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Author Topic: Rhodium Archive  (Read 936 times)

Locked

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Re: Rhodium Archive
« Reply #20 on: March 10, 2010, 05:05:09 AM »
Not worth the effort? Why are we still typing about that site? Because it is worth the effort and having one compiled center of drug knowledge is awesome.

I think the problem is that the torch was not passed to the next caretaker. Of the online world I feel that the people here are the best choice now. That's why I brought it up.

Naf1

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Re: Rhodium Archive
« Reply #21 on: March 10, 2010, 05:20:25 AM »
That problem has been fixed btw, if you find anymore please let me know!

Vesp

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Re: Rhodium Archive
« Reply #22 on: March 10, 2010, 05:24:41 AM »
Yeah, I'm just not sure if the comments idea is very good. The other ideas are great, however and should be implemented.
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Enkidu

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Re: Rhodium Archive
« Reply #23 on: March 11, 2010, 09:16:11 AM »
Some links in the archive go directly to the DEA website. Not cool.

Naf1

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Re: Rhodium Archive
« Reply #24 on: March 11, 2010, 11:00:03 PM »
Fixed, I have removed the the links (well added hxxp) to any DEA or USDOJ links in there. I have missed any please let me know.

timecube

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Re: Rhodium Archive
« Reply #25 on: March 12, 2010, 12:24:25 AM »
Rhodium frequently added helpful inline corrections and suggestions.  It would be nice if the documents could be kept in their original forms, but with non-intrusive links to footnotes that could offer corrections and links to additional information.

A subforum could be setup for discussing additions and corrections, so it could work a bit like a peer reviewed system.  Then there could be a sticky thread for simple, easily verifiable errors and additions like math errors, incorrectly cited lit. values, dead links, etc.

As pointed out of course it takes a lot less effort to suggest these things than to implement them.

no1uno

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Re: Rhodium Archive
« Reply #26 on: March 12, 2010, 02:56:34 AM »
Let's play with it a little - I am pretty confident we could shorten the page by having one or three dropdown boxes that take the user where they want to be...

say for example, first dropdown would be Medicinal/Instrumentation/ etc.

then we use Ajax (esp. the xmlhttprequest and php to populate dropdown menu two, which for medicinal would be PEA's/Analgetics/etc.

Say we chose PEA's, then we'd have a third menu - Stimulants/Enactogens/Hallucinogens

Click a choice on that and it could parse a response with the simple CSS based onclick show the full abstract of each article pertaining to that subject, topic & sub-topic

here is a simple Ajax/PHP/MySQL script to do exactly what I just suggested above (well, apart from parsing the response to show the link (CSS styled to look like a button) with the other relevant HTML parsed in as well).

Play with that and we'll have a Web2.0 library in no time - plus with the use of keywords (which is how the drop-down lists are populated) an article may well show up in several different searches, in each response it would be relevant because the keywords (accessible by the AJAX/PHP query on the MySQL database would see the keywords).

Don't even think about saving large-blobs of information in the MySQL db, just save the URI/URL of where the item is uploaded and saved/accessible from, all you need in the DB is the Title, Keyword(s), Author(s), Abstract and the link to where the full-text article can be found
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timecube

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Re: Rhodium Archive
« Reply #27 on: March 12, 2010, 03:42:26 AM »
On a side note, I know I'm pissing all over holy canon, but am I the only one who's always been frustrated by the illegibility of this page caused by the background?

http://127.0.0.1/rhodium/Rhodium/chemistry/index.html

Enkidu

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Re: Rhodium Archive
« Reply #28 on: March 12, 2010, 04:23:05 AM »
^ it has slightly annoyed me as well.
« Last Edit: March 12, 2010, 04:24:57 AM by Enkidu »

no1uno

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Re: Rhodium Archive
« Reply #29 on: March 12, 2010, 06:26:21 AM »
Here is a quick bodgied up html form to update a database with the pertinent information for journal articles, which would allow users to (1) search (a) keywords; (b) author(s); etc. and/or use dropdown menus to follow the whole Subject, Topic, Sub-topic (where pertinent) - thereby allowing people to surf through the whole site and they can access pages that are categorised under more than one heading (like methylenation and safrole or demethylation & methylenation, etc.).

The simple DB upload form attached needs a PHP/MySQL mirror (so that the values recorded in the form can be placed into the DB in the relevant columns) and then we'll need to use the XMLHTTPRequest to get them from the DB as and when required (no page reload), making for a solid, Web2.0 application.

Anyone want to help out with the coding? ;)
"...     "A little learning is a dang'rous thing;
    Drink deep, or taste not the Pierian spring:
    There shallow draughts intoxicate the brain,
    And drinking largely sobers us again.
..."

timecube

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Re: Rhodium Archive
« Reply #30 on: March 12, 2010, 07:28:26 AM »
Each instance of id="" needs to be replaced with name=""

'id' is just used for browser-side referencing, while 'name' is used in actual form submissions (I know this because I spent a lot of time once trying to figure out why my form variables weren't submitting correctly  :).)

There may be some broken browsers like IE that submit ids as names, but they're not supposed to.

no1uno

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Re: Rhodium Archive
« Reply #31 on: March 12, 2010, 11:57:45 AM »
Quote from: timecube on March 12, 2010, 07:28:26 AM
Each instance of id="" needs to be replaced with name=""

'id' is just used for browser-side referencing, while 'name' is used in actual form submissions (I know this because I spent a lot of time once trying to figure out why my form variables weren't submitting correctly  :).)

There may be some broken browsers like IE that submit ids as names, but they're not supposed to.

Et tu, yeah I can never remember which one to use... But the general idea is the same - use the form to populate the DB (via the called PHP script), then use the DB (via another PHP script) to populate the dropdown menu's and etc. etc.

Parse the XML coming out of the DB, assigning each as the relevant Div, etc. so the .css styles it appropriately - avoid jscript where possible, a lot of people browse with it off (I know I do).

EDIT

Aptana 2.0 is being an utter bitch with php, bear with me

Now, we got any PHP code wizards here? I'd like to be able to iterate through the arrays generated by the $authors and $keywords, so that they can be stored in the DB and called upon (ie. everything with $author=Shulgin pops up with everything he has written and so on and so forth, more to the point, the $keywords would be useful.

« Last Edit: March 13, 2010, 04:56:46 AM by no1uno »
"...     "A little learning is a dang'rous thing;
    Drink deep, or taste not the Pierian spring:
    There shallow draughts intoxicate the brain,
    And drinking largely sobers us again.
..."

no1uno

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Re: Rhodium Archive
« Reply #32 on: March 13, 2010, 07:54:46 AM »
can I use preg_split() (split_string is deprecated)? It would appear to be the easiest and cleanest route to keeping the input form nice & uncluttered, while returning the separate names/keywords as arrays within the variable, therefore they can be retrieved using the drop-boxes/search engine...

Anyone want to jump in?

Righto, what tables do we want? Or more properly, what information do we want to store in "A" table or a series of tables, whichever the fuck is easier to code for the response(s) we want

Title - gotta allow at least 100 characters for that sucker (and even that might be too short)

DOI/PMID - what, they are under 20 characters? Anyone seen them any longer?

Author(s) - that one is gonna have to be made to allow for multiple entries (ie. an array)

Keywords - as above

Abstract URL - thirty characters - any longer and you'll have to use tinyurl

Full text URL - as above

Abstract - going to have be several hundred characters - I've seen 'em go to 300-odd words

Journal - 20 characters should do it

Volume - 4 integers

Year - 4 integers

Issue 2 integers

pages - 10 integers

Now, design wise, we want to be able to access each and every article for each and every subject it arises on, some arise multiple times (that is what the keywords are for). We also want to be able to access via citation or DOI/PMID, so that has to be in there. The keywords we can program in so that they are filled from dropdown menus, we aren't all that interested in how to grow forests in the lower danube valley, so the number of relevant subjects will be pretty small.
 


« Last Edit: March 13, 2010, 10:29:34 AM by no1uno »
"...     "A little learning is a dang'rous thing;
    Drink deep, or taste not the Pierian spring:
    There shallow draughts intoxicate the brain,
    And drinking largely sobers us again.
..."

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Re: Rhodium Archive
« Reply #33 on: March 13, 2010, 04:33:54 PM »
Quote from: no1uno on March 13, 2010, 07:54:46 AM
Author(s) - that one is gonna have to be made to allow for multiple entries (ie. an array)

Keywords - as above

(snip)

Now, design wise, we want to be able to access each and every article for each and every subject it arises on, some arise multiple times (that is what the keywords are for).

I strongly recommend having a "keyword" table with two fields, "id" and "keyword", then having a link table, "paper_keyword", linking the "paper" and "keyword" tables -- it would have the fields "paper_id" and "keyword_id". From an SQL perspective this is the cleanest way to do this kind of search (it's called a link table).

The SQL would look like this:

SELECT paper.title, paper.abstract, paper.link FROM paper, keyword, paper_keyword WHERE keyword = $searchterm AND keyword.id = paper_keyword.keyword_id AND paper_keyword.paper_id = paper.id;

You can do the exact same thing for multiple authors.

On the subject of keywords: does the chemistry literature in general have an established keyword ontology? IEEE and ACM for computer science do, and PubMed for health/medicine does, but I am not real familiar with the chemistry literature yet. However I deal with databases and ontologies for money. :)

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Re: Rhodium Archive
« Reply #34 on: March 13, 2010, 07:59:01 PM »
Holy shit most of that is over my head, but if one was to supply an example, I could help out a bit. Like if someone could make a generic to fill in...

hrefwhateveridontunderstand..///(PUT_JOURNAL_NAME_HERE)
a=blabbabittywhizbang(PUT_ABSTRACT_HERE)

Then just put exactly how the journal should be named, I'm in. I have been naming my personal journal copies sort of like we ask for them; journal, numbers, title. I agree that to have the first part of the name be the DOI makes the most computer sense. Whatever, we need to pick a format and go with it and that includes the requested journal uploads as well just to streamline this whole operation.

That star background has pissed me off forever and I might have even mentioned something a long time ago.

Vesp

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Re: Rhodium Archive
« Reply #35 on: March 13, 2010, 09:45:02 PM »
Off Topic-ish: But if you guys see any posts, threads, procedures on this site please let me know and I will post a copy of them here: http://127.0.0.1/talk/index.php/board,32.0.html

This is to eventually turn them into HTML and PDF files... I think it is important we separate out the really impressive or useful posts from the everyday ones just for the sake of convenience and preservation.
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Naf1

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Re: Rhodium Archive
« Reply #36 on: March 13, 2010, 10:10:45 PM »
"On a side note, I know I'm pissing all over holy canon, but am I the only one who's always been frustrated by the illegibility of this page caused by the background?"

http://127.0.0.1/rhodium/Rhodium/chemistry/2index.html

The above URL was made for you, it is an exact copy of the original minus the starfield.

Wizard X

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Re: Rhodium Archive
« Reply #37 on: March 14, 2010, 12:00:36 AM »
Quote from: Vesp on March 13, 2010, 09:45:02 PM
Off Topic-ish: But if you guys see any posts, threads, procedures on this site please let me know and I will post a copy of them here: http://127.0.0.1/talk/index.php/board,32.0.html

This is to eventually turn them into HTML and PDF files... I think it is important we separate out the really impressive or useful posts from the everyday ones just for the sake of convenience and preservation.

Free PDF Converter. It's a simple HTML to PDF Converter. No need to install any applications on your computer.

http://html-pdf-converter.com/

Or, use this? http://download.cnet.com/Free-HTML-to-PDF-Converter/3000-18497_4-10691753.html
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Enkidu

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Re: Rhodium Archive
« Reply #38 on: March 14, 2010, 06:10:54 AM »
Quote from: Naf1 on March 13, 2010, 10:10:45 PM
"On a side note, I know I'm pissing all over holy canon, but am I the only one who's always been frustrated by the illegibility of this page caused by the background?"

http://127.0.0.1/rhodium/Rhodium/chemistry/2index.html

The above URL was made for you, it is an exact copy of the original minus the starfield.


The problem actually surrounds the color of the text and the color of the background. Dark links on a dark background make for difficult reading...

no1uno

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Re: Rhodium Archive
« Reply #39 on: March 14, 2010, 10:44:09 AM »
Quote from: Naf1 on March 13, 2010, 10:10:45 PM
"On a side note, I know I'm pissing all over holy canon, but am I the only one who's always been frustrated by the illegibility of this page caused by the background?"

http://127.0.0.1/rhodium/Rhodium/chemistry/2index.html

The above URL was made for you, it is an exact copy of the original minus the starfield.


PM me the login please ??? Mine ain't working
"...     "A little learning is a dang'rous thing;
    Drink deep, or taste not the Pierian spring:
    There shallow draughts intoxicate the brain,
    And drinking largely sobers us again.
..."
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