Details pages -- conventions

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

1. Keep lines in the source page to 100 characters or less (occasional exceptions are OK, such as for long links).

The 100-char limit is dictated by the coding standards for the entire kent/src tree with the intention of improving code readability.

1. Try to use lowercase html, <a>...</a> versus upper-case <A>...</A>.
2. Quotes, ampersands, less than and greater than signs, and degree symbols should be represented with their [html names]. For example " for " and & for & and < for < and > for > and ° for °.
3. 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.
4. A track description page's "Display Conventions and Configuration" section should cover all track types.
5. For ENCODE track description pages, the page should include contact information for the submitting lab.
6. Links to pages outside of the Genome Browser should open in a new window (target="_blank").
7. Do not include punctuation in link names. For example: target="_blank">link name</a>. NOT target="_blank">link name.</a>
8. Links to our own SOE pages should use ".soe." in the URL, not ".cse." E.g., http://hgdownload.soe.ucsc.edu/
9. When referencing User Interface settings, try to make the wording appear similar and bold the text. For instance, see the Wiggle Help page and how we bold Draw indicator lines: similar to how it appears on the UI page.

See the general style recommendations entry for similar related information.

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, which you can find by searching pubmed.
   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 between <p> ... </p> 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>

Referring to BLAT

• The tool = “BLAT” (if you can substitute the phrase “the BLAT tool”)
  • Thus, the target database of BLAT is not a set of GenBank sequences,...
  • ...note that BLAT results are limited to 16 results per chromosome strand...

• The noun = “Blat”
  • Due to the high demand on our Blat servers…
  • Blat source and executables are freely available...

• The verb = “blat”
  • When blatting on the command line....".
  • (unless it starts a sentence) “Blat the sequence...".

• The commandline = “blat”
  • blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 database.2bit query.fa output.psl

• The hgBlat CGI = “*hgBlat*”
  • ...some small differences between the hgBlat/gfServer and...