Biomine help

Introduction

Biomine integrates and indexes data from several publicly available biological databases with the aim of aiding explorative discovery of non-trivial connections between biological entities, such as genes and phenotypes.

Frequently Asked Questions

In addition to this help page, a list of frequently asked questions is available.

Searching with Biomine

You can make Biomine queries by selecting one or more biological entities as search terms. To select search terms, use the search field at the top of the Biomine search page to type in an entity name (e.g. the name of a gene or protein, such as APOE), a search term (e.g. Alzheimer), or a database identifier (e.g. MIM:194470). You will then be presented with a list of suggested search terms, from which you can pick one or more terms from that list, and/or type in a different keyword to see other suggestions.

If the list of suggested search terms contains a term of interest, click the title of term to select it. If you wish to see a suggested search term in the source database from which Biomine has indexed it, click the database identifier to the right of the term's title.

Once you have selected one or more search terms, which will be listed on the right, you can click the “Discover connections” button to start a Biomine search. Biomine will then search for entities connecting your search terms. If only one search term is given, Biomine finds entities directly and undirectly related to the term.

If you cannot find the entity you are looking for, try one of the following:

• Change what you wrote in the search field to get different suggestions.
  • Suggestions include only entities which match the typed phrase.
• Browse for more entities by type (e.g. protein, phenotype) by clicking on a type heading in the suggestions list.
• Browse for more entities by organism, where applicable (e.g. human or mouse genes), by clicking on an organism heading in the suggestions list.
  • Note: In order to to pick an organism, it may be necessary to first select a type. The initial list of suggestions contains organisms only if there are organism-specific nodes suggested, and may not contain the complete list of organisms for the suggestions even so. The complete list of organisms is available once a specific node type is selected.

If no suggestions are displayed, and no message is shown stating that nothing matched the phrase typed in the search field, your browser might not be configured to support JavaScript. Please consult the FAQ for information on Biomine system requirements.

Data indexed by Biomine

Entities and their identifiers in the Biomine database

Entity type(s)	Database	Record ID	Example	Remarks
Gene	EntrezGene	Entrez GeneId	EntrezGene:351	Official symbols of genes can be used directly, e.g. “APOE”.
	HGNC	HGNC id	HGNC:620
Protein	UniProt	accession number (primary or secondary)	UniProt:P05067	Official symbols of proteins can be used directly, e.g. “A4_HUMAN”.
	EntrezProtein	Entrez protein id	EntrezProtein:112927
Phenotype, Locus, Allelic variant	MIM	OMIM ID	MIM:159300	Any id prefix (e.g. #, +, or %) must be omitted. The symbols of some phenotypes can be used directly, e.g. “AD” for Alzheimer Disease.
Cellular component, Structural element, Molecular function	GO	GO:ID	GO:GO:0008201
Family, Domain, Site, Repeat	InterPro	accession number	InterPro:IPR001254
Homology group	HomoloGene	HomoloGene id	HomoloGene:11438
Article	PubMed	PubMed id	PubMed:9463312	The articles themselves are not stored in the Biomine database, only links to referred biological entities.

Currently data concerning only the following organisms is indexed by Biomine:

• Homo sapiens (hsa)
• Mus musculus (mmu)
• Rattus norvegicus (rno)
• Drosophila melanogaster (dme)
• Caenorhabditis elegans (cel)

Identifiers associated with organisms other than those listed above are not recognised, even though they may be present in the source databases.

Using Biomine search results

After a Biomine search has completed, the query page shows a thumbnail of the resulting graph. Click on this graph to open it in an interactive Java applet, where nodes are hyperlinks to individual records. To use this applet, your browser must support Java 1.5 or later (usually by means of an up-to-date Java plugin).

In the interactive view you can:

• Access search results:
  • select a node by a mouse click (for further operations from the menu)
    • select multiple nodes by holding down Shift when clicking
    • copy the ids of selected nodes to clipboard (e.g. for further queries) from the menu (may require setting Java applet security policy to allow clipboard access)
  • open a node context menu by right-clicking (or Ctrl-clicking on Macintosh) and:
    • see more information about the node
    • open a WWW record/entity from the context menu
• Modify the graph layout:
  • drag and drop nodes to manually modify the layout
  • release a node for automatic layout (after dragging) from the context menu
• Navigate the graph structure:
  • highlight a node and its immediated neighbors by placing mouse over the node
  • zoom the view to a node and its immediate neighbors by a double click on the node
  • zoom the view to fit all nodes by a double click on the background
  • zoom the view by the mouse scroll wheel (or right click and drag on the background)