[MOBY-l] PubFetch - MOBY

[Vijay Narayanasamy]

Hi,

The PubFetch initial version is available via BioMOBY 

A Quick ReadMe 
--------------

1. Go to http://mobycentral.cbr.nrc.ca/cgi-bin/Client/MOBY-Client05.cgi 
2. Select the Namespace "Global_Keyword" from the drop-down menu
3. Enter Keywords (one per line) in the text area e.g. cancer, calpain,
diabetes
4. Click "Initialize with this seed data" button.
5. In the next page choose the service "Search PubMed for given query and
get PMIDs"
6. Select the Objects (key words) that you want to send and click "Send
Selected Objects to Service"
You will get PubMed IDs as "String" objects with Namespace "PMID" in the
next page
7. Choose the service "Get Documents in MEDLINE Display Format for given
PMIDs"
8. Select the Objects (PMID String) that you want to send and click "Send
Selected Objects to Service"
You will get the articles in MEDLINE display format in next page



I also need some suggestions

1. Is Global_Keyword a good Namespace for PubMed query? Or can we have
"PubMed/Query"
2. Should I return "PMID" as an Object from the PubMed for given query
instead of "String" with "PMID" as Namespace
3. I think it is a good idea to register a "PubMed/Medline" object for
article returned from PubMed in Medline format. Like wise we can register
"PubMed/XML" for article returned in XML format from PubMed,
"PubMed/Summary" for article summary retrieved from PubMed ...
4. Also is it a good idea to have "PubMed/ID" as namespace for PubMed ID
object instead of "PMID"?
 
Can a service accept more than one namespace or object as input or output
(to have flexibility and to make better use of other services available in
BioMOBY)?

--Vijay

Vijay Narayanasamy
Bioinformatics Research Center
Medical College of Wisconsin
8701, W. Watertown Plank Road
Milwaukee, WI 53226
414-456-8026