revisiting AGRICOLA in GO.xrf_abbs (was RE: [MOBY-l] NameSpac
e for AGRICOLA? (fwd))
Vijay Narayanasamy
VNarayan at mail.brc.mcw.edu
Mon Sep 8 16:45:12 EDT 2003
Hi all,
Thanks Barbara for the explanation. What Mike and Suparna are referring to
AGRICOLA id is in fact the "AGRICOLA accession number" (MARC TAG 016).
But still I feel that from an "Information Retrieval" angle I do not know
how to get the accession numbers for a given query?
Only then I can use those accession numbers for retrieval of the records
from the database.
Currently I can retrieve the "bib" number (MARC TAG 035) for a given query
(using a parser). I can use those "bib" numbers for forming a URL to
uniquely retrieve a record.
Also I want to use the publicly available AGRICOLA. I do not want to use a
subscription service like Community of Science (COS).
I would like to have a Namespace for AGRICOLA for this purpose.
Vijay
---------Mike Cherry wrote:--------------------
> There is a better source of AGRICOLA information than directly from the
> National Ag Library. I think its a bit odd that NAL doesn't seem to
> use their own unique IDs. Anyway you can get this information from the
> Community of Science (COS) site. The AGRICOLA ids seem to start with
> 'IND'.
>
> The AGRICOLA search page is at:
>
> http://agricola.cos.com/
>
> Examples of links to reference are:
>
> Yen JT & Pond WG (1984)
> http://agricola.cos.com/cgi-bin/getRec?id=IND84014403
>
> Nowak J & Steinkraus KH:
> http://agricola.cos.com/cgi-bin/getRec?id=IND89038399
>
> TAIR is using AGRICOLA and the 'IND' IDs in their gene association
> file, however they add a space 'IND '.
>
> -Mike
>
-----Original Message-----
From: Barbara Buchanan [mailto:bbuchana at nal.usda.gov]
Sent: Monday, September 08, 2003 2:46 PM
To: 'Sue Rhee'; Midori Harris
Cc: Vijay Narayanasamy; Barbara Buchanan
Subject: RE: revisiting AGRICOLA in GO.xrf_abbs (was RE: [MOBY-l] NameSpac e
for AGRICOLA? (fwd))
Hello everyone,
Yes the NAL call numbers are unique. The citations you reference below are
all journal articles. The journal article itself does not get a unique NAL
call number but the journal as a whole does. These 5 articles are all from:
NAL CALL NO: RC620 A1N8
Indexed: p
Title: Nutrition reports international.
Publisher: Los Altos, Calif.
Description: 40 v. : ill. ; 23 cm.
Note: Vol. 1, no. 1 (Jan. 1970)-v. 40, no. 6 (Dec. 1989)
Note: NAL holdings: v.1, 1970-
LC Subject: Nutrition -- Biological chemistry -- Research.
Other Author: Albanese, Anthony August, 1908-
Related Work: CONTINUED BY
Journal of nutritional biochemistry -- 0955-2863 (DLC)
90640852 (OCoLC)21104658
If you want a unique identifier for your database you should consider using
the AGRICOLA accession number. That number is unique to the article. I
provide this number to other database curators but I don't know if they use
it or some other method for unique identification.
So to recap the NAL call number is unique but only at the journal or book
title level. It is not unique for journal articles, proceedings chapters,
book chapters etc.
Regarding the relationship between Agricola and the NAL (National
Agricultural Library) -- The NAL indexes the publications and produces the
Agricola records here at the NAL.
The NAL then makes the sale tape of records available for the commercial
vendor.
If I can be of any additional assistance, please let me know. I hope this
clears up this confusion and does not just add to it.
Barbara Buchanan
-----Original Message-----
From: Sue Rhee [mailto:rhee at acoma.Stanford.EDU]
Sent: Monday, September 08, 2003 2:47 PM
To: Midori Harris
Cc: Vijay Narayanasamy; bbuchana at nal.usda.gov
Subject: Re: revisiting AGRICOLA in GO.xrf_abbs (was RE: [MOBY-l] NameSpace
for AGRICOLA? (fwd))
Hi, Midori
I think perhaps Barbara Buchanan at NAL could address these questions. I'm
ccing her here.
Sue
On Mon, 8 Sep 2003, Midori Harris wrote:
> Hi,
>
> Some of you may remember that there was a bit of confusion about an entry
> for the AGRICOLA database in the GO.xrf_abbs file. We thought we'd sorted
> it out, because Linda Hannick provided a NAL entry (included in the
> forwarded exchange, below), which mentions AGRICOLA. NAL is the
> abbreviation, and the object is 'call number'. But now another
> complication has arisen: according to Vijay, whose message I'm forwarding,
> one NAL call number may identify more than one publication, i.e. they are
> not unique IDs.
>
> Could those who are familiar with NAL and AGRICOLA comment on what we
> should change in GO.xrf_abbs? In particular, would the 'bib' that Vijay
> uses work as the unique ID for our purposes? And how should we represent
> the relationship between NAL and AGRICOLA?
>
> Cheers,
> Midori
>
> ---------- Forwarded message ----------
> Date: Fri, 5 Sep 2003 10:13:34 -0500
> From: Vijay Narayanasamy <VNarayan at mail.brc.mcw.edu>
> To: Midori Harris <midori at ebi.ac.uk>
> Subject: RE: [MOBY-l] NameSpace for AGRICOLA?
>
>
> On Fri, 5 Sep 2003, Vijay Narayanasamy wrote:
>
> > Hi Midori,
> >
> > Thanks. But NAL Call number does not appear to be unique. See the
following.
> > Same Call number for 5 records.
> >
> > Heading
> > Information
> >
> > Call number
> >
> > RC620
> > A1N8
> >
> > AUTHOR
> > Yen, J.T. USDA, ARS, Roman L. Hruska U.S. Meat Animal
> >
> > TITLE
> > Response of weanling pigs to dietary supplementation of
> >
> > Call number
> >
> > RC620
> > A1N8
> >
> > AUTHOR
> > Nowak, J.
> > Cornell University, Geneva, NY.
> >
> > TITLE
> > Effect of tempeh fermentation of peas on their potential
> >
> > Call number
> >
> > RC620
> > A1N8
> >
> > AUTHOR
> >
> > Newman, C.W.
> > Montana State University, Bozeman.
> >
> >
> > TITLE
> >
> > A comparison of Alaskan fish meals to soybean meals as
> >
> > Call number
> >
> > RC620
> > A1N8
> >
> > AUTHOR
> >
> > Brown, W.F. University of Florida, Ona, FL.
> >
> >
> > TITLE
> >
> > Intake and digestibility of, and performance by, cattle
> >
> >
> > Call number
> >
> > RC620
> > A1N8
> >
> > AUTHOR
> >
> > Yokogoshi, H. The
> > University of Shizuoka, Shizuoka, Japan.
> >
> >
> > TITLE
> >
> > Acute effects of various carbohydrates on brain serotonin
> >
> >
> > What I am using to uniquely identify and retrieve a record is
> > "bib" from the URL
> >
> > For example bib=0000-05160 in the following URL
> >
> > http://www.nal.usda.gov/cgi-bin/agricola-ind?bib=0000-05160&conf=010000
> >
> > "bib" value has a tag "035" in MARC record.
> >
> > Since NAL is reserved for call number. I would like to get another
namespace
> > for AGRICOLA.
> >
> > Any suggestions?
> >
> > Thanks,
> >
> > Vijay
> >
> > Vijay Narayanasamy
> > Project Programmer / Analyst
> > Bioinformatics Program, Human and Molecular Genetics Center
> > Medical College of Wisconsin
> > 8701, W. Watertown Plank Road
> > Milwaukee, WI 53226
> > 414-456-8026
> > vnarayan at mcw.edu
> > http://brc.mcw.edu/
> >
> >
> > -----Original Message-----
> > From: Midori Harris [mailto:midori at ebi.ac.uk]
> > Sent: Friday, September 05, 2003 3:32 AM
> > To: Vijay Narayanasamy
> > Cc: MOBY (moby-l at biomoby.org)
> > Subject: Re: [MOBY-l] NameSpace for AGRICOLA?
> >
> > Hi,
> >
> > This is in go/doc/GO.xrf_abbs:
> >
> > abbreviation: NAL
> > database: AGRICOLA
> > object: call number
> > example: NAL:TP248.2 P76 v.14
> > generic_url: http://www.nal.usda.gov/ag98/ag98.html
> >
> > I got the information from Linda Hannick at TIGR; I think it's this way
> > round (rather than abbreviation:AGRICOLA) because the IDs are NAL call
> > numbers.
> >
> > Midori
> >
> > On Thu, 4 Sep 2003, Vijay Narayanasamy wrote:
> >
> > > Hi,
> > >
> > > Is there any namespace for articles from AGRICOLA database? I propose
> > > AGRICOLA. Any suggestions?
> > >
> > > I have a MOBY Service running in my local MOBY Central that retrieves
> > > AGRICOLA MARC records for a given query, parses them to produce
documents in
> > > MEDLINE Display format.
> > >
> > > I need a new namespace for AGRICOLA.
> > >
> > > --Vj
> > >
> > >
> > > Vijay Narayanasamy
> > > Project Programmer / Analyst
> > > Bioinformatics Program, Human and Molecular Genetics Center
> > > Medical College of Wisconsin
> > > 8701, W. Watertown Plank Road
> > > Milwaukee, WI 53226
> > > 414-456-8026
> > > vnarayan at mcw.edu
> > > http://brc.mcw.edu/
> > >
> > >
> > > _______________________________________________
> > > moby-l mailing list
> > > moby-l at biomoby.org
> > > http://biomoby.org/mailman/listinfo/moby-l
> > >
>
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