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The NCBI BioSystems database

por matias leo (2019-02-02)


INTRODUCTION

Biological molecular databases often contain relationships between records based on computational inference of similarity, such as links between sequences deemed homologous in protein and nucleotide databases. Less frequently do they explicitly log relationships between records that are experimentally derived, such as the genes interacting in a biological pathway, even though knowledge of these relationships is crucial for understanding living systems and for 카지노사이트 performing biological research. Fortunately, a considerable number of resources have been created to address this issue: the Pathguide (1) resource lists nearly 300 pathway resources alone, including KEGG (2), Reactome (3), PID (4), PharmGKB (5), GenMAPP (6), Biocyc (7)

 

and many others. While there is some degree of overlap between such resources, there may be significant numbers of unique records available from many of the underlying datasets. However, because of the diverse history of these databases and resources, integration with commonly used molecular database resources, such as NCBI's Entrez search engine, is done on a case-by-base basis. To address this issue, we have created the NCBI BioSystems 온라인카지노 database that functions as a clearinghouse for these databases by integrating their data into the existing NCBI Entrez databases (8), such as Gene, Protein, PubMed and PubChem, and linking back to the original database web site for more detailed information and analysis (Figure 1). Centralizing and linking the existing biosystems databases potentially increase their usefulness by integrating their pathways and

 

systems into a resource that is accessed by a significant number of scientists. It also enables users to quickly find and categorize proteins, genes and small molecules by pathway, disease state, etc., instead of requiring time-consuming inference of biological relationships from other evidence, e.g. by examining a 3D structure.

Figure 1.A schematic representation of the integration of the BioSystems database with various NCBI resources and with resources publically available from the depositor.

 

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A schematic representation of the integration of the BioSystems database with various NCBI resources and with resources publically available from the depositor.

 

 

A schematic representation of the integration of the BioSystems database with various NCBI resources and with resources publically available from the depositor.  OVERVIEW OF CONTENT

A BioSystem record is defined as a biologically related list of gene, protein and small molecule identifiers, along with the characterization of interactions, citations and other annotations, where none of these items are mandatory. This definition is not limited to metabolic- or signaling pathways: for example, a BioSystems disease record may contain susceptibility genes, biomarkers and drugs used for treatment.

 

The BioSystems database is archival and each BioSystem record receives a unique identifier known as a bsid that is intended to remain constant over the lifetime of the record. Each new version of a BioSystem record is assigned a version number.

Presently, NCBI BioSystems contains  카지노사이트추천 pathways from KEGG (2), Human Reactome (3) and EcoCyc (9) for a total of about 100 000 BioSystem records. These BioSystems records link to over 2 million protein records, nearly 900 000 gene records and several thousands PubChem records.

An example record, shown in Figure 2, describes the COX portion of the human arachidonic acid metabolism pathway, which metabolizes lipids into prostaglandins that are involved in a host of regulatory mechanisms via binding to and activating G protein-coupled receptors. This pathway has an important role in pain and inflammation. Specifically, the protein encoded by human PTGS1 gene is involved in the conversion of prostaglandin PGG2 into inflammation-causing prostaglandin PGH2. Aspirin has been shown to bind to the PTGS1 gene product (prostaglandin-endoperoxide synthase 1), blocking that enzyme's ability to produce PGH2 and thereby reducing pain and 바카라사이트 inflammation. The NCBI BioSystems record lists these genes, their associated proteins and the small molecules involved in the pathway. The BioSystems records also contain annotations such as taxonomy, description, pathway images and citations. Finally, links to and from other NCBI Entrez databases are listed, including links between BioSystems records. Links between BioSystems records are specified by the depositor and also generated computationally for BioSystems that list overlapping sets of proteins.

Figure 2.An example BioSystems record display for the COX portion of the arachidonic acid metabolism pathway, which metabolizes lipids that are commonly found in the cell membrane into prostaglandins. The display includes a thumbnail image, links back to the depositor's web site, and lists of the molecular identifiers and annotations associated with the pathway.View largeDownload slide

An example BioSystems record display for the COX portion of the arachidonic acid metabolism pathway, which metabolizes lipids that are commonly found in the cell membrane into prostaglandins. The display includes a thumbnail image, links back to the depositor's web site, and lists of the molecular identifiers and annotations associated with the pathway.

 

 An example BioSystems record display for the COX portion of the arachidonic acid metabolism pathway, which metabolizes lipids that are commonly found in the cell membrane into prostaglandins. The display includes a thumbnail image, links back to the depositor's web site, and lists of the molecular identifiers and annotations associated with the pathway.  

Currently, we distinguish between two major record types, organism-specific biosystems and conserved biosystems. Organism-specific biosystems correspond to particular instances of a biological system, such as the arachidonic acid 카지노사이트 pathway in human. Conserved biosystems are canonical biosystems that are used to group together orthologous, organism-specific biosystems. Currently, these records are derived from reference pathways in the KEGG database.