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:

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:

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: