PubCrawler Info: Watching your neighbours
Scan for new database entries that are related to your favourite papers
or sequences!
IMPORTANT: Due to changes on the NCBI website we are currently unable to search for related sequences in GenBank! For more information see the WWWW-Service News.
PubCrawler allows you to use NCBI's feature of Related
Articles (PubMed) or Neighbors
(GenBank) in your search for new publications. Scan for new articles
that are related to your own papers, or to other papers that interest you,
or scan for new sequences that are similar to ones of interest.
To set this up, you first need to know the identifier number
of your target (the article or sequence whose neighbours you want
to watch). Put the identifier into your PubCrawler configuration.
After the first run you will get all related articles and sequences. The
following times you will only get hits that have been newly-designated
by NCBI as neighbours of the target.
How to get the identifier:
First,
query
PubMed to find your target article (choose PubMed) and note its identifier:
-
For neighbourhood searches of PubMed entries you need to specify
the PubMed Identifier (PMID)
of the target article. It is specified in the PubMed/Medline entry.
It is important to use the PMID and not the UI (Medline Unique Identifier) because in the future citations will only be assigned PubMed UIs (PMID).
If you only know the UI of an article, put it into the query box and click on 'Go'. A summary of the article should come up which shows the PMID number as well.
Example: 4599080
(PMID) .
How to set up neighbourhood queries:
Start from PubCrawler's
WWW-Service, enter your user name and password and click on 'Modify
Queries and Options'. This will load your current configuation
into the PubCrawler
Configurator. For each database (PubMed and GenBank) there is a table
where you build your queries. The bottom row is for neighbourhood searches.
Just change the alias (in the green field) to something meaningful (keyword
from paper title or sequence name) and enter the identifier(s) into the
box in the next column. Press 'Submit' to process the form. You can now
'Check' or 'Modify' your queries by clicking the corresponding button.
If you are happy with them keep clicking the 'Submit'-button until you
arrive at a page where you can 'Store' your profile onto our server
(you will be asked again for your user name and password).
Neighbours of multiple targets:
A single search can scan for new neighbours of any number of documents
or sequences. Just enter a list of identifiers, separated by commas
(all numbers have to relate to the same database -- PubMed or GenBank!).
This will retrieve all the neighbours as a single group. Alternatively,
you can set up as many separate neighbour searches as you like, on separate
lines in the Configurator.
NOTE: A PubMed article typically has about 100 neighbours. If you put
several target identifiers into a list, make sure that the total number
of neighbours retrieved does not exceed the maximum allowed (maxdocs
parameter in your configurator profile). If you exceed this limit
you risk missing some important documents. Instead, put the identifiers
on separate lines and merge them by using the same alias name for all of
them.
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Last modified at $Date: 2018/05/25 12:12:10 $