Dima, Oana and Lu, Fachuang
             and Van de Peer, Yves and Vanholme, Ruben and Ralph, John
             and Vanholme, Bartel and Boerjan, Wout},
  title   = {Systematic Structural Characterization of Metabolites in
             Arabidopsis via Candidate Substrate-Product Pair Networks},
  journal = {The Plant Cell},
  volume  = {26},
  number  = {3},
  pages   = {929--945},
  year    = {2014},
  doi     = {10.1105/tpc.113.122242},
}
@article{chandrasekaran,
  author  = {Chandrasekaran, Sriram and Price, Nathan D.},
  title   = {Probabilistic integrative modeling of genome-scale metabolic and
             regulatory networks in {Escherichia} coli and {Mycobacterium}
             tuberculosis},
  journal = {Proceedings of the National Academy of Sciences},
  volume  = {107},
  number  = {41},
  pages   = {17845--17850},
  year    = {2010},
  doi     = {10.1073/pnas.1005139107},
}
@article{fernie,
  author   = {Fernie, Alisdair R.},
  title    = {The future of metabolic phytochemistry: Larger numbers of
              metabolites, higher resolution, greater understanding}
  journal  = {Phytochemistry},
  volume   = {68},
  number   = {22-24},
  pages    = {2861--2880},
  year     = {2007},
  doi      = {10.1016/j.phytochem.2007.07.010},
}

If you want your entries to be numbered by order of citation, you need to use sorting=none. See Biblatex citation order.

moewe
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