Details pages -- conventions: Difference between revisions

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#  All references to websites not in our domain require the <code>target="_blank"</code> that will open a new tab for the reference.
#  All references to websites not in our domain require the <code>target="_blank"</code> that will open a new tab for the reference.
#  Papers are referenced with outlinks in one place at the bottom of the page only, not in the text above.  In the text we simply say something like "Euskirchen, <EM> et al.</EM>, 2007".  Particularly if the paper is in preprint or Epub, we then only have to change the ref in one place.
#  Papers are referenced with outlinks in one place at the bottom of the page only, not in the text above.  In the text we simply say something like "Euskirchen, <EM> et al.</EM>, 2007".  Particularly if the paper is in preprint or Epub, we then only have to change the ref in one place.
#  Refs are in PubMed format (see [[CBSE_citation_format]]).
#  Refs with many authors are truncated to 10 authors and ''et al'' (which should be italicized).
#  Refs are in alphabetical order by first author's last name.
#  Refs are in alphabetical order by first author's last name.
#  Refs are in PubMed format (see [[CBSE_citation_format]]). We have a script /cluster/bin/scripts/getTrackReferences that will generate this from a provided PMID. That you can find by searching www.pubmed.com
##  Refs with many authors are truncated to 10 authors and ''et al'' (which should be italicized).
## Example running of the getTrackReferences script on a Browser Paper with the [http://www.ncbi.nlm.nih.gov/pubmed/?term=The+UCSC+Genome+Browser+database%3A+extensions+and+updates+2013. PMID: 23155063 found at pubmed] where the resulting html can be pasted into a Track Description Page.
<pre>
$ getTrackReferences 23155063
Accessing http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=Pubmed&id=23155063
<p>
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead
B <em>et al</em>.
<a href="http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&amp;pmid=23155063" target="_blank">
The UCSC Genome Browser database: extensions and updates 2013</a>.
<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D64-9.
PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/23155063" target="_blank">23155063</a>; PMC: <a
href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531082/" target="_blank">PMC3531082</a>
</p>
</pre>

Revision as of 18:29, 18 August 2016


Details pages should be consistent from track to track. To ease the burden on QA, developers are requested to:

  1. Keep lines in the source page to 100 characters or less.
  2. Try to use lowercase html, <a>...</a> versus upper-case <A>...</A>. It is OK if an older page has mixed types.
  3. Quotes, ampersands, less than and greater than signs, and degree symbols should be represented with their [html names]. For example &quot; for " and &amp; for & and &lt; for < and &gt; for > and &deg; for °.
  4. Email addresses should go through Hiram's sanitizer (encodeEmail.pl). It turns the address into an encrypted HREF "mailto:" address that makes it harder for spammers to use.
  5. The "Display Conventions and Configuration" section should cover all track types.
  6. For ENCODE tracks, the page should include contact information for the submitting lab.
  7. Links to pages outside of the Genome Browser should open in a new window.
  8. Do not include punctuation in link names. For example:
 target="_blank">link name</a>.

not 

 target="_blank">link name.</a>
  1. Links to our own SOE pages should use ".soe." in the URL, not ".cse." E.g., http://hgdownload.soe.ucsc.edu/

Grammar/punctuation notes:

  1. Units should be separated from the numbers by a space: "200 bp", not "200bp".
  2. We are using data as a plural noun. "Data are" not "Data is."
  3. "It's" means "It is." "Its" is possessive.
  4. Use American spellings: analyze, minimize, color, etc.

References

  1. All references to websites not in our domain require the target="_blank" that will open a new tab for the reference.
  2. Papers are referenced with outlinks in one place at the bottom of the page only, not in the text above. In the text we simply say something like "Euskirchen, et al., 2007". Particularly if the paper is in preprint or Epub, we then only have to change the ref in one place.
  3. Refs are in alphabetical order by first author's last name.
  4. Refs are in PubMed format (see CBSE_citation_format). We have a script /cluster/bin/scripts/getTrackReferences that will generate this from a provided PMID. That you can find by searching www.pubmed.com
    1. Refs with many authors are truncated to 10 authors and et al (which should be italicized).
    2. Example running of the getTrackReferences script on a Browser Paper with the PMID: 23155063 found at pubmed where the resulting html can be pasted into a Track Description Page.
$ getTrackReferences 23155063
Accessing http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=Pubmed&id=23155063


<p>
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead
B <em>et al</em>.
<a href="http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=23155063" target="_blank">
The UCSC Genome Browser database: extensions and updates 2013</a>.
<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D64-9.
PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/23155063" target="_blank">23155063</a>; PMC: <a
href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531082/" target="_blank">PMC3531082</a>
</p>
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