Re: [Connotea-code-devel] Re: same abstract page viewed in different sessions

[Suresh K. <ss...@co...>]

Hi Sonya,

I find bookmarking a page with collected links somewhat less preferable =20
for at least two reasons: first, it defeats the purpose of community =20
tagging since the references themselves are no longer visible to the =20
tagging system, only a collected references page that can only be accesse=
d =20
by the person who created it is visible. Secondly, it is less useful if =20
one wants to export the references in an RIS file and perform operations =
=20
on them locally.

Using EUtils is definitely the "user-side" way to fix the problem; but it=
 =20
will require a little bit of programming for which I do not have the time=
 =20
at the moment. The "connotea-side" way would be to fix the link that gets=
 =20
added or recognize the PMID; I have not looked into the connotea code, bu=
t =20
it sounds like something that could be done easily at least for the =20
commonly used cases. Right now, I have to manually "fix" every link I add=
 =20
 from Pubmed.

Thanks,

Suresh


On Fri, 21 Apr 2006 00:36:28 -0400, Sonya <msr...@ea...> wrot=
e:

>> Message: 1
>> To: con...@li...
>> From: "Suresh Krishna" <ss...@co...>
>> Date: Thu, 20 Apr 2006 00:37:10 -0400
>> Subject: [Connotea-code-devel] (no subject)
>>
>>
>> Hi,
>>
>> I now have some more information about the query_hl=3D field that ofte=
n
>> shows up when i click on pubmed abstracts from a search query. This =20
>> field
>> is a session dependent
>> reference to the search history, and therefore of no use for permanent
>> linking in a connotea library. It would be great if it could be
>> automatically parsed out of the
>> link by connotea... An alternative would be to actually recognize pubm=
ed
>> abstract pages via their PMID.
>>
>> The problem is that the same abstract page viewed in different session=
s
>> are treated as two different references by connotea, and therefore my
>> library is littered with
>> duplicate references that share the same PMID.
>>
>> See for instance:
>>
>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&db=3Dpubm=
ed&dopt=3DAbstract&list_uids=3D13054692&query_hl=3D18&itool=3Dpubmed_docs=
um
>> and
>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DRetrieve&db=3Dpubm=
ed&dopt=3DAbstract&list_uids=3D13054692&query_hl=3D18&itool=3Dpubmed_docs=
um
>>
>> Thanks much, Suresh
>>
>>
>>
>> --__--__--

>
> PubMed Sessions time out after 24 hours.
>
> I don't know if what I do, will or will not,  help you.
> It's just what I do. I have a PUBMED account, I save all my abstracts
> into a saved query.
>
> It goes into my
>
> "My Saved Searches and Collections"
>
> I assign it a title
> Then I go into Connotea, and click add a bookmark, get that link for
> that saved search, and add that link...
> just that ONE link for all of my abstracts, the lot of them, the  70 of
> the abstracts (or whatever it may be)
> then I go into Connotea and link it all together.....
>
> "Influenza and Climate" MyNCBI Search Query Entrez PubMed
> <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DSelect+from+Histor=
y&query_key=3D18&WebEnv=3D01eHYaEuCx1vi-j_czp5QQ2dmHvS7ulS5BssyPX1p4RJF5f=
ow-tIAa%40Wl2qyIIOFlkAAC0aH5YAAAAL&WebEnvRq=3Dtrue&term=3Dinfluenza%20and=
%20climate&db=3Dpubmed>
> (info <http://www.connotea.org/uri/fdc4a71beeedbea36b550d0664b8fac7>)
> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=3DSelect+from+History=
&query
> _key=3D18&WebEnv=3D01eHYaEuCx1vi-j_czp5QQ2dmHvS7ulS5BssyPX1p4RJF5fow-tI=
Aa%40Wl2
> qyIIOFlkAAC0aH5YAAAAL&WebEnvRq=3Dtrue&term=3Dinfluenza%20and%20climate&=
db=3Dpubme
> d
> 74 items Ecological sources of zoonotic diseases, influenza epidemics
> with global climate variability, environmental
>  risk factors in the emergence of infectious diseases, Environmental
> influences on emerging infectious diseases, mortality and temperature
> Posted by msredsonyas <http://www.connotea.org/user/msredsonyas> to
> PubChem PubMed <http://www.connotea.org/tag/PubChem%20PubMed> Climate
> Sciences <http://www.connotea.org/tag/Climate%20Sciences> Sonya's
> Database Query Runs
> <http://www.connotea.org/tag/Sonya%27s%20Database%20Query%20Runs>
> Ecological Sciences <http://www.connotea.org/tag/Ecological%20Sciences>
>  Medical Sciences <http://www.connotea.org/tag/Medical%20Sciences>
> Environmental <http://www.connotea.org/tag/Environmental> influenza
> <http://www.connotea.org/tag/influenza> on Fri Mar 10 2006
> <http://www.connotea.org/date/2006-03-10> at 08:23 UTC
>
>
> To make it easier to find these, I always save these type of searches
> and queries under my title "Sonya's Database Query Runs", because
> I have several of these types of  accounts with NASA Harvard, and other
> places, and I do the very same thing with those.
>
>
> You also might want to have a look at NIH's Utlilties which is one of
> the projects that works on PUBMED citations.
>
>
> "UMLS Knowledge Source Server (UMLSKS)" UMLSKS Version 5.0 Unified
> Medical Language System
> <http://umlsks.nlm.nih.gov/kss/servlet/Turbine/action/KssLogin;jsession=
id=3DAC9F23E4FDB977A6F3801BD4582A05FF.kss3>
> (info <http://www.connotea.org/uri/41a3425f23f494969d341985764b7740>)
> http://umlsks.nlm.nih.gov/kss/servlet/Turbine/action/KssLogin;jsessioni=
d=3DAC
> 9F23E4FDB977A6F3801BD4582A05FF.kss3
> UMLS Releases: 2003AA 2003AB 2003AC 2004AA 2004AB 2004AC 2005AA 2005AB
> 2005AC [Metathesuarus=AE, Semantic Network,
>  and SPECIALIST Lexicon] "..hierarchies for the Semantic Network..."The
> UMLS Knowledge Source Server (UMLSKS) is a
> computer application that provides Internet access to the Knowledge
> Sources and other related resources made available
>  by developers using the UMLS. Its purpose is to make UMLS data more
> accessible to users, and in particular to system developers.
> The system architecture allows remote site users (individuals as well a=
s
> computer programs) to send requests to a server at the
> National Library of Medicine (NLM). Access to the system is provided
> through the World Wide Web, an Extensible Markup Language
>  (XML)-based socket programming interface, and through an Application
> Programmer Interface (API). "...
>  {Users are responsible for compliance with UMLS copyright restrictions=
}
>
>
> "PubMed ESummary XML update" Utilities-announce ncbi.nlm.nih.gov 1-26-0=
6
> <http://www.ncbi.nlm.nih.gov/mailman/private/utilities-announce/2006-Ja=
nuary/000049.html>
> (info <http://www.connotea.org/uri/a0a982bf213d6ee5c52bd37f283d6bfe>)
> http://www.ncbi.nlm.nih.gov/mailman/private/utilities-announce/2006-Jan=
uary
> /000049.html
> "The ESummary XML for PubMed citations will soon be updated to include =
a
> new item, LastAuthor, e.g.,"
>
>
> "Entrez Utilities" NIH
> <http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html>
> (info <http://www.connotea.org/uri/4de5d21e66216497f1fbe4bee3b915b8>)
> http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
> .."Entrez Programming Utilities are tools that provide access to Entrez
> data outside of the
> regular web query interface and may be helpful for retrieving search
> results for future use in another environment."..