Style Error: biomed-central

o.briet
Biomed central has a different style for complete books than for a book in a series [http://www.biomedcentral.com/authors/instprepdoc#style]:

Examples are given:
Complete book
9. Margulis L: Origin of Eukaryotic Cells. New Haven: Yale University Press; 1970.
Where the title is italic title case

Monograph or book in a series
10. Hunninghake GW, Gadek JE: The alveolar macrophage. In Cultured Human Cells and Tissues. Edited by Harris TJR. New York: Academic Press; 1995:54-56. [Stoner G (Series Editor): Methods and Perspectives in Cell Biology, vol 1.]
Where the main title is bold (not title case), and the series title is italic title case.

Zotero does not (yet?) differentiate between item type 'book' and 'book in a series', so biomed-central.csl generates everything as a type 'book'. Is it possible to fix this?

Thanks,
Olivier
  • adamsmith
    Zotero _can_ distinguish between book and book in a series - simply by adding series information to a book item.
    As for the citations above: there are two things about this:
    - The second example is actually a chapter from an edited volume (Book section in Zotero terms), not a monograph (if you check, it's the same as the book chapter example on that page)
    - It's followed by the series information in square brackets. Obviously Zotero can do that, but I'd like to see an example where that's actually used in a journal - this strikes me as quite uncommon as bibliographies go.
  • o.briet
    Thanks for your response. The biomed-central.csl does not (yet) differentiate, but it is great to know that, in principle, it could.

    I agree that the example they give is far fetched, but now, also the first bit (without the series information bit in square brackets) is not implemented.

    Given that the biomed-central style is common to 220 journals, it might be worth to include it.
  • adamsmith
    The first part _is_ implemented. It's also unrelated to this being in a series or not. As I say above, all book chapters should be cited that way and are in the biomed central style. If it doesn't come out that way, you've entered the data in Zotero incorrectly.
  • o.briet
    Yes sorry, you are right. Coming back to your query: below some examples of series I found in actual Biomed-Central journal articles (with links).

    Some good examples:
    http://www.ethnobiomed.com/content/8/1/3
    Elias SA: The use of insect fossils in archaeology. In Advances in quaternary entomology. Edited by Elias SA. Amsterdam: Elsevier; 2010:89-121.
    [van der Meer JJM (Series Editor): Developments in Quaternary Science, vol 12.]

    Ramos-Elorduy J: Insects in the diet of tropical forest peoples in Mexico. In Food and Nutrition in the Tropical Forest. Biocultural Interactions and Applications to Development. Edited by Hladik CM, Hladik A, Linares OF, Pagezy H, Semple A, Hadley M. Paris: UNESCO; 1993:205-212.
    [Jeffers JNR (Series editor): Man and the Biosphere vol 13.]

    Other examples:
    http://www.biomedcentral.com/1471-2105/9/195
    Figueiredo M: Unsupervised sparse regression. In Nonlinear Estimation and Classification. Volume 171. Edited by Denison DD, Hansen MH, Holmes CC, Mallick B, Yu B. Springer-Verlag; 2003:474. [Lecture Notes in Statistics]

    Kiiveri HT: A Bayesian approach to variable selection when the number of variables is very large. In Science and Statistics: A Festschrift for Terry Speed. Volume 41. Edited by Goldstein DR. Hayward, California , Institute of Mathematical Statistics; 2003:127-143. [Davison A (Series Editor): IMS Lecture Notes - Monograph Series]

    http://www.ojrd.com/content/4/1/3
    Leigh PN: Amyotrophic lateral sclerosis. In Motor Neuron Disorders and related diseases. Volume 82. Edited by Eisen AA, Sham PJ. Amsterdam: Elsevier; 2007:249-268.
    [Aminoff MJ, Boller F, Swaab DF (Series Editor): Handbook of Clinical Neurology]

    http://ccforum.com/content/16/1/R4
    Frank JA, Yumiko I, Slutsky AS: Pathogenesis of ventilator-induced lung injury. In Acute Respiratory Distress Syndrome. Volume 179. Edited by Matthay M. Marcel Dekker. Boca Raton, FL: CRC Press; 2003:201-244.
    [Lenfant C (Series Editor) Lung Biology in Health and Disease]


    http://www.trialsjournal.com/content/11/1/37
    The influence of the pharmaceutical industry; formal minutes, oral and written evidence. Volume 2. London: Stationery Office; 2005.
    [House of Commons, Health Committee (Series Editor): Report of session 2004-05; vol 4]

    http://www.molecularneurodegeneration.com/content/7/1/53
    Bockstael O, Foust KD, Kaspar B, Tenenbaum L: Recombinant AAV Delivery to the Central Nervous System. Volume 807 edition. Edited by Snyder RO, Moullier P. Humana Press; 2011:159-177.
    [Walker JM (Series Editor): Methods in Molecular Biology]

    http://www.ethnobiomed.com/content/4/1/4
    Paluch A: Świat roślin w tradycyjnych praktykach leczniczych wsi polskiej. Wrocław: Wydawnictwo Uniwersytetu Wrocławskiego; 1984.
    [Staniszewska M (Series Editor): Acta Universitatis Wratislaviensis, vol 752]

    http://www.biomedcentral.com/1471-2148/7/197
    Hauser L, Ward RD: Population identification in pelagic fish: the limits of molecular markers. In Advances in Molecular Ecology pp 191-224. Edited by Carvalho GR. Amsterdam , IOS Press; 1998. [Science Series NATO (Series Editor): Series A: Life Sciences]

    http://www.biomedcentral.com/1471-2105/6/172
    Bujnicki JM: Molecular phylogenetics of restriction endonucleases. In Restriction Endonucleases. Volume 14. Edited by Pingoud A. Berlin, Springer-Verlag; 2004:63-87. [Gross HJ (Series Editor): Nucleic Acids and Molecular Biology]
  • adamsmith
    OK, that's plenty - I'll implement that asap and let you know when it's done. Thanks for reporting.
  • o.briet
    Thanks very much for willing to do this. Please refer to the biomed central site http://www.biomedcentral.com/authors/instprepdoc#style, as some of the formatting was lost in the copying in this forum.
    I got confused by their example title
    "Monograph or book in a series" because example 10 is actually a 'book chapter in a book in a series'..
  • adamsmith
    The style is now fixed. The updated version will appear on the repository within 30mins (check the timestamp). Update your copy of the style by re-installing it from the repository. (See here if you need instructions for installing styles in standalone.)
    Any further problems please let us know.
  • o.briet
    Thanks again. I noticed there are still a few issues with the biomed-central style. I have tried to address these as explained below. I have created a group library with the examples given by biomed central: http://www.zotero.org/groups/biomedcentralexamples
    The three things I was unable to address were:
    1) For books, chapters, etc, the volume should be in italic "Volume 1." just before "2nd edition". Now it appears just as a bold number before the page numbers (as it should be for journal articles).
    2) The thesis reference.
    3) The "in press" reference (now, if ", in press" is filled in the "Date" slot, one space too many remains. I understand that this will be addressed in future releases.
    Could you please have a look at the Volume problem (and also check my suggested improvements)?

    Problems and proposed solutions (for biomed central examples, in order of listing):
    1 No periods in journal abbreviations! “strip-periods="true"” added
    2 Supplement should be between brackets not bold. Specified as “issue” in reference file, and “






    “ was commented in.
    3 Should mention “, in press”. This is added in the reference info in the “year”. But notice the space too many between the journal abbreviation and the comma. Apparently this will be resolved in future Zotero releases.
    4 OK
    5 Edited should be with capital, added after info:


    Edited by

    (Ed)
    (Eds)


    Series editor
    Series editors



    Volume font-style="italic"
    Volumes font-style="italic"



    5. Period after last editor. “ ” changed to “ ” in line 32
    6 See 5. Also: Volume should be “Volume 2.”. Not bold “2”like it is a journal volume.
    7 Editors should be mentioned in the beginning
    “

  • o.briet
    <?xml version="1.0" encoding="utf-8"?>
    <style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
    <info>
    <title>BioMed Central</title>
    <id>http://www.zotero.org/styles/biomed-central</id>;
    <link href="http://www.zotero.org/styles/biomed-central" rel="self"/>
    <link href="http://www.biomedcentral.com/bmcbioinformatics/authors/instructions/researcharticle#formatting-references" rel="documentation"/>
    <!-- This documentation link contains incorrect information about the number of authors for supplemental info; it was confirmed directly by BMC that the correct max number of authors to list is 30, see also https://github.com/citation-style-language/styles/issues/190
    <link href="http://www.biomedcentral.com/authors/instprepdoc#refs" rel="documentation"/>
    -->
    <author>
    <name>Robert M Flight</name>
    <email>rflight79@gmail.com</email>
    </author>
    <category citation-format="numeric"/>
    <category field="medicine"/>
    <category field="biology"/>
    <updated>2013-01-12T23:55:23+00:00</updated>
    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
    </info>
    <terms>
    <locale xml:lang="en">
    <term name="editor" form="verb">Edited by</term>
    <term name="editor" form="short">
    <single>(Ed)</single>
    <multiple>(Eds)</multiple>
    </term>
    <term name="collection-editor" form="short">
    <single>Series editor</single>
    <multiple>Series editors</multiple>
    </term>
    <!-- Not sure if this does anything -->
    <term name="volume" form="short">
    <single>Volume font-style="italic" </single>
    <multiple>Volumes font-style="italic" </multiple>
    </term>
    </locale>
    </terms>
    <macro name="author">
    <names variable="author" suffix=": ">
    <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
    <substitute>
    <names variable="editor"/>
    <label form="short" prefix=" "/>
    </substitute>
    </names>
    </macro>
    <macro name="editor">
    <names variable="editor" suffix=".">
    <label form="verb" suffix=" "/>
    <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
    </names>
    </macro>
    <macro name="publisher">
    <text variable="publisher-place" suffix=": "/>
    <text variable="publisher" suffix="; "/>
    </macro>
    <macro name="container-title">
    <text variable="container-title" font-weight="normal" font-style="italic" vertical-align="baseline" form="short" strip-periods="true"/>
    </macro>
    <macro name="title">
    <choose>
    <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
    <text variable="title" font-weight="normal" font-style="italic" suffix="" text-case="title"/>
    </if>
    <else>
    <text variable="title" suffix="" font-weight="bold"/>
    </else>
    </choose>
    </macro>
    <macro name="volume">
    <text variable="volume" font-weight="bold" font-style="normal"/>
    </macro>
    <macro name="edition">
    <choose>
    <if is-numeric="edition">
    <group delimiter=" ">
    <number variable="edition" form="ordinal"/>
    <text term="edition" form="long" suffix="."/>
    </group>
    </if>
    <else>
    <text variable="edition" suffix="."/>
    </else>
    </choose>
    </macro>
    <citation collapse="citation-number">
    <sort>
    <key variable="citation-number"/>
    </sort>
    <layout prefix="[" suffix="]" delimiter=", ">
    <text variable="citation-number"/>
    </layout>
    </citation>
    <bibliography et-al-min="31" et-al-use-first="30">
    <layout>
    <text variable="citation-number" suffix=". "/>
    <choose>
    <if type="webpage">
    <!-- The webpages will be the bane of my existence -->
    <text macro="title"/>
    <text variable="URL" prefix=" [" suffix="]"/>
    </if>
    <else>
    <!-- Now for everything else -->
    <group suffix=".">
    <text macro="author"/>
    <text macro="title" suffix=". "/>
    <choose>
    <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
    <text macro="edition" prefix=" " suffix=" "/>
    <text macro="publisher" prefix=" "/>
    </if>
    <else-if type="chapter paper-conference" match="any">
    <text term="in" text-case="capitalize-first" suffix=" "/>
    <text macro="container-title" suffix=". "/>
    <text macro="edition" suffix=". "/>
    <text macro="editor"/>
    <text macro="publisher" prefix=" "/>
    </else-if>
    <else>
    <text macro="container-title" suffix=" "/>
    </else>
    </choose>
    <date variable="issued">
    <date-part name="year"/>
    </date>
    <text macro="volume" prefix=", "/>
    <!-- This was to deal with supplemental issues, but is-numeric evaluates to true if there is a number in there at all, so for right now, this is commented out RMF Dec 4, 2008 -->

    <choose>
    <if is-numeric="issue">

    </if>
    <else>
    <text variable="issue" prefix="(" suffix=")"/>
    </else>
    </choose>

    <text variable="page" prefix=":"/>
    </group>
    <group prefix =" [" suffix="]" delimiter=": ">
    <names variable="collection-editor">
    <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
    <label prefix=" (" suffix=")" form="short"/>
    </names>
    <group delimiter=", ">
    <text variable="collection-title" font-style="italic" text-case="title"/>
    <choose>
    <if is-numeric="collection-number">
    <text variable="collection-number" prefix="vol. "/>
    </if>
    <else>
    <text variable="collection-number"/>
    </else>
    </choose>
    </group>
    </group>
    </else>
    </choose>
    </layout>
    </bibliography>
    </style>
  • o.briet
    Here again the list of problems and solutions (some code not visible in the first posting due to posting as html).
    1 No periods in journal abbreviations! “strip-periods="true"” added
    2 Supplement should be between brackets not bold. Specified as “issue” in reference file, and “ <!-- This was to deal with supplemental issues, but is-numeric evaluates to true if there is a number in there at all, so for right now, this is commented out RMF Dec 4, 2008 -->
    <choose>
    <if is-numeric="issue">
    </if>
    <else>
    <text variable="issue" prefix="(" suffix=")"/>
    </else>
    </choose> “ was commented in.
    3 Should mention “, in press”. This is added in the reference info in the “year”. But notice the space too many between the journal abbreviation and the comma. Apparently this will be resolved in future Zotero releases.
    4 OK
    5 Edited should be with capital, added after info:
    <terms>
    <locale xml:lang="en">
    <term name="editor" form="verb">Edited by</term>
    <term name="editor" form="short">
    <single>(Ed)</single>
    <multiple>(Eds)</multiple>
    </term>
    <term name="collection-editor" form="short">
    <single>Series editor</single>
    <multiple>Series editors</multiple>
    </term>
    <!-- Not sure if this does anything -->
    <term name="volume" form="short">
    <single>Volume font-style="italic" </single>
    <multiple>Volumes font-style="italic" </multiple>
    </term>
    </locale>
    </terms>
    5. Period after last editor. “ <names variable="editor" suffix="">” changed to “ <names variable="editor" suffix=".">” in line 32
    6 See 5. Also: Volume should be “Volume 2.”. Not bold “2”like it is a journal volume.
    7 Editors should be mentioned in the beginning
    “ <substitute>
    <names variable="editor"/>
    <label form="short" prefix=" "/>
    </substitute>
    </names>”
    Put in “<macro name="author"> section”
    8 See 7
    9 OK
    10 Book title should be title case . “text-case="title"”added to line 47 This should also be added to the series information towards the end. collection editor changed from “long” to “short”.
    <term name="collection-editor" form="short">
    <single>Series editor</single>
    <multiple>Series editors</multiple>
    </term>
    11 OK
    12 Completely missing thesis info
    13 OK
  • adamsmith
    thanks - I'll take a look asap - as a general note, rather than redefining terms, just style them when they come up (e.g. use text-case="title" on the edited by, use prefix="(" suffix=")" text-case="title" on the ed and eds etc.
  • adamsmith
    edited February 1, 2013
    The style is now fixed. The updated version will appear on the repository within 30mins (check the timestamp). Update your copy of the style by re-installing it from the repository. (See here if you need instructions for installing styles in standalone.)

    I've taken most of your suggestions, changed some around and also fixed issues 1 and 2 that you weren't able to address.
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