Oncogene Style
Hello everybody,
Recently I have started writing a manuscript which I plan to send to 'Oncogene', but the style is not matching with the prescribed format. I am giving a link to the page describing the style.http://mts-onc.nature.com/cgi-bin/main.plex?form_type=display_auth_instructions
The Oncogene style is a combination of American Journal of Physical Anthropology and Cold Spring Harbor Laboratory Press with some additional modifications (Taken from a thread started by unique317).
A prototype as seen in almost all 'Oncogene' papers is as follows:
Klefstrom J, Vastrik I, Saksela E, Valle J, Eilers M and Alitalo K. (1994). EMBO J., 13, 5442 – 5450.
The main points are:
1. Within the text, a reference should be cited by author and date; not more than two authors may be cited per reference; if there are more than two authors cite one author and et al.
2. At the end of the manuscript the citations should be typed in alphabetical order, with the authors' surnames and initials inverted.
3. All authors should be quoted for papers with up to six authors; for papers with more than six authors, the first six only should be quoted followed by et al.
4. References should include, in the following order: authors' names, year, article title, journal, volume number (in bold font), inclusive page numbers, and name and address of publisher (for books only).
5. The name of the journal should be abbreviated according to the International List of Periodical Title World Abbreviations and underlined to indicate italics.
6. References to web-only journals should give authors, article title and journal name as above, followed by url in full - or doi if known - and the year of publication in parentheses.
As I know absolutely nothing about how to create or edit styles (no idea at all!) I would be extremely grateful if somebody can help me. I have tried using the EndNote version of Oncogene but that also does not work properly. Thanks to all of you for having spent your time in reading my discussion. Thanks.
Recently I have started writing a manuscript which I plan to send to 'Oncogene', but the style is not matching with the prescribed format. I am giving a link to the page describing the style.http://mts-onc.nature.com/cgi-bin/main.plex?form_type=display_auth_instructions
The Oncogene style is a combination of American Journal of Physical Anthropology and Cold Spring Harbor Laboratory Press with some additional modifications (Taken from a thread started by unique317).
A prototype as seen in almost all 'Oncogene' papers is as follows:
Klefstrom J, Vastrik I, Saksela E, Valle J, Eilers M and Alitalo K. (1994). EMBO J., 13, 5442 – 5450.
The main points are:
1. Within the text, a reference should be cited by author and date; not more than two authors may be cited per reference; if there are more than two authors cite one author and et al.
2. At the end of the manuscript the citations should be typed in alphabetical order, with the authors' surnames and initials inverted.
3. All authors should be quoted for papers with up to six authors; for papers with more than six authors, the first six only should be quoted followed by et al.
4. References should include, in the following order: authors' names, year, article title, journal, volume number (in bold font), inclusive page numbers, and name and address of publisher (for books only).
5. The name of the journal should be abbreviated according to the International List of Periodical Title World Abbreviations and underlined to indicate italics.
6. References to web-only journals should give authors, article title and journal name as above, followed by url in full - or doi if known - and the year of publication in parentheses.
As I know absolutely nothing about how to create or edit styles (no idea at all!) I would be extremely grateful if somebody can help me. I have tried using the EndNote version of Oncogene but that also does not work properly. Thanks to all of you for having spent your time in reading my discussion. Thanks.
You could either:
- contact unique317 to obtain the latest version of the style he was building
- decide if American Journal of Physical Anthropology or Cold Spring Harbor Laboratory Press or some other style is most similar to the style you want
You can then enumerate specific modifications that need to be made to a particular style to get it to output what you want.I have already started doing that and I don,t know how much time will it take before I get something useful. However, yes, I will try and contact unique317. Thanks.
I have managed to tweak the existing CSH Press style to look similar to Oncogene but now I cannot validate it. Can somebody tell me what is wrong in it and how to do it?
<?xml version="1.0" encoding="UTF-8"?>
<style xmlns="http://purl.org/net/xbiblio/csl" xml:lang="en" class="in-text" >
<info>
<title>Oncogene(dev)</title>
<id>http://www.zotero.org/styles/cshlp</id>
<link href="http://www.zotero.org/styles/cshlp"/>
<author>
<name>Julian Onions</name>
<email>julian.onions@gmail.com</email>
</author>
<contributor>
<name>Richard Karnesky</name>
<email>karnesky+zotero@gmail.com</email>
<uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
</contributor>
<contributor>
<name>Indranil Paul</name>
<email>indranil.res@gmail.com</email>
</contributor>
<category term="biology"/>
<category term="author-date"/>
<updated>2010-09-24T02:21:30+00:00</updated>
<summary>A style for all journals by CSHLP</summary>
<rights>This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License: http://creativecommons.org/licenses/by-sa/3.0/</rights>
</info>
<macro name="editor">
<names variable="editor">
<label form="short" text-case="lowercase" suffix=". " />
<name and="text" delimiter=", " initialize-with="." text-case="capitalize-first"/>
</names>
</macro>
<macro name="series-editor">
<names variable="original-author">
<label form="short" text-case="capitalize-first" suffix=". "/>
<name and="text" delimiter=", "/>
</names>
</macro>
<macro name="author">
<names variable="author">
<name and="text" name-as-sort-order="all" sort-separator=", " delimiter=", " delimiter-precedes-last="always" initialize-with="."/>
<label form="short" prefix=", " suffix="." text-case="lowercase"/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
</macro>
<macro name="author-short">
<names variable="author">
<name form="short" and="text" delimiter=", "/>
<substitute>
<names variable="editor"/>
<names variable="translator"/>
</substitute>
</names>
</macro>
<macro name="access">
<group>
<text variable="URL"/>
<group prefix=" (" suffix=")">
<text term="accessed" text-case="capitalize-first" suffix=" "/>
<date variable="accessed">
<date-part name="month" suffix=" "/>
<date-part name="day" suffix=", "/>
<date-part name="year"/>
</date>
</group>
</group>
</macro>
<macro name="title">
<choose>
<if type="thesis">
<text variable="title"/>
</if>
<else-if type="book">
<text variable="title" font-style="italic"/>
</else-if>
<else>
<text variable="title"/>
</else>
</choose>
</macro>
<macro name="publisher">
<group delimiter=", " >
<text variable="publisher"/>
<text variable="publisher-place"/>
</group>
</macro>
<macro name="year-date">
<date variable="issued">
<date-part name="year"/>
</date>
</macro>
<macro name="day-month">
<date variable="issued">
<date-part name="month"/>
<date-part name="day" prefix=" "/>
</date>
</macro>
<macro name="page">
<label variable="page" suffix=". " form="short"/>
<text variable="page"/>
</macro>
<macro name="edition">
<choose>
<if is-numeric="edition">
<group delimiter=" ">
<number variable="edition" form="ordinal"/>
<text term="edition" form="short" suffix="."/>
</group>
</if>
<else>
<text variable="edition" suffix="."/>
</else>
</choose>
</macro>
<citation>
<option name="et-al-min" value="1"/>
<option name="et-al-use-first" value="1"/>
<option name="et-al-subsequent-min" value="3"/>
<option name="et-al-subsequent-use-first" value="1"/>
<option name="disambiguate-add-year-suffix" value="true"/>
<option name="disambiguate-add-names" value="true"/>
<option name="disambiguate-add-givenname" value="true"/>
<option name="collapse" value="year"/>
<layout prefix="(" suffix=")" delimiter="; ">
<group delimiter=", ">
<group delimiter=" ">
<text macro="author-short"/>
<text macro="year-date"/>
</group>
<text variable="locator"/>
</group>
</layout>
</citation>
<bibliography>
<option name="hanging-indent" value="false"/>
<option name="et-al-min" value="6"/>
<option name="et-al-use-first" value="6"/>
<sort>
<key macro="author"/>
<key variable="title"/>
</sort>
<layout suffix=".">
<group delimiter=" ">
<text macro="author" suffix="."/>
<text macro="year-date" prefix="(" suffix=")."/>
</group>
<choose>
<if type="article-newspaper article-magazine" match="any">
<group delimiter=" ">
<text macro="title" prefix=" " suffix="."/>
</group>
<group prefix=" " delimiter=", ">
<text variable="container-title" font-style="italic"/>
<text macro="day-month"/>
<text variable="edition"/>
</group>
</if>
<else-if type="thesis">
<text macro="title" prefix=" " suffix="."/>
<group prefix=" " delimiter=", ">
<text macro="edition"/>
<text macro="editor" suffix="."/>
<text variable="genre"/>
<text macro="publisher"/>
</group>
</else-if>
<else-if type="book">
<group delimiter=" ">
<text macro="title" prefix=" " suffix="."/>
<text macro="edition"/>
<text macro="editor" suffix="."/>
<text macro="publisher"/>
</group>
</else-if>
<else-if type="chapter">
<group delimiter=" ">
<text macro="title" prefix=" " suffix="."/>
<group class="container" delimiter=", ">
<group delimiter=" ">
<text term="in" text-case="capitalize-first"/>
<text variable="container-title" font-style="italic"/>
<text macro="editor" prefix=" (" suffix=")"/>
</group>
<group delimiter=" ">
<text variable="volume" prefix="Vol. " suffix=" of"/>
<text variable="collection-title" font-style="italic"/>
<text macro="series-editor"/>
</group>
<text macro="page"/>
<text macro="publisher" prefix=" "/>
</group>
</group>
</else-if>
<else>
<group suffix="." >
<text macro="title" prefix=" " />
<text macro="editor" prefix=" "/>
</group>
<group class="container" prefix=" " suffix="." delimiter=" ">
<text variable="container-title" form="short" font-style="italic"/>
<group delimiter=": ">
<text variable="volume" font-weight="bold"/>
<text variable="page"/>
</group>
</group>
</else>
</choose>
<text prefix=" " macro="access" suffix="."/>
</layout>
</bibliography>
</style>
-------------------
Thanks.
edit: that said, you should change the <id> and <link> e
I uploaded my file (in .txt) in Validator.nu and got an 'error'. Can you please tell me how to do it step by step? What are Preset, Parser, etc., etc. options?
OR if you can spare some of your time then I can send this file to you? I have uploaded it.
http://gist.github.com/594955
second, if you paste it into the window you need
Schemas: http://bitbucket.org/bdarcus/csl-schema/raw/83f9cf9b53bd/csl.rnc
Preset: None
Parsing: XML, don't load external entitites
and the Box for "be lax about html content type" schould be checked.
leave XMLNS filter blank
One last problem! I have saved it as a .csl file and it looks like this "Oncogene.csl". But after opening it into a firefox window the page is displayed but nothing is happening. I suppose some kind of "Install" option will appear but I cannot see anything except just the displayed page.
Thank you very much for all your patient and kind help. And how to make it available to all so that everybody can use it?
Get it back into Zotero section here:
http://www.zotero.org/support/csl_simple_edits
especially with respect to hidden extensions
I got it! Actually my file was like "Oncogene.csl.txt" .txt being hidden. The trick was to simply delete .txt part. Thank you for your help. It is amazing that so many knowledgeable guys are out there ready to help you waiting for just your asking. Its excellent. Thanks again.
Yes sure. But there are still two caveats:
1. All the "et al" in citations and bibliography should be in italics which I couldn't make.
2. In bibliographies (not citations) the style puts a "comma" after the "last author" and before the "et al" (as shown below) which should not be there. I am unable to do it after so many tries.
Welcker M, Orian A, Jin J, Grim JA, Harper JW, Eisenman RN, et al. (2004). The Fbw7 tumor suppressor regulates glycogen synthase kinase 3 phosphorylation-dependent c-Myc protein degradation. Proc Natl Acad Sci U S A 101: 9085 -9090.
The style would be perfect with these two rectified.
You can find the style at http://gist.github.com/594955
In that case the style for Oncogene at the address given above should be final from my side and can be submitted to the repository as adamsmith suggested.
Thank you all for your excellent suggestions.
An improved 1.0 version with et al in italics and no comma before et al is on the 1.0 repository:
https://github.com/citation-style-language/styles