PubCrawler Terms

Profile

The PubCrawler Profile contains all of the user-specific information. This includes user name, password, e-mail address as well as search queries, PubCrawler options, and schedule information. Most of this data is stored during the registration process. It is protected by a password, supplied by the user.
To set up or modify a profile, please use the WWW PubCrawler page.

Search Query

To use PubCrawler, one or more search queries have to be set up. These will determine which articles to look for in the library.
Each query consist of

the name of the database from which to extract information (genbank or pubmed)
an optional alias
pairs of search term/search query, which can be combined with boolean operators.

Options

Options enable fine tuning of PubCrawler results. They determine amongst others how many reports to retrieve, how many full abstracts to show, etc.
You can change the options every time you have finished using PubCrawler Configurator and are prepairing to store your searches on the public server.

Schedule

The schedule is a time table for your own PubCrawler jobs. You can determine at which weekdays and at which times your searches should be carried out.
To change the schedule, go to PubCrawler's WWW-Service, enter your username and password and click on 'Modify Personal Data & Schedule'.

Registration

To make avail of PubCrawlers WWW-service you have to be a registered user. For this you have to choose a user name (3 - 12 alpha-numerical characters) and a password (4 - 14 alpha-numerical characters). Please note that these are case sensitive!
It is also necessary to give an e-mail address. This will be used for important notifications, PubCrawler results (if requested) and also to get your password sent, in case you'll forget it - so please supply a valid e-mail address!
There are two ways to register:

Use the WWW PubCrawler page.
Use the PubCrawler Configurator to create a configuration file and at the final stage use the button labelled 'Store Profile' to enter the registration process.

Easy Check

The results, logs and configuration of each WWW-PubCrawler user are protected by passwords. Everytime they are accessed the username and password has to be typed in.
When the 'Easy Check' option is activated, cookies are transferred to the user's web browser and the authentication will be carried out automatically when the following site is accessed: http://pubcrawler.gen.tcd.ie/cgi-bin/pubcrawler.results
This only works

if you have cookies enabled in your browser (which is the default for most of them)
for one user per browser (other people using the same browser on the same computer could overwrite another person's cookies);

The 'Easy Check' option can be activated during registration process or afterwards through PubCrawler's WWW-Service and click on 'Modify Personal Data & Schedule'.

First Visit

In their results file people often find lines like the following:

800 hits after first visit for '50000:350000[SLEN] '

The term 'first visit' relates to a stage in a typical PubCrawler run, where numerical id's of all reports matching a given search query are retrieved from PubMed or GenBank. These will then be compared with the local database and only for the ones that haven't been seen before, a full report is requested during a second visit to NCBI.
There are more details available about how PubCrawler works.

Alias

An alias can be optionally specified for each search query. They serve two purposes:

In the output file an alias is used as a short description for a long search term. It replaces the query with a suitable name.
The same alias given to multiple queries combines their individual results into a single one. Therefore, very long queries can be split into several small ones, and results from queries covering similar research fields can be seen together.

NOTE: Only queries directed to the same database can share the same alias!

PubCrawler Terms

INDEX

EXPLANATION