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I'm writing a report in which I'm citing several different works. When I find a paper that I need to cite, I look up the bibTex reference to get this...

Query Results from the ADS Database





Retrieved 1 abstracts, starting with number 1.  Total number selected: 1.



@ARTICLE{1990PASP..102.1181B,

   author = {{Bessell}, M.~S.},

    title = "{UBVRI passbands}",

  journal = {pasp},

 keywords = {Astronomical Photometry, Spectral Bands, Ubv Spectra, Charge Coupled Devices, Reference Stars, Stellar Color, Stellar Magnitude},

     year = 1990,

    month = oct,

   volume = 102,

    pages = {1181-1199},

      doi = {10.1086/132749},

   adsurl = {http://adsabs.harvard.edu/abs/1990PASP..102.1181B},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}

...which I copy and paste into my bib file. Thus, my bib file looks like this:

@ARTICLE{chj+17,

   author = {{Curran}, S.~J. and {Hunstead}, R.~W. and {Johnston}, H.~M. and 

    {Whiting}, M.~T. and {Sadler}, E.~M. and {Allison}, J.~R. and 

    {Bignell}, C.},

    title = "{Further Observational Evidence for a Critical Ionising Luminosity in Active Galaxies}",

  journal = {ArXiv e-prints},

archivePrefix = "arXiv",

   eprint = {1706.06508},

 keywords = {Astrophysics - Astrophysics of Galaxies},

     year = 2017,

    month = jun,

   adsurl = {http://adsabs.harvard.edu/abs/2017arXiv170606508C},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}



@article{cd18,

author = {Curran, S J and Duchesne, S W},

title = {The mid-infrared properties and gas content of active galaxies over large lookback times},

journal = {Monthly Notices of the Royal Astronomical Society},

volume = {476},

number = {3},

pages = {3580-3590},

year = {2018},

doi = {10.1093/mnras/sty443},

URL = {http://dx.doi.org/10.1093/mnras/sty443},

eprint = {/oup/backfile/content_public/journal/mnras/476/3/10.1093_mnras_sty443/2/sty443.pdf}

}



@article{bes05,

author = {Bessell, Michael S.},

title = {Standard Photometric Systems},

journal = {Annual Review of Astronomy and Astrophysics},

volume = {43},

number = {1},

pages = {293-336},

year = {2005},

doi = {10.1146/annurev.astro.41.082801.100251},

URL = {https://doi.org/10.1146/annurev.astro.41.082801.100251},

eprint = {https://doi.org/10.1146/annurev.astro.41.082801.100251,}



@INPROCEEDINGS{sanders99,

   author = {{Sanders}, D.~B.},

    title = "{Infrared Emission from AGN}",

booktitle = {Activity in Galaxies and Related Phenomena},

     year = 1999,

   series = {IAU Symposium},

   volume = 194,

   eprint = {astro-ph/9903445},

   editor = {{Terzian}, Y. and {Khachikian}, E. and {Weedman}, D.},

    pages = {25},

   adsurl = {http://adsabs.harvard.edu/abs/1999IAUS..194...25S},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}



@ARTICLE{wu04,

   author = {{Wu}, X.-B. and {Zhang}, W. and {Zhou}, X.},

    title = "{Color-Redshift Relations and Photometric Redshift Estimations of Quasars in Large Sky Surveys}",

  journal = {cjaa},

   eprint = {astro-ph/0307418},

 keywords = {galaxies: photometry, quasars: general, quasars: emission lines, surveys},

     year = 2004,

    month = feb,

   volume = 4,

    pages = {17-27},

      doi = {10.1088/1009-9271/4/1/17},

   adsurl = {http://adsabs.harvard.edu/abs/2004ChJAA...4...17W},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}



@ARTICLE{bes90,

   author = {{Bessell}, M.~S.},

    title = "{UBVRI passbands}",

  journal = {pasp},

 keywords = {Astronomical Photometry, Spectral Bands, Ubv Spectra, Charge Coupled Devices, Reference Stars, Stellar Color, Stellar Magnitude},

     year = 1990,

    month = oct,

   volume = 102,

    pages = {1181-1199},

      doi = {10.1086/132749},

   adsurl = {http://adsabs.harvard.edu/abs/1990PASP..102.1181B},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}

Once I've saved the file, I enter

bibliography{QSO_bibliography2}

bibliographystyle{ieeetr}

into my tex file. After compiling, my bbl file contains

begin{thebibliography}{1}



bibitem{bes90}

M.~S. {Bessell}, ``{UBVRI passbands},'' {em pasp}, vol.~102, pp.~1181--1199,

  Oct. 1990.



bibitem{bes05}

M.~S. Bessell, ``Standard photometric systems,'' {em Annual Review of

  Astronomy and Astrophysics}, vol.~43, no.~1, pp.~293--336, 2005.



bibitem{chj+17}

S.~J. {Curran}, R.~W. {Hunstead}, H.~M. {Johnston}, M.~T. {Whiting}, E.~M.

  {Sadler}, J.~R. {Allison}, and C.~{Bignell}, ``{Further Observational

  Evidence for a Critical Ionising Luminosity in Active Galaxies},'' {em ArXiv

  e-prints}, June 2017.



bibitem{cd18}

S.~J. Curran and S.~W. Duchesne, ``The mid-infrared properties and gas content

  of active galaxies over large lookback times,'' {em Monthly Notices of the

  Royal Astronomical Society}, vol.~476, no.~3, pp.~3580--3590, 2018.



end{thebibliography}

and then I insert the citation with something like cite{bes05}. However, only some of the inline citations are recognized. I'm also getting the following error message from the bbl file:

Undefined control sequence. ...Bessell}, ``{UBVRI passbands},'' {em pasp

So my question is: why doesn't the bbl file contain all of the references I've put into the bib file; why are only some of my citations recognized; and why do I get an error message in the bbl file when I copied the code directly from the reference database?

This happens whether I'm using BibTex or BibLaTex, so I'm not sure how to fix it.

I'm sorry for the confused question, but there's a lot going on behind the scenes that I don't know about.

As you've already noted in a comment, it's necessary to provide definitions for the macros pasp and cjaa that occur in some of the bib entries. Given that these macros are not likely to ever be encountered outside a bibliographic context, it makes sense to stick their definitions into the bib file itself, via a @preamble{ " ... " } directive; see below for the details. By including the macro definitions in the bib file that uses them, LaTeX will always have access to the macro definitions whenever they're needed.

A second thought: I believe it's pretty much standard nowadays to provide hyperlinks to the publications assuming, of course, that they're available online. The ieeetr bibliography style is quite ancient -- so ancient, in fact, that it's not programmed to do anything with fields such as url and doi. If you want to make your paper more reader-friendly, I suggest you (a) switch to the IEEEtran bibliography style and (b) load the url and hyperref packages with suitable options; see below for the details. Some of your bib entries don't contain a url field. However, they do contain an adsurl field. Just change the field names from adsurl to url as needed. Of course, if for some reason you prefer not to show the URLs in the formatted bibliographic entries, you shouldn't switch to the IEEEtran bibliography style.

RequirePackage{filecontents}

begin{filecontents}{mybib.bib}

@preamble{"

   providecommand{pasp}{Publications of the Astronomical Society of the Pacific}

   providecommand{cjaa}{Chinese Journal of Astronomy~& Astrophysics}

"}



@ARTICLE{chj+17,

   author = {Curran, S. J. and Hunstead, R. W. and Johnston, H. M. and 

             Whiting, M. T. and Sadler, E.~M. and Allison, J.~R. and 

             Bignell, C.},

    title = "Further Observational Evidence for a Critical Ionising 

             Luminosity in Active Galaxies",

  journal = {ArXiv e-prints},

archivePrefix = "arXiv",

   eprint = {1706.06508},

 keywords = {Astrophysics - Astrophysics of Galaxies},

     year = 2017,

    month = jun,

      url = {http://adsabs.harvard.edu/abs/2017arXiv170606508C},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}



@article{cd18,

author  = {Curran, S J and Duchesne, S W},

title   = {The mid-infrared properties and gas content of active galaxies 

           over large lookback times},

journal = {Monthly Notices of the Royal Astronomical Society},

volume  = {476},

number  = {3},

pages   = {3580-3590},

year    = {2018},

doi     = {10.1093/mnras/sty443},

URL     = {http://dx.doi.org/10.1093/mnras/sty443},

eprint  = {/oup/backfile/content_public/journal/mnras/476/3/10.1093_mnras_sty443/2/sty443.pdf}

}



@article{bes05,

author  = {Bessell, Michael S.},

title   = {Standard Photometric Systems},

journal = {Annual Review of Astronomy and Astrophysics},

volume  = {43},

number  = {1},

pages   = {293-336},

year    = {2005},

doi     = {10.1146/annurev.astro.41.082801.100251},

URL     = {https://doi.org/10.1146/annurev.astro.41.082801.100251},

eprint  = {https://doi.org/10.1146/annurev.astro.41.082801.100251,}

}



@INPROCEEDINGS{sanders99,

   author = {Sanders, David B.},

    title = {Infrared Emission from {AGN}},

booktitle = {Activity in Galaxies and Related Phenomena},

     year = 1999,

   series = {IAU Symposium},

   volume = 194,

   eprint = {astro-ph/9903445},

   editor = {Terzian, Y. and Khachikian, E. and Weedman, D.},

    pages = {25},

      url = {http://adsabs.harvard.edu/abs/1999IAUS..194...25S},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}



@ARTICLE{wu04,

   author = {Wu, X.-B. and Zhang, W. and Zhou, X.},

    title = {Color-Redshift Relations and Photometric Redshift 

             Estimations of Quasars in Large Sky Surveys},

  journal = {cjaa},

   eprint = {astro-ph/0307418},

 keywords = {galaxies: photometry, quasars: general, quasars: 

             emission lines, surveys},

     year = 2004,

    month = feb,

   volume = 4,

    pages = {17-27},

      doi = {10.1088/1009-9271/4/1/17},

      url = {http://adsabs.harvard.edu/abs/2004ChJAA...4...17W},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}



@ARTICLE{bes90,

   author = {Bessell, Michael S.},

    title = {{UBVRI} passbands},

  journal = {pasp},

 keywords = {Astronomical Photometry, Spectral Bands, Ubv Spectra, 

             Charge Coupled Devices, Reference Stars, Stellar Color, 

             Stellar Magnitude},

     year = 1990,

    month = oct,

   volume = 102,

    pages = {1181-1199},

      doi = {10.1086/132749},

      url = {http://adsabs.harvard.edu/abs/1990PASP..102.1181B},

  adsnote = {Provided by the SAO/NASA Astrophysics Data System}

}

end{filecontents}



documentclass{article}

usepackage[english]{babel}

usepackage[numbers]{natbib}

bibliographystyle{IEEEtran} % 'ieeetr' bib style is ancient

usepackage[hyphens,spaces,obeyspaces]{url}

usepackage[colorlinks,allcolors=blue]{hyperref}



begin{document}

nocite{*}

bibliography{mybib}

end{document}

ref should be cite. ref points to labels in the document, not to cite keys in .bib files.