2

The journal article should look like this:

Pensole G, Gissi C, Lanave C, Saccone C. 1995. Glutamine synthetase gene evolution in bacteria. Mol Biol Evol. 12:189-197

Longer journal titles should be abbreviated and after the volume number a colon.

(The formats for CSE posted are from 2012 and do not have abbreviations or the colon.)

Update 8/14/14: I cannot get the posted CSE style to work but the followed CBE style needs the following changes to Journal citations which I am not sure how to make:

  1. Not full capitalization in the last name
  2. No comma after the last name
  3. No periods after the initials
  4. Abbreviated long Journal titles (such as Mol Biol Evol., with only a period after the last word) in accordance with ISO 4 standards on ISSN.org
  5. No period after full journal names such as Nature or Science.
  6. No italicization of journal name.
  7. No comma between name and date for in-text citations, including after et al.

The rest can remain the same. More specific info about the format of end references can be found here http://writing.wisc.edu/Handbook/DocCSE_NameYear.html#article.

CBE Style:

ENTRY
  { address
    author
    booktitle
    chapter
    edition
    editor
    howpublished
    institution
    journal
    key
%    month      not used in apalike
    note
    number
    organization
    pages
    publisher
    school
    series
    title
    type
    volume
    year
  }
  {}
  { label extra.label sort.label }

INTEGERS { output.state before.all mid.sentence after.sentence after.block }

FUNCTION {init.state.consts}
{ #0 'before.all :=
  #1 'mid.sentence :=
  #2 'after.sentence :=
  #3 'after.block :=
}

STRINGS { s t }

FUNCTION {output.nonnull}
{ 's :=
  output.state mid.sentence =
    { ", " * write$ }
    { output.state after.block =
    { add.period$ write$
      newline$
      "\newblock " write$
    }
    { output.state before.all =
        'write$
        { add.period$ " " * write$ }
      if$
    }
      if$
      mid.sentence 'output.state :=
    }
  if$
  s
}

FUNCTION {output}
{ duplicate$ empty$
    'pop$
    'output.nonnull
  if$
}

FUNCTION {output.check}
{ 't :=
  duplicate$ empty$
    { pop$ "empty " t * " in " * cite$ * warning$ }
    'output.nonnull
  if$
}

%                   apalike needs this function because
%                   the year has special punctuation;
%                   apalike ignores the month
FUNCTION {output.year.check}
{ year empty$
    { "empty year in " cite$ * warning$ }
    { write$
      " " year * extra.label *
      mid.sentence 'output.state :=
    }
  if$
}

FUNCTION {output.bibitem}
{ newline$
  "\bibitem[" write$
  label write$
  "]{" write$
  cite$ write$
  "}" write$
  newline$
  ""
  before.all 'output.state :=
}

FUNCTION {fin.entry}
{ add.period$
  write$
  newline$
}

FUNCTION {new.block}
{ output.state before.all =
    'skip$
    { after.block 'output.state := }
  if$
}

FUNCTION {new.sentence}
{ output.state after.block =
    'skip$
    { output.state before.all =
    'skip$
    { after.sentence 'output.state := }
      if$
    }
  if$
}

FUNCTION {not}
{   { #0 }
    { #1 }
  if$
}

FUNCTION {and}
{   'skip$
    { pop$ #0 }
  if$
}

FUNCTION {or}
{   { pop$ #1 }
    'skip$
  if$
}

FUNCTION {new.block.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.block
  if$
}

FUNCTION {field.or.null}
{ duplicate$ empty$
    { pop$ "" }
    'skip$
  if$
}

FUNCTION {emphasize}
{ duplicate$ empty$
    { pop$ "" }
    { "{\em " swap$ * "}" * }
  if$
}

FUNCTION {smallcaps}
{ duplicate$ empty$
    { pop$ "" }
    { "{\sc " swap$ * "}" * }
  if$
}

INTEGERS { nameptr namesleft numnames }

FUNCTION {format.names}
{ 's :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr "{vv~}{ll}{, jj}{, f.}" format.name$ 't :=   % last name first
      nameptr #1 >
    { namesleft #1 >
        { ", " * t * }
        { numnames #2 >
        { "," * }
        'skip$
          if$
          t "others" =
        { " et~al." * }
        { " and " * t * }
          if$
        }
      if$
    }
    't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {format.editor.names}
{ 's :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr "{f. }{vv~}{ll}{, jj}" format.name$ 't :=   % last name first
      nameptr #1 >
    { namesleft #1 >
        { ", " * t * }
        { numnames #2 >
        { "," * }
        'skip$
          if$
          t "others" =
        { " et~al." * }
        { " and " * t * }
          if$
        }
      if$
    }
    't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {format.authors}
{ author empty$
    { "" }
    { author format.names smallcaps }
  if$
}

FUNCTION {format.key}           % this function is just for apalike
{ empty$
    { key field.or.null }
    { "" }
  if$
}

FUNCTION {format.editors}
{ editor empty$
    { "" }
    { editor format.editor.names
      editor num.names$ #1 >
    { " (eds.)" * }
    { " (ed.)" * }
      if$
    }
  if$
}

FUNCTION {format.title}
{ title empty$
    { "" }
    { title "t" change.case$ }
  if$
}

FUNCTION {n.dashify}
{ 't :=
  ""
    { t empty$ not }
    { t #1 #1 substring$ "-" =
    { t #1 #2 substring$ "--" = not
        { "--" *
          t #2 global.max$ substring$ 't :=
        }
        {   { t #1 #1 substring$ "-" = }
        { "-" *
          t #2 global.max$ substring$ 't :=
        }
          while$
        }
      if$
    }
    { t #1 #1 substring$ *
      t #2 global.max$ substring$ 't :=
    }
      if$
    }
  while$
}

FUNCTION {format.btitle}
{ title %emphasize
}

FUNCTION {tie.or.space.connect}
{ duplicate$ text.length$ #3 <
    { "~" }
    { " " }
  if$
  swap$ * *
}

FUNCTION {either.or.check}
{ empty$
    'pop$
    { "can't use both " swap$ * " fields in " * cite$ * warning$ }
  if$
}

FUNCTION {format.bvolume}
{ volume empty$
    { "" }
    { "volume" volume tie.or.space.connect
      series empty$
    'skip$
    { " of " * series emphasize * }
      if$
      "volume and number" number either.or.check
    }
  if$
}

FUNCTION {format.number.series}
{ volume empty$
    { number empty$
    { series field.or.null }
    { output.state mid.sentence =
        { "number" }
        { "Number" }
      if$
      number tie.or.space.connect
      series empty$
        { "there's a number but no series in " cite$ * warning$ }
        { " in " * series * }
      if$
    }
      if$
    }
    { "" }
  if$
}

FUNCTION {format.edition}
{ edition empty$
    { "" }
    { output.state mid.sentence =
    { edition "l" change.case$ " edition" * }
    { edition "t" change.case$ " edition" * }
      if$
    }
  if$
}

INTEGERS { multiresult }

FUNCTION {multi.page.check}
{ 't :=
  #0 'multiresult :=
    { multiresult not
      t empty$ not
      and
    }
    { t #1 #1 substring$
      duplicate$ "-" =
      swap$ duplicate$ "," =
      swap$ "+" =
      or or
    { #1 'multiresult := }
    { t #2 global.max$ substring$ 't := }
      if$
    }
  while$
  multiresult
}

FUNCTION {format.pages}
{ pages empty$
    { "" }
    { pages multi.page.check
    { "pp." pages n.dashify tie.or.space.connect }
    { "p." pages tie.or.space.connect }
      if$
    }
  if$
}

FUNCTION {format.vol.num.pages}
{ volume field.or.null
  pages empty$
    'skip$
    { duplicate$ empty$
    { pop$ format.pages }
    { ":" * pages n.dashify * }
      if$
    }
  if$
}

FUNCTION {format.chapter.pages}
{ chapter empty$
    { "" }
    { type empty$
    { "chapter" }
    { type "l" change.case$ }
      if$
      chapter tie.or.space.connect
    }
  if$
}

FUNCTION {format.in.ed.booktitle}
{ booktitle empty$
    { "" }
    { editor empty$
%   { "{\em In} " booktitle emphasize * }
%   { "{\em In} " format.editors * ", " * booktitle emphasize * }
    { "{\em In} " booktitle * }
    { "{\em In} " format.editors * ", " * booktitle * }
      if$
    }
  if$
}

FUNCTION {format.thesis.type}
{ type empty$
    'skip$
    { pop$
      type "t" change.case$
    }
  if$
}

FUNCTION {format.tr.number}
{ type empty$
    { "Technical Report" }
    'type
  if$
  number empty$
    { "t" change.case$ }
    { number tie.or.space.connect }
  if$
}

FUNCTION {format.article.crossref}
{ "In"                          % this is for apalike
  " \cite{" * crossref * "}" *
}

FUNCTION {format.book.crossref}
{ volume empty$
    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
      "In "
    }
    { "Volume" volume tie.or.space.connect
      " of " *
    }
  if$
  "\cite{" * crossref * "}" *               % this is for apalike
}

FUNCTION {format.incoll.inproc.crossref}
{ "In"                          % this is for apalike
  " \cite{" * crossref * "}" *
}

FUNCTION {article}
{ output.bibitem
  format.authors "author" output.check
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { journal emphasize " " * format.vol.num.pages * output
    }
    { format.article.crossref output.nonnull
      format.pages output
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {book}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
      editor format.key output
    }
    { format.authors output.nonnull
      crossref missing$
    { "author and editor" editor either.or.check }
    'skip$
      if$
    }
  if$
  output.year.check             % special for apalike
  new.block
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      new.block
      format.number.series output
      new.sentence
      publisher "publisher" output.check
      address output
    }
    { new.block
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  new.block
  note output
  fin.entry
}

FUNCTION {booklet}
{ output.bibitem
  format.authors output
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title "title" output.check
  new.block
  howpublished output
  address output
  new.block
  note output
  fin.entry
}

FUNCTION {inbook}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
      editor format.key output
    }
    { format.authors output.nonnull
      crossref missing$
    { "author and editor" editor either.or.check }
    'skip$
      if$
    }
  if$
  output.year.check             % special for apalike
  new.block
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      format.chapter.pages "chapter and pages" output.check
      new.block
      format.number.series output
      new.sentence
      publisher "publisher" output.check
      address output
    }
    { format.chapter.pages "chapter and pages" output.check
      new.block
      format.book.crossref output.nonnull
    }
  if$
  format.edition output
  new.block
  note output
  fin.entry
}

FUNCTION {incollection}
{ output.bibitem
  format.authors "author" output.check
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title "title" output.check
  format.pages output
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.bvolume output
      format.number.series output
      format.chapter.pages output
      new.sentence
      publisher "publisher" output.check
      address output
      format.edition output
    }
    { format.incoll.inproc.crossref output.nonnull
      format.chapter.pages output
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {inproceedings}
{ output.bibitem
  format.authors "author" output.check
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.bvolume output
      format.number.series output
      format.pages output
      address output                    % for apalike
      new.sentence                  % there's no year
      organization output               % here so things
      publisher output                  % are simpler
    }
    { format.incoll.inproc.crossref output.nonnull
      format.pages output
    }
  if$
  new.block
  note output
  fin.entry
}

FUNCTION {conference} { inproceedings }

FUNCTION {manual}
{ output.bibitem
  format.authors output
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.btitle "title" output.check
  organization address new.block.checkb
  organization output
  address output
  format.edition output
  new.block
  note output
  fin.entry
}

FUNCTION {mastersthesis}
{ output.bibitem
  format.authors "author" output.check
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title "title" output.check
  new.block
  "Master's thesis" format.thesis.type output.nonnull
  school "school" output.check
  address output
  new.block
  note output
  fin.entry
}

FUNCTION {misc}
{ output.bibitem
  format.authors output
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title output
  new.block
  howpublished output
  new.block
  note output
  fin.entry
}

FUNCTION {phdthesis}
{ output.bibitem
  format.authors "author" output.check
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.btitle "title" output.check
  new.block
  "PhD thesis" format.thesis.type output.nonnull
  school "school" output.check
  address output
  new.block
  note output
  fin.entry
}

FUNCTION {proceedings}
{ output.bibitem
  format.editors output
  editor format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.btitle "title" output.check
  format.bvolume output
  format.number.series output
  address output                % for apalike
  new.sentence                  % we always output
  organization output               % a nonempty organization
  publisher output              % here
  new.block
  note output
  fin.entry
}

FUNCTION {techreport}
{ output.bibitem
  format.authors "author" output.check
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title "title" output.check
  new.block
  format.tr.number output.nonnull
  institution "institution" output.check
  address output
  new.block
  note output
  fin.entry
}

FUNCTION {unpublished}
{ output.bibitem
  format.authors "author" output.check
  author format.key output              % special for
  output.year.check                 % apalike
  new.block
  format.title "title" output.check
  new.block
  note "note" output.check
  fin.entry
}

FUNCTION {default.type} { misc }

MACRO {jan} {"January"}

MACRO {feb} {"February"}

MACRO {mar} {"March"}

MACRO {apr} {"April"}

MACRO {may} {"May"}

MACRO {jun} {"June"}

MACRO {jul} {"July"}

MACRO {aug} {"August"}

MACRO {sep} {"September"}

MACRO {oct} {"October"}

MACRO {nov} {"November"}

MACRO {dec} {"December"}

MACRO {acmcs} {"ACM Computing Surveys"}

MACRO {acta} {"Acta Informatica"}

MACRO {cacm} {"Communications of the ACM"}

MACRO {ibmjrd} {"IBM Journal of Research and Development"}

MACRO {ibmsj} {"IBM Systems Journal"}

MACRO {ieeese} {"IEEE Transactions on Software Engineering"}

MACRO {ieeetc} {"IEEE Transactions on Computers"}

MACRO {ieeetcad}
 {"IEEE Transactions on Computer-Aided Design of Integrated Circuits"}

MACRO {ipl} {"Information Processing Letters"}

MACRO {jacm} {"Journal of the ACM"}

MACRO {jcss} {"Journal of Computer and System Sciences"}

MACRO {scp} {"Science of Computer Programming"}

MACRO {sicomp} {"SIAM Journal on Computing"}

MACRO {tocs} {"ACM Transactions on Computer Systems"}

MACRO {tods} {"ACM Transactions on Database Systems"}

MACRO {tog} {"ACM Transactions on Graphics"}

MACRO {toms} {"ACM Transactions on Mathematical Software"}

MACRO {toois} {"ACM Transactions on Office Information Systems"}

MACRO {toplas} {"ACM Transactions on Programming Languages and Systems"}

MACRO {tcs} {"Theoretical Computer Science"}

READ

FUNCTION {sortify}
{ purify$
  "l" change.case$
}

INTEGERS { len }

FUNCTION {chop.word}
{ 's :=
  'len :=
  s #1 len substring$ =
    { s len #1 + global.max$ substring$ }
    's
  if$
}

%           There are three apalike cases: one person (Jones),
%           two (Jones and de~Bruijn), and more (Jones et~al.).
%           This function is much like format.crossref.editors.
%
FUNCTION {format.lab.names}
{ 's :=
  s #1 "{vv~}{ll}" format.name$
  s num.names$ duplicate$
  #2 >
    { pop$ " et~al." * }
    { #2 <
    'skip$
    { s #2 "{ff }{vv }{ll}{ jj}" format.name$ "others" =
        { " et~al." * }
        { " and " * s #2 "{vv~}{ll}" format.name$ * }
      if$
    }
      if$
    }
  if$
}

FUNCTION {author.key.label}
{ author empty$
    { key empty$
    { cite$ #1 #3 substring$ }
    'key                    % apalike uses the whole key
      if$
    }
    { author format.lab.names }
  if$
}

FUNCTION {author.editor.key.label}
{ author empty$
    { editor empty$
    { key empty$
        { cite$ #1 #3 substring$ }
        'key                % apalike uses the whole key
      if$
    }
    { editor format.lab.names }
      if$
    }
    { author format.lab.names }
  if$
}

FUNCTION {editor.key.label}
{ editor empty$
    { key empty$
    { cite$ #1 #3 substring$ }
    'key            % apalike uses the whole key, no organization
      if$
    }
    { editor format.lab.names }
  if$
}

FUNCTION {calc.label}      % this function came from ASTRON.BST (ARR)
{ type$ "book" =
  type$ "inbook" =
  or
    'author.editor.key.label
    { type$ "proceedings" =
        'editor.key.label                       % apalike ignores organization
        'author.key.label                       % for labeling and sorting
      if$
    }
  if$
  "\protect\astroncite{" swap$ * "}{"                   % these three lines are
  *                                                     % for apalike, which
  year field.or.null purify$ #-1 #4 substring$          % uses all four digits
  *                       % the mathing closing "}" comes in at the reverse.pass
  'label :=
}

FUNCTION {sort.format.names}
{ 's :=
  #1 'nameptr :=
  ""
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { nameptr #1 >
    { "   " * }
    'skip$
      if$                       % apalike uses initials
      s nameptr "{vv{ } }{ll{ }}{  f{ }}{  jj{ }}" format.name$ 't := % <= here
      nameptr numnames = t "others" = and
    { "et al" * }
    { t sortify * }
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {sort.format.title}
{ 't :=
  "A " #2
    "An " #3
      "The " #4 t chop.word
    chop.word
  chop.word
  sortify
  #1 global.max$ substring$
}

FUNCTION {author.sort}
{ author empty$
    { key empty$
    { "to sort, need author or key in " cite$ * warning$
      ""
    }
    { key sortify }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {author.editor.sort}
{ author empty$
    { editor empty$
    { key empty$
        { "to sort, need author, editor, or key in " cite$ * warning$
          ""
        }
        { key sortify }
      if$
    }
    { editor sort.format.names }
      if$
    }
    { author sort.format.names }
  if$
}

FUNCTION {editor.sort}
{ editor empty$
    { key empty$
    { "to sort, need editor or key in " cite$ * warning$
      ""
    }
    { key sortify }
      if$
    }
    { editor sort.format.names }
  if$
}

%           apalike uses two sorting passes; the first one sets the
%           labels so that the `a's, `b's, etc. can be computed;
%           the second pass puts the references in "correct" order.
%           The presort function is for the first pass. It computes
%           label, sort.label, and title, and then concatenates.
FUNCTION {presort}
{ calc.label
  label sortify
  "    "
  *
  type$ "book" =
  type$ "inbook" =
  or
    'author.editor.sort
    { type$ "proceedings" =
    'editor.sort
    'author.sort
      if$
    }
  if$
  #1 entry.max$ substring$  % for
  'sort.label :=        % apalike
  sort.label            % style
  *
  "    "
  *
  title field.or.null
  sort.format.title
  *
  #1 entry.max$ substring$
  'sort.key$ :=
}

ITERATE {presort}

SORT        % by label, sort.label, title---for final label calculation

STRINGS { last.label next.extra }   % apalike labels are only for the text;

INTEGERS { last.extra.num }     % there are none in the bibliography

FUNCTION {initialize.extra.label.stuff} % and hence there is no `longest.label'
{ #0 int.to.chr$ 'last.label :=
  "" 'next.extra :=
  #0 'last.extra.num :=
}

FUNCTION {forward.pass}
{ last.label label =
    { last.extra.num #1 + 'last.extra.num :=
      last.extra.num int.to.chr$ 'extra.label :=
    }
    { "a" chr.to.int$ 'last.extra.num :=
      "" 'extra.label :=
      label 'last.label :=
    }
  if$
}

FUNCTION {reverse.pass}       % this function came from ASTRON.BST (ARR)
{ next.extra "b" =
    { "a" 'extra.label := }
    'skip$
  if$
  label extra.label * "}" * 'label :=
  extra.label 'next.extra :=
}

EXECUTE {initialize.extra.label.stuff}

ITERATE {forward.pass}

REVERSE {reverse.pass}

%               Now that the label is right we sort for real,
%               on sort.label then year then title.  This is
%               for the second sorting pass.
FUNCTION {bib.sort.order}
{ sort.label
  "    "
  *
  year field.or.null sortify
  *
  "    "
  *
  title field.or.null
  sort.format.title
  *
  #1 entry.max$ substring$
  'sort.key$ :=
}

ITERATE {bib.sort.order}

SORT        % by sort.label, year, title---giving final bibliography order

FUNCTION {begin.bib}
{ preamble$ empty$              % no \etalchar in apalike
    'skip$
    { preamble$ write$ newline$ }
  if$
  "\begin{thebibliography}{}" write$ newline$       % no labels in apalike
}

EXECUTE {begin.bib}

EXECUTE {init.state.consts}

ITERATE {call.type$}

FUNCTION {end.bib}
{ newline$
  "\end{thebibliography}" write$ newline$
}

EXECUTE {end.bib}
  • CSE is Council of Science Editors. I have checked, it seems to be the only one that does not exist. – Nicole Aug 14 '14 at 0:37
  • 1
    Unfortunately, with that kind of information it is hard to produce a style that is the exact replica of what you are after. For starters one would need to know about formatting volume and (issue) number of an article (or is the issue number always dropped?) What about other entry types? If you are referring to this as the posted 2012 styles, then please come up with an MWE and explain what exactly you need to have altered. – moewe Aug 14 '14 at 4:51
  • 1
    You do notice though that what you posted is a BibTeX style, not a biblatex style. What exactly did not work with the biblatex style linked to above. – moewe Aug 15 '14 at 4:05
  • 1
    I've added the tag 'bibtex' but have left 'biblatex' for now. – Mico Aug 15 '14 at 4:51
  • 3
    It looks to me like the CSE is really trying to sell its book, Scientific Style and Format, for $$ and hence may have decided to refrain from circulating a bibliography style file that implements its formatting guidelines for BibTeX users. Anyway, the guidelines appear to be pretty clear, and it should be straightforward to run the makebst utility (of the custom-bib package) to create a bibliography style file from scratch. Note that the CSE's citation-related guidelines are best set through natbib-related options. – Mico Aug 15 '14 at 5:07

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