ONLINE MENDELIAN INHERITANCE IN ANIMALS

PHENES OF THE MAJOR DOMESTIC ANIMAL SPECIES


HELP


BIRX

Online Mendelian Inheritance in Animals (OMIA) uses the BIRX database searching software (obtained from NCBI). This is a WWW-compatible interface for the IRX (Information Retrieval eXperimental workbench) database searching program.

The Search Query

OMIA contains references on Phenotype Genes (phenes) in the major domestic animal species, i.e. documented phenotypes of inherited traits.

As currently implemented, the database contains principally bibliographic material. Species names (i.e. common names) and phene names have been added to the database. In some cases, additional information, such as Across-Species Synonyms, MIM Number, Species Synonyms, Species Summary, Inheritance and Molecular Genetics, is available.

As a result of your query you will retrieve a list of documents. Click on the document icon beside any name in the list to view the entry.

Field Restrictions

The query form consists of sixteen Field Restriction check boxes followed by four query input boxes. Each of the sixteen fields of the database (Titles + Species, MIM number, Species Synonyms, etc.) can be searched independently of (or in conjunction with) one another. Most of the information is contained within the Titles + Species and References fields.

To restrict your search to particular fields, check one or more of the check buttons beside Titles + Species, References, MIM number, etc.

You must then check off the Field Restriction button in front of an input box.

If no buttons are checked all fields will be searched.

For any input box you may choose whether or not to apply field restrictions. However, if you do apply field restrictions you may only apply one pattern across all input boxes, e.g. if you choose the field restrictions Species Synonyms and Across-Species Synonyms for the first input box, all other boxes for which you mark Field Restriction will be restricted to the Species Synonyms and Across-Species Synonyms fields.

Input Boxes

Each input box is preceded by a "Field Restriction" check button and followed by a choice of the Boolean Operators AND or OR (last box excepted). The Boolean operator combines the results generated by the preceeding input box with the results of the next box.

Usually, single input boxes are used for entering phrases or other combinations of words you expect to occur together. Words entered within a single input box will generate a match only if all the words occur within a single field of the document.

In contrast, a Boolean operator (AND, OR) between query input boxes combines documents without respect to fields. Therefore, entering words within a single input box is more restrictive than entering them across boxes.

Boolean Operators

Boolean operators are used to combine the results from different query input boxes.

The Boolean operators are:

Therefore, the AND operator is used to narrow the query output and the OR operator is used to expand the query output. The default is AND.

1st 100

The "nth 100" button is used to specify which subset of the query output is to be returned to the user.

You should normally select the "1st 100" documents to be returned. Usually, this will be all you need. If your query finds more than 100 documents, you can resubmit it to retrieve the next 100 documents or you can request that all of the documents be retrieved. However, be aware that it can take a long time and use a lot of memory to load and transfer large numbers of documents over the network. We do not recommend using the "all" button unless you feel that it is necessary.

Note that, as with IRX, BIRX ranks the returned documents in order so that those first returned will be most relevant to your query (will contain most instances of the input words).

Run Query

The "Run Query" button causes the current query to be executed.

Clear Input

The "Clear Input" button resets the contents of the query form to their original state.

Results

After the query has been submitted, you will receive a table of contents of the documents retrieved. Each document is prefixed with an icon. Selecting that icon will retrieve the text for that document.