Entrez BioSystems interface redesign

[20 SEP 2011]  NCBI's BioSystems database now has a revised home page, search interface, and search results display, to have functions similar to those available in PubMed. Changes include: (a) a streamlined home page with links to related resources; (b) an "Advanced Search" page, which provides the ability to build a query one term at a time, browse the index of any search field, and combine earlier searches; and (c) new search results displays that provide links in the right margin to search filters, related data, and tools.

Additional KEGG data now available in BioSystems

[25 AUG 2011]  The BioSystems database now includes additional records from KEGG, including pathway modules, which represent subsets of larger pathways, as well as structural complexes and functional sets. (See the Biosystems help document for more information about the various record types.)

Instant links from gene expression data to ranked list of pathways

[15 MAR 2011]  Gene expression data in the GEO Profiles database now link to associated records in the BioSystems database. A button on the GEO Profiles search results page will automatically perform a multiple step FLink operation that retrieves pathways containing one or more of the genes represented in the expression data. The pathways can be ranked by frequency (illustrated example) or percent (%) coverage (illustrated example). More about FLink's ranking methods...

WikiPathways data now available in BioSystems

[03 MAR 2011]  WikiPathways data are now available in the BioSystems database. WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community. Its data can be retrieved from the BioSystems database by doing a search for: wikipathways[sourcename], or by clicking on the WikiPathways data statistic in the "database statistics" box on this page. In addition, the BioSystems database continues to be updated weekly, as new data become available from the source databases.

Entrez Gene records link to BioSystems

[04 JAN 2011]  Records in the Entrez Gene database now link to corresponding pathways in the NCBI BioSystems database and allow you to view the gene within the context of the pathway diagram. The BioSystems links are available in two places:

(1) The "General Gene Information: Pathways from BioSystems" section of a gene record lists the pathways from the NCBI BioSystems database that have been associated with the gene. Each link opens a context-sensitive view of the corresponding biosystem record, where the gene of interest is listed at the top of the "genes" folder tab and its checkbox is selected by default. From there, you can view the gene within the context of the pathway diagram, if that function is provided by the source database of the biosystem record.

(2) The "Links" menu in the right margin of a gene record will open a list of all the associated pathways from the NCBI BioSystems database. The "Selected BioSystems" box in the upper right corner of the resulting display provides some aggregate information about the set of biosystems, and you can click on any biosystem of interest to open a standard view (not context-sensitive) of its record.

As an example of the first approach, view the "general gene info" for GeneID 7157 (human tumor protein p53) and scroll down to "Pathways from BioSystems." Follow the link for "Amyotrophic lateral sclerosis (ALS), organism-specific biosystem (from KEGG)" and notice that GeneID 7157 (TP53), from which we started, appears at the top of the Genes folder tab and its checkbox is activated. Then click on "Highlight selected records in source database" to view the location of the selected gene within the pathway diagram, where the gene will be displayed with a red outline. (Note that the highlight function is currently available only for KEGG records.) The pathways were associated with the genes using the method described in the data processing section of the BioSystems help document.

Reactome data for non-human organisms now available in BioSystems

[12 AUG 2010]  The non-human subset of Reactome is now available in the BioSystems database. Reactome is a curated knowledge base of biological pathways for human and chicken and also includes computed pathways for other organisms. Its data can be retrieved from the BioSystems database by doing a search for: reactome[sourcename], or by clicking on the Reactome data statistic in the "database statistics" box on this page. In addition, the BioSystems database continues to be updated weekly, as new data become available from the source databases.

Public release of FLink

[29-JUL-2010]   FLink is now publicly available. Developed to handle large quantities of input and output data, it is a tool that enables you to traverse from a group of records in a source database to a ranked list of associated records in a destination database. For example, it can accept up to 100,000 protein sequence, gene, or small molecule identifiers as input and retrieve a ranked list of up to 100,000 biosystems. An illustrated quick start guide shows the easy 1-2-3 step process for using the tool. The help document also provides details about the proper formatting of the (1) input UID list, the features of the (2) review + select display and (3) output display, and a list of supported databases.

Pathway Interaction Database (PID) and additional BioCyc databases now available in BioSystems

[31 MAR 2010]  The NCBI BioSystems Database has been expanded to include the Pathway Interaction Database (PID) and all BioCyc Tier 1 (EcoCyc and MetaCyc) and Tier 2 databases (previously, only the EcoCyc subset of BioCyc was included). Data from these resources can be retrieved from the BioSystems database by doing a search for: "pathway interaction database"[sourcename] or for biocyc[sourcename], or by clicking on the statistic for either source in the "database statistics" box on this page. In addition, the BioSystems database continues to be updated weekly, as new data become available from the source databases.

Reactome data for human now available in BioSystems

[14 SEP 2009]  The human subset of Reactome is now available in the BioSystems database. Reactome is a curated knowledge base of biological pathways and its data can be retrieved from the BioSystems database by doing a search for: reactome[sourcename], or by clicking on the Reactome data statistic in the "database statistics" box on this page. In addition, the BioSystems database continues to be updated weekly, as new data become available from the source databases.

Public release of BioSystems database into Entrez

[30 APR 2009]  The NCBI BioSystems Database was made public in the Entrez system in order to provide integrated access among biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. The database contains biological pathways from two source databases, KEGG and the EcoCyc subset of BioCyc, and is designed to accommodate other types of biosystems such as diseases as data about them become available. more...