The new page would allow wiki-based annotation of the information
from the other site, which is PubMed...so, yes it has a very nice and
heavily trafficked web interface indeed!
For example, the web service at Pubmed provide the abstract and links
to full text (at yet another website) for a publication. My users
would want to add things like:
"This paper describes a resource that turned out to be useful for
doing X" or
"Figure 1 in this paper shows this thing that the authors didn't
notice" or
"The xxx gene described in this paper is also known as yyy; they were
shown to be the same 10 years later"
etc.
These are kinds of knowledge that are scattered throughout the
scientific community. My wikis are hoping to gather some of that
distributed wisdom.
Also, the page in my wiki would collect what other pages in the wiki
refer to that item via the "what links here" capability.
If you'd like to see the kind of content I'm talking about, check out
Pubmed. There's a long url, but I usually just use http:pubmed.com,
which redirects. If you're in the US, your tax dollars support
PubMed, and we're grateful for that! Mediawiki already recognizes
this as a major resource, since typing a PMID <idnum> in a page
automatically creates an external link to PubMed...it's an Easter Egg
that we stumbled across.
http://en.wikipedia.org/wiki/Wikipedia:PMID
=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
On Feb 7, 2007, at 3:40 PM, Jim Wilson wrote:
That makes sense, though I wonder, does the
web-service already have a
web-interface? I guess what I'm getting at is, if the information
already
exists on another web site, why do you want to duplicate it in your
own
wiki?
(Not sure I understand all the problem parameters - I want to help,
I'm just
trying to get a grasp of what's involved. Thanks in advance.)
On 2/7/07, Jim Hu <jimhu(a)tamu.edu> wrote:
Hi Jim,
The content will come from a query to an external web service, which
will be used to fill the template. This is based on the page title
being parsed to look for an accession to the external database.
Does that make sense?
Jim
=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
On Feb 7, 2007, at 12:06 PM, Jim Wilson wrote:
Hi Jim,
You mention that you might want to have the reference pages created
'on
demand' - if so, how do you know what content to put into those
pages? Is
it simply static text as read from a Template? And if so, what
would that
Template say?
-- Jim R. Wilson
On 2/7/07, Jim Hu <jimhu(a)tamu.edu> wrote:
Hi,
I'm thinking about writing an extension...and I haven't really done
one totally from scratch yet, so please forgive the waste of
bandwidth if I'm missing something in the documentation...and the
length of this message.
Here's what I want to do and why. I'm running some wikis
related to
biology/genomics. We use Cite.php, and I'd like to automatically
create pages for the references cited by citations in Cite. php.
I've already modified Cite so that if someone enters "PMID:<id
number>" as either the input text or the name= part, a block of
code
(essentially an extension of Cite where I've added a "hook" in
Cite.php) goes to Pubmed, retrieves the detailed information about
the citation and substitutes the reference text.
For example, if you have
<ref name='PMID:2167309'/>
as the third citation, the reference that shows up is
3. ↑ Rathod PK & Khatri A (1990) Synthesis and
antiproliferative
activity of threo-5-fluoro-L-dihydroorotate. J Biol Chem
265:14242-9
PMID:2167311
I like this because it reduces markup clutter that is a
criticism of
Cite. The next thing I want to do is change the external link to
Pubmed to an internal link to a page in the wiki, where users
can add
commentary about the reference. These pages will be stubbed with
more information from Pubmed, including a template, the
abstract, and
the reference. I'm thinking of two possible strategies:
1) Run something that creates the page (if needed) when the parser
renders a page with a <ref> tag.
2) Run something that creates the page (if needed) when a user
clicks
on the link in the references section
These aren't mutually exclusive, of course, but what I like
about #2
is that I don't create pages unless someone actually wants to
look at
them (upon reflection, this may create pages when the search
engines
hit the links, but that may be OK) and, more importantly, I think
this can be done so that the page will be created if someone
searches
for the reference and the citation doesn't already exist.
The way I'm thinking of doing this is to hook into AlternateEdit
and
branch off to something that grabs the desired template from the
templates namespace, populates the wikitext with data, saves it,
and
redirects to the saved page. Questions:
Q1) Am I nuts? (default=true) Is there anything that I'm forgetting
that will make this blow up?
Q2) Is that the right place to hook?
Q3) What's the best way to do the create/save/redirect step?
Q4) Has anyone already done something like this that I can adapt?
Q5) Would this be useful to anyone else?
For Q2 and Q3, I don't want the user to see the edit form. I
want it
to look like the page was there all along. For #3 I have a kludgy
way to do it: create the page as XML and run maintenance/
importDump.
There must be a better way, right? Thanks for any advice.
Jim
=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054
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