Using the OMIM WAIS server

[Ken Fasman]

Here is the basic help file for accessing the OMIM Wide Area Information 
Server (WAIS).  Please contact GDB User Support if you have more specific 
questions on this service, or OMIM in general.


Ken Fasman
Director of Informatics
Genome Data Base
Johns Hopkins University School of Medicine
2024 E. Monument St.
Baltimore MD  21205

ken at library.welch.jhu.edu

===================================================

Welcome to the help file for using WAIS to search the Online Mendelian
Inheritance in Man (OMIM) database.

OMIM is also accessible interactively through GDB (Genome Data Base).  It is 
available there as a full text database running under the National Library 
of Medicine's IRX software.  For information on accessing OMIM through GDB, 
or if you have any questions about OMIM, please send mail to 
help at welch.jhu.edu, or call (410) 955-7058.

OMIM is listed in the directory of WAIS servers as: 
online-mendelian-inheritance-in-man.src  

Open this source to query the database, or you may type "omim" 
in the Query box and the directory of servers will retrieve the 
source for you.

OMIM WAIS is updated daily at 9:00 am ET.  If you attempt to search the
database at this time, you may receive a message stating that
OMIM is unavailable.  Please retry your search after 9:30 am ET.

--How to Search OMIM via WAIS--

1.	Type your query in the "Tell me about:" box.
	For example, to search for any information in OMIM on Marfan
	syndrome, type:
		marfan

	(You do not need to use capital letters or include the word
	 "syndrome."  Your query will bring back better results if 
	 commonly found terms such as "syndrome" or "disease" are not 
	 used.  See Search Strategies below for more information.)

2.	Select the "Search" button.

	Your results will be returned to you.  OMIM returns the most
	relevant result at the top of the list.  The number in the
	far left column shows the "weight" or importance of the entry.
	Note that the weight descends as you move down the list.  The 
	weighting is determined by the number of times that the search 
	terms occur in the document.
  

3.	Select a document to read and press the "View" button.

	A window will appear with the six-digit OMIM document number
	and the document title.  Your query terms will be highlighted 
	in the document.  When you are finished reading the document,
	you may either select the "Done" button, if you do not wish to save
	the document, or the "Save to File" button, if you would like to 
	save the file to your computer.  If you have created an 
	omim directory, select the omim directory from your list.  
	The omim directory will be appended to the directory list above
	the source file list.  Then type in a *unique* name for every
	file you save, e.g., marfan1, marfan2, etc.  If you save all of 
	the documents to the same file, you will overwrite every previously 
	saved file with the most recently saved file. 

To erase search terms from the Query box, use the <Backspace> or <Delete> key. 
Pressing the <Return> key will begin searching on the question (if any)
that is currently in the Query button.

--OMIM via WAIS Search Strategies--

Searching OMIM via WAIS works differently than OMIM via IRX (the OMIM
retrieval software included with the GDB application).  

-How to Phrase a Query-
Use only the most important word(s) in your query.  If you are searching
for documents on colon cancer, typing:

Query: colon

retrieves documents that are more closely related to your search than

Query: colon cancer

The second query retrieves documents mentioning either colon or cancer.
To search SPECIFICALLY for lung cancer, type the following:

Query: "lung cancer"

Note the quotation marks around the phrase.  They are very important for 
eliminating unwanted entries.  As in the example above, if you leave off the quotation marks, you will retrieve entries which contain either the word 
"lung" OR "cancer" (or both).

Quotation marks should also be used to surround search terms containing 
punctuation marks, such as "Tay-Sachs."  Otherwise, WAIS will ignore 
the punctuation and improper entries may be retrieved.

-How WAIS Searches for Query Terms-
NOTE:  OMIM via WAIS does *not* automatically stem words. For example:

Query: pig

retrieves documents that contain the word pig.  Words containing the 
word pig, such as pigmentation, are *not* retrieved when searching OMIM
via WAIS.  Documents containing these words would be automatically 
retrieved when searching OMIM via IRX.  If you did want to retrieve 
documents containing variations of the word pig, you would need to 
type:

Query: pig, pigs, pigment, pigmentation

However, plural stemming does occur: e.g., dystrophies become dystrophy.

-Excluding Certain Documents From Retrieval-

It is possible to exclude certain documents from being retrieved in 
your search.  If you are searching a general subject, such as cancer,
but do not want to retrieve documents on certain kinds of cancer, type:

Query: cancer not colon not breast not ovarian

No documents referring to colon, breast, or ovarian cancer will be retrieved.
Be careful when using "not" in a retrieve, as you will exclude documents from
your search which also mention other cancers if they mention the terms you
are excluding.  If a document refers to both breast and lymphatic cancer,
it will not be retrieved. 

-Locating Your Search Terms Within a Document-

To move directly to the places in the current document that 
show your highlighted query terms, select the "Find Key" button.  Select
the "Find Key" button to move to the next occurrence of your query terms.
When there are no more occurrences of your query terms in the document, 
you will see the following message in the Status box:

Status: Could not find any more keywords.

--Searching Both GDB and OMIM--

If you search both GDB and OMIM WAIS versions simultaneously, you will 
receive a mixture of OMIM and GDB document headlines.  OMIM entries will 
contain the 6 digit MIM number in the document description, while GDB 
entries will start with "Locus," "Probe," etc.


Typing:

marfan

retrieves the OMIM headline for the Marfan Syndrome entry and the
the locus headline for the FBN1 locus both weighted at 1000.  The
rest of the headlines consist of GDB citation headlines.  Search 
OMIM separately to retrieve additional OMIM Marfan Syndrome 
information.			

-- End of help file --