Displaying publications on the website about mimic-website HOT 8 CLOSED

As I explained to Tom, the publications are generated by a script that I run whenever I update .bib files. I can adapt the script to spit out various subsets of the publications list, e.g, only MIMIC-related, based on information in the "funded by" field.

I strongly feel that we should maintain a single set of bib files that list publications, and generate lists from them. It would be a nightmare to cross-check lists that are separately maintained.

My tuppence.
K

On 9/2/15 12:52 AM, Tom Pollard wrote:

Should the website display a list of MIMIC-related articles? For example, see:
https://mimic.physionet.org/about/publications.html

If so, how should the list of articles be generated?

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#8

from mimic-website.

I strongly feel that we should maintain a single set of bib files that list publications, and generate lists from them. It would be a nightmare to cross-check lists that are separately maintained.

Yes, that makes sense. We can use a similar to system to the current one. The references are imported into the current publications page from brp_references.html using the following chunk of code (thanks for emailing it across):

<?php

$path = JPATH_ROOT . "/brp_references.html";
require_once($path);

?>

The source of brp_references.html includes the following comment, so am I right in thinking that the original list is a .bib file?

<!-- Generated by: /home/lcp/references/bib2xhtml-v3.0-15-gf506/bib2xhtml -s 
plain -r -c -e nosize,nopages -D pdf 
temp_journal-2014.bib /home/lcp/html/brp_references.html -->

If so, we should be able to set up the site so that all you need to do is upload the original bib file. We can then automatically import the references into the website in a style of your choosing.

from mimic-website.

bib files are in https://physioforge.csail.mit.edu/reposkrb/bibdb/trunk/ . There are a bunch of them; the script I use looks at these eight:

brp_theses.bib Last-Modified: Fri, 18 Feb 2011 18:16:54 GMT
lcp_journal.bib Last-Modified: Tue, 18 Aug 2015 19:37:13 GMT
lcp_theses.bib Last-Modified: Mon, 08 Jun 2015 14:28:53 GMT
brp_journal.bib Last-Modified: Mon, 18 Mar 2013 21:52:23 GMT
brp_conferences.bib Last-Modified: Fri, 20 May 2011 15:58:55 GMT
lcp_conferences.bib Last-Modified: Fri, 23 Jan 2015 20:06:43 GMT
lcp_books_and_chapters.bib Last-Modified: Thu, 22 Jan 2015 23:05:34 GMT

The brp* files are no longer updated, since the brp project has ended. I don't know whether we want/need to keep that brp bibliography for archival purposes, or just use one publication list, i.e. the one at http://lcp.mit.edu/publications.shtml .

What is wrong with continuing the current procedure of simply using the html that I generate, styling it as you see fit?

K

(the snippet from Dan's joomla page works, I think, because he had a cron job that copied the brp_references.html file from ariadne once a day.)

On 9/2/15 2:35 PM, Tom Pollard wrote:

I strongly feel that we should maintain a single set of bib files that list publications, and generate lists from them. It would be a nightmare to cross-check lists that are separately maintained.

Yes, that makes sense. We can use a similar to system to the current one. The references are imported into the current publications page from brp_references.html using the following chunk of code (thanks for emailing it across):

<?php

$path = JPATH_ROOT . "/brp_references.html";
require_once($path);

?>

The source of brp_references.html includes the following comment, so am I right in thinking that the original list is a .bib file?

<!-- Generated by: /home/lcp/references/bib2xhtml-v3.0-15-gf506/bib2xhtml -s
plain -r -c -e nosize,nopages -D pdf
temp_journal-2014.bib /home/lcp/html/brp_references.html -->

If so, we should be able to set up the site so that all you need to do is upload the original bib file. We can then automatically import the references into the website in a style of your choosing.

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#8 (comment)

from mimic-website.

We can definitely use the HTML if this is easiest for you. The only benefit of a .bib file is that the structure makes it easier to parse if we want to extract specific information (e.g. if we wanted to extract just a list of DOIs then we would know to look in the "DOI:" field), but this is a very minor issue.I don't have a strong preference either way, and was just suggesting the alternative because I thought it would remove a step (generating the HTML) from the process.

from mimic-website.

Publications are imported from the brp_references file at:
https://github.com/MIT-LCP/mimic-website/tree/master/layouts/partials/brp_references.html

This issue relates to #14.

The stylesheets will need to be updated to render the content correctly (e.g. no line break after titles).

from mimic-website.

This doesn't seem quite right. Where does this file come from? If it's the one that was on the old website, then it's essentially static, since it includes only papers funded by the brp project, now complete. At I mentioned earlier, it would be preferable either to pull the full lcp publications file, or to use a custom-generated subset. I can adust the script that generates these files. Please let me know what you'd like.
K

On 9/18/15 12:11 PM, Tom Pollard wrote:

Publications are imported from the brp_references file at:
https://github.com/MIT-LCP/mimic-website/tree/master/layouts/partials/brp_references.html

This issue relates to #14.

The stylesheets will need to be updated to render the content correctly (e.g. no line break after titles).

---

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#8 (comment)

from mimic-website.

This doesn't seem quite right. Where does this file come from? If it's the one that was on the old website, then it's essentially static

The page imports the same HTML snippet that was used previously (https://github.com/MIT-LCP/mimic-website/blob/master/layouts/partials/brp_references.html).

it would be preferable either to pull the full lcp publications file, or to use a custom-generated subset

Either of these would be fine, so perhaps we should have a quick chat to work out what is best. My preference is for whichever involves the least manual input.

The page template imports publication lists added to the /layouts/partials/ directory. If preferred it could retrieve the list from a database directly (e.g. if the LCP list is maintained in a database).

from mimic-website.

The main question is, What criteria should be in place for deciding whether a publication is listed or not? Once that's settled, we can figure out whether to set up new .bib files or not, and how to flag desired publcations in our current .bib files. Should be straightforward.

On 9/20/15 8:58 PM, Tom Pollard wrote:

This doesn't seem quite right. Where does this file come from? If it's the one that was on the old website, then it's essentially static

The page imports the same HTML snippet that was used previously (https://github.com/MIT-LCP/mimic-website/blob/master/layouts/partials/brp_references.html).

it would be preferable either to pull the full lcp publications file, or to use a custom-generated subset

Either of these would be fine, so perhaps we should have a quick chat to work out what is best. My preference is for whichever involves the least manual input.

The page template imports publication lists added to the /layouts/partials/ directory. If preferred it could retrieve the list from a database directly (e.g. if the LCP list is maintained in a database).

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#8 (comment)

from mimic-website.