This help document answers the following questions about the References Query Form:

• What can I use the References Query Form to find?
• How do I fill in this query form?
• How do the sort options work?
• What values are acceptable in each of the fields?
• How do I interpret the summary results of my query?
• How can I view a more detailed result?
• How do I interpret the detail results?
• Are there examples of queries and results?

What can I use the References Query Form to find?

By far, most data in the database are extracted from the scientific literature. You can search the collection of references and access links to related data in MGI. The References query form enables you to retrieve information related to one or more references. MGI is "reference driven" in that most data are extracted from journal articles and other documents. The references comprise a "master bibliography" for the database.

Some kinds of data, such as mouse physical mapping data from MIT, are downloaded from external databases. Appropriate references for these data are also provided.

How do I fill in this query form?

Enter enough information in the search fields to narrow the search to a few records. Use the Author(s), First Author, Abstract, or Title fields to focus your search. Use the Year and Journal fields with other fields to further limit the scope of the search. If you anticipate multiple query results, select the sort option most suitable to your needs. When you select a detail view of the query result, you can follow links to additional information about this reference throughout the database.

After entering values in the form fields, click Search to submit the query. Click Reset to clear the fields and return any default values.

How do the sort options work?

First Author	References are sorted in alphabetical order by first author.
J number	References are by J number in ascending order. The J number is an MGI accession ID format for references. References are assigned J numbers sequentially, beginning with J:1; currently (late 2007), MGI contains over 120,000 references, so the most recent J numbers are somewhere in the J:120,000+ range.
Year (default sort option)	References are ordered by year with the newest articles at top of list.
Max number of items returned	You can speed your query by limiting the number of results returned; the default is 100.
Summarize results	By default, the system summarizes the results of your query; a list of References without abstracts appears. When you click an item on the list, the full reference appears in PubMed format with abstract, if available.

What values are acceptable in each of the fields?

Reference Accession ID | First Author | Authors | Journal | Year | Volume | Pages | Title | Abstract | Chromosome

How do I interpret the summary results of my query?

If you expect multiple records from a search, it may be helpful to generate a concise listing of query results. By default, the Summarize results option is selected. Click the box beside this option to select or deselect it. The References Query Results -- Summary page orders the items by year (the most recent items appear first). Each line contains the following information: J number, author(s), title, journal, publication date, volume/issue, pages.

Click a record in the summarized list to see the full PubMed format Reference and abstract (if available).

How can I view a more detailed result?

The References Query Results -- Summary report provides links to detailed results. Click the desired item to see its References Query Results -- Detail report.

How do I interpret the detail results?

Click a category to retrieve the related information. On these pages, you can follow links to browse additional areas of MGI or other databases; you can always go back to the original list of reference results.

• The References Query Results -- Detail report displays the full PubMed format reference with an abstract or full text link, if available.
• The PubMed ID number is linked to the record found in ENTREZ.
• The detailed results include information about the MGI Accession ID, J Number, Other Accession IDs, (usually PubMed), Title, Authors, Journal, Volume, Issue, Year, Pages, Review Status, Abstract/Full Text (if available), and Additional Information (if available).
• The Review Status field indicates whether the article comes from a peer-reviewed journal or a nonpeer-reviewed publication or data submission.
• The Full Text link displays any short, unpublished scientific articles associated with your query.
• Items under Additional Information link to any MGI data extracted from that paper. If present, a number in parentheses indicates how many data items of that type to expect. Related records may include marker descriptions, sequences, orthologies, molecular probes, mapping data, expression data (for example, n results,  n assays,  n tissues), antibodies (associated with expression assays), or phenotypic alleles.

Are there examples of queries and results?

The following examples show the field values to set for the query. Default values for other fields are assumed.

1. Find a paper in MGI describing a methodology for large-scale sequence analysis with J number J:45711.

   Reference Accession ID J:45711
   This query finds an article entitled Comparative sequence analysis of a gene-rich cluster at human chromosome 12p13 and its syntenic region in mouse chromosome 6, J number, 45711 and MGI ID accession ID, MGI:1194866.

2. Find all the papers published after 2001 authored by Carninci, though you are not sure of the first name.

   First Author BEGINS Carninci
   Year >2001
   This query finds all articles written by any first author whose last name begins Carninci published after 2001.

3. Find all the papers written by Carninci in 2002 and published in the journal Genomics.

   First Author BEGINS carninci
   Journal BEGINS gen
   Year = 2002
   The query results include all articles written by Carninci in 2002 published in Genomics, Genetics (or any other journal whose name begins with Gen).

4. Find papers published in 2003 that include an author named Clemente or Clementi; you are not sure which.

   Author(s) CONTAINS clemen
   Year = 2003
   

   The query finds the articles published in 2003 written by several authors. In each case, one of the author names contains the letters clemen (for example, Clemens and Clemente).

5. There is an article on cystic fibrosis by a researcher whose last name is something-Bell or Bell-something. You are pretty sure that cystic fibrosis is in the title.

   First Author BEGINS bell
   Title CONTAINS cystic
   This query finds several references to articles by Campbell, Bellacosa, and Abella with cystic or Cystic in the title.

6. Some important research on kidney disease was reported by Cohen. Get a list of references by him/her pertaining to kidney.

   Summarize Results?: No
   First Author: BEGINS cohen
   Abstract: kidney or renal
   The query retrieves references displayed in full format so that you can view all of them on the same web page, search all the contents, or print out all the results.

Note: Be wary of the following searches:

1. Title CONTAINS murine
   This search uses a common term found in many titles and requires looking at every title in the bibliography table. If you set No Limit on Max number of items returned, the result is a display of over six thousand references. If this is not your intent, either limit the maximim number of returns or use more words and additional criteria to narrow your query.



2. First Author = Nadeau J
   Using the = (equals) operator in a text field results in a search for the precise string of characters you enter. This search returns any reference attributed to Nadeau J and excludes those by Nadeau JH.