1. Select the type of search by clicking the navigation tab:

   Use 'Free Text Search' to search by keywords, genes, diseases, or strings of genes.
   Use 'List Search' to search with a list of genes by name or ID.
   Use 'Query Interactions' to search for specific protein interactions.
   

2. Enter your genes, gene list, search terms or phrase.

   In Free Text Search, use any phrases or operators permitted by Lucene (See below for example queries). Specify if you want MiMI to search for your terms in only certain fields by adding the field prefix : cellularComponent:nucleus. (For gene lists, click the radio button to specify names or ID, upload a file and copy it if you are using a file).

   For more detailed instructions for using Lucene queries visit: http://lucene.apache.org/java/2_4_0/queryparsersyntax.html

3. Press submit. The results appear in a summary table.

1. Scan results and confirm them. Details on merging logic and source databases can be found in the User Manual.

2. For details on a given gene, click the the gene name.

   To see information about the GO terms describing the gene’s cellular components, biological processes, or molecular functions, click the term link.
   To see all interactors with a gene, click the # under Int
   To see all articles about a gene, click the # under Doc
   To see related pathways, click the # under Path
   

3. To open and close any of the information sections, click on the section icon or Show/Hide

4. To go back and forth in MiMI, use the back and forward buttons in your browser.

5. To link out to other sources and return, click the desired hyperlink and use the browser’s back button to return to MiMI.

NOTE: Breadcrumbs for navigation are slated for the next version.

1. Find basic gene details and gene attributes in the Molecule Details section (open by default)

2. Examine interactions and literature about interactions by opening the Protein Interactions section

   Get a list of all articles about these interactions by clicking the documents hyperlink. From there, click the See Text link to view the abstract.

   See the article citations on one interaction by clicking the number under the Lit Count column. From there, you can click on the See Text link to see the article abstract.

3. Examine literature about the selected gene by opening the Literature section.

   Click the page numbers to move through the list.
   Click the PMID to go to the PubMed abstract page.
   Click View under the See Mined Text column to see other genes associated with this gene in the article.
   Click Search Google Scholar to go directly to results from a Google search on the gene.

4. Examine pathways in which the gene resides by opening the Pathways section.

   Click KEGG ID or Image to see details or a network.
   Click View Related under Genes Related to the Pathways to see a list of all genes related to the pathway.
   From there, click “Show Genes in this pathway that interact” (under theDescription header), to see interacting genes within and outside the pathway.
   NOTE: This may be a large set and take time to load.

5. Link out to other biological databases such as NCBI Entrez Gene, EMBL-EBI, and others .

6. Use integrated tools from NCIBI to extend your investigation.

For a complete listing of NCIBI Tools visit the NCIBI Web Site.

For additonal MiMI support and/or any questions regarding MiMI email mimi-help@umich.edu.