# Presentation: 042688

## Aquaculture Web Resources and Bibliographies

**BUILDING THE DATA **

**Notes:**
Introduce myself
Talk about the AIC and its program
Introduce the focus on bibs. Since we have a number of varied products.

## Slide 2

**Notes:**
This Department of Commerce Aquaculture web site has been created to provide the broadest possible access to the National Oceanic and Atmospheric Administration/Department of Commerce information on aquaculture. 

Information found at this site includes information on the research projects funded through the NOAA/DOC aquaculture initiative, summaries of  orkshops and meetings that occurred under the auspices of DOC and NOAA, notices of funding opportunities, governmental services and organizational material that will be helpful to those interested in our aquaculture programs, short subject bibliographies and content based pages, and information on NOAA international panels dealing with aquaculture issues .

The Center works closely with existing information services that are already supported by NOAA/DOC such as the AQUANIC electronic information service housed at Purdue University in Indiana, the National Sea Grant Library on the University of Rhode Island Bay Campus in Narragansett, RI, the 28 NOAA libraries across the United States, and the National Marine Fisheries Service, Office of Industry and Trade.

## “But where are the Internet librarians?  Google and its friends don’t come close...query results are the equivalent of ripping out 50,000 pages from books, periodicals, brochures, and random snippets of jetsam...and ...stacking them in front of the patron.  HP ran an ad:  ‘What the Internet needs is an old-fashioned librarian.’ ...” 

- 				*WIRED magazine *04/2003

**Notes:**
Bibs. Not anything new.  
But, one of the few tools left that are unique—

Many people using Internet for research but bibs are not yet replaced by Internet.

## Slide 4

**Notes:**
Sometime finds something on the Internet and if not bookmarked can’t find again using the same seach

Sometime going through hundreds of possible sources

Still much hidden,  still not full text, etc.

Bib just one tool to make web pages better.

## Who is the audience?

**What do they want?**
**Do they know what they want?**
***What do they expect?***
***What should they get?***

**Notes:**
THE VERY FIRST ITEM IS TO CONSIDER WHO THE PRODUCT IS FOR.  (Before design, ease of use, scale, scope....)
Sometimes the audience is selected for you—NOAA staff working on an ongoing project—participants in a workshop
Sometimes you have to define the audience as you identify an issue or subject
Sometimes you have to create the audience as you gain perspective on the movement of an area of interest or as you “market” information.

Bibs. Replacing what used to be first-line  ref questions in a special library

Does the audience know what it wants?  Probably (most of the time) with the broad Internet availability and the sophistication of NOAA audiences  

If you complete a general Internet search sometimes can determine where bib would be useful
Only if the audience knows what is out there can they determine if the bib will be useful.  They may not know and you may not know—especially if your audience it global and broad—in reality you may have more than one aud.

## Getting specific or general?

**Basics**
**Issues**
**User driven**
**NOAA driven**
**Time as a factor **

**Notes:**
From the perspective of developing a web page of tools:
Basics:
What is already out there?—Primary resource for aquaculture is AquaNIC
	Don’t duplicate
	But DO link to them
	What is out there that is not well done—do it better
Issues
Conference titles and proceedings
Discussions on listservs—”Safety and hydrogen Sulfide”

User Driven:  also comes from listservs—talking to people—email questions
	Maria’s users wanted Tilapia information

NOAA DRIVEN:  Policies, programs, etc. (oyster issue)

Time Restricted:  limited by time and resources as always

## The “searchable bibliography” project motivated by professional enthusiastic people...

## CREATING THE SEARCHABLE BIBLIOGRAPHIES

**MySQL – NOAA Miami Library (Open source database)**
**PROCITE Software from ISI for importing online bibliographic data**
- Import references directly from online databases, copy and paste from online citations, or manually type in the reference
**HTML for intro page and looks**

**Notes:**
I.  Searchable bibs:  (Clickable text)
Use primarily ASFA database—permission to put up limited # of abstracts.  Negotiated and begun with NOAA Miami library. (300-400)
Currently treat the bib like a buffer---edit when bib gets too large.

MySQLsoftware used by NOAA Miami Library and they offered to assist with project on Tilapia feeds and feeding for their patrons.

Much of the editing work is done by Maria Bello who is now ??
I start my ASFA search and then bring in to Procite software—version 5
Procite emphasizes use with Web of Science (ISI) but can use ASFA

Must use a configuration files—we use one specifically for ASFA from Procite.

## The search strategy

- I. (Tilapia aurea or Sarotherodon aureus or Oreochromis aureus or Tilapia niloticus or Sarotherodon niloticus or Oreochromis niloticus or Tilapia mossamibica or Sarotherodon mossambicus or Oreochromis mossambicus)
-  and
- (genetic* or gene or reproduc* or hatch*)
- II
- (Tilapia aurea or Sarotherodon aureus or Oreochromis aureus or Tilapia niloticus or Sarotherodon niloticus or Oreochromis niloticus or Tilapia mossamibica or Sarotherodon mossambicus or Oreochromis mossambicus) and (feed* or nutrition or supplement* or meal or digest* or diet*)
***WHAT ARE THE LIMITS AND LIMITATIONS?***

**Notes:**
Define the scope of the subject AND
First, develop the search strategy.

## The Search - ASFA

**The Search - ASFA**

**Notes:**
As stated primary database is ASFA.
Mark records and email or save selected citations to PC
These are then saved as an ascii text file

May add other citations but need to avoid using abstracts or get permission.

The hard part within the Procite database is keeping new data separate and being aware that duplicates can be missed.

## PROCITE

**PROCITE**

**Notes:**
Created a name for the database
Procite will create two database files -- .pdt (primary database file) and .pdx (key file) file. 
Then select a configuration file—the ASFA one was provided by Procite.
Select the transfer button
Sometimes the workform file needs to be modified from the default
(this is just a file that sets what you see in the records database window) 

## Slide 12

**Notes:**
If it is successful you get a window providing information on how many files were transferred as well as how many duplicates were identified.

## These are the new citations ...all enter with marks

**These are the new citations ...all enter with marks**

**Theoretically**

**“****Subdatabase” goes to Miami**

**Notes:**
The new citations come in as marked records when imported.  This allows you to identify the new files from the files that may already be in the database.
If you select these marked files and then “group” them under a subname, this will help you keep these records unique.  I do this so that I don’t send the entire database to Miami.
Note that I have “theoretically” above the duplicate tab.  The configuration file that I use does not always catch duplicates.
Time has been an issue in getting this straightend out.

## WORKFORMS

**WORKFORMS**

**Notes:**
What is shown is the Journal Long Form  This works out as best standard to start with.   (There are dozens of pre-defined WORKforms with fields.)

This sample is just to show the difficulty in data being automatically loaded to correct fields. (go over the data problems shown)

As citations are edited—can put select other workform for each citation

Can ALSO customize the form and give it a name of your own.

## The journal list

**The journal list**

**Notes:**
A very nice feature of Procite is the indexing that it provides in several  fields.

Those shown with arrows.  All of the fields with drop down arrows have indexed lists.

Due to the various bibs created in aquaculture ...now have a standard journal list that I use.  I have saved this file and call it “aquaticscience.”

This is particularly useful when encountering abbreviated lists or foreign titles and trying to maintain accuracy.

## Slide 16

**Notes:**
Here is a sample of the drop down list that appears when I click on the arrow.  A user can have both abbreviations and full titles or either.

## Files Go to Miami

**Files Go to Miami**

**Here the real work begins:**
**	****Check for duplicates**
**	****Convert the records from Procite to ****	****text in comma delimeter format     ****	****using an output style created in ****	****Procite to match the database**
**	****Import the records into miniSQL**

**Notes:**
How this all got started?
	Janice mentioned their database?
	Maria her interest in aquaculture (tilapia)?

Maria Bellow and Linda Pikula were very happy to work togther on bibs.
First asked if I would be interested in creating a Tilapia bib for their users.  
Large amount of information—so needed to narrow scope
Fish is freshwater and somewhat out of scope— but gave me ability to request their tools for other subjects for searchable bibs.
Still substantial work on the part of the mySQL users at the other end

## Whaaa  happened?

**Citation is not complete**
**Still some data in wrong fields**
**File is then saved:**
- as text format using an output style created in Procite to accommodate the fields in the table for that database in MiniSQL database
- reveals extra spaces for removal

**Notes:**
Maria still finds the above problems when I send her the Procite files.

(Bullets)

## TA-DAA !!

**TA-DAA !!**

**Notes:**
This is an example of the Sustainable Aquaulture Bib front page.
Search engine allows searching on all fields??  Maria?

## Modifying and Filtering

**Limiting the scope**
**Limiting the date range**
**Getting as comprehensive as possible**
**Making the data amorphous**
**The online part**
**Hitting the target...**

**Notes:**
Some issues with all of the types of bibs.
Do to copyright issues with ASFA I am limiting scope and date on the searchable bibs.  Citations cannot build into large database.
Another approach with as with the oyster bibliography involved finding as much information as possible—much in Japanese.  Corresponding with Japanese researchers, etc., putting up some full text.

What do I mean by making it amorphous? (not a strict bib in most cases, include links, graphs, pictures, videos, etc.)
These are not static bibliographies in the tradition sense.  These are elements that react to each other and to their environment.

Online means a larger audience and more opportunity for feedback.

The target may be moving—so pages have to be revisited more often than with paper products.

## Non-searchable - traditional

**Issue Driven**
**Highly specialized **

## Issue driven: using both citations and online links

**Issue driven: using both citations and online links**

**Notes:**
Non-searchable bibliographies reside on the website as well

Issue driven—Safety Issues in Aquaculture---Hydrogen Sulfide

In Van Halen mode—nothing stays the same.

## Comprehensive BUT with an Internet themeand “interactive”

**Comprehensive BUT with an Internet theme****and “interactive”**

**Notes:**
Oyster bib due to interest in reviving oyster industry in Chesapeake Bay

Crassostrea Gigas—prone to disease issues 
	industry virtually gone
Crassostrea Ariakensis being considered--Japan
	only as triploid due to introduction issues

Real challenge getting information—our close work with Japanese through UJNR made it easier.

Probably the most comprehensive

Interactive in the sense that researchers need it and contribute

## Thanks for your attention!

**Questions?**