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GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction.

Browne F, Wang H, Zheng H, Azuaje F - Source Code Biol Med (2009)

Bottom Line: Extraction of these data can be both complex and time consuming.A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae.Manual construction of reference datasets can be a time consuming process requiring programming knowledge.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK. hy.wang@ulster.ac.uk.

ABSTRACT

Background: Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of new therapeutic interventions. Efforts have been made to map interactions on a proteomic-wide scale using both experimental and computational techniques. Reference datasets that contain known interacting proteins (positive cases) and non-interacting proteins (negative cases) are essential to support computational prediction and validation of protein-protein interactions. Information on known interacting and non interacting proteins are usually stored within databases. Extraction of these data can be both complex and time consuming. Although, the automatic construction of reference datasets for classification is a useful resource for researchers no public resource currently exists to perform this task.

Results: GRIP (Gold Reference dataset constructor from Information on Protein complexes) is a web-based system that provides researchers with the functionality to create reference datasets for protein-protein interaction prediction in Saccharomyces cerevisiae. Both positive and negative cases for a reference dataset can be extracted, organised and downloaded by the user. GRIP also provides an upload facility whereby users can submit proteins to determine protein complex membership. A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae.

Conclusion: GRIP is developed to retrieve information on protein complex, cellular localisation, and physical and genetic interactions in Saccharomyces cerevisiae. Manual construction of reference datasets can be a time consuming process requiring programming knowledge. GRIP simplifies and speeds up this process by allowing users to automatically construct reference datasets. GRIP is free to access at http://rosalind.infj.ulst.ac.uk/GRIP/.

No MeSH data available.


Related in: MedlinePlus

Description of the complex matching algorithm used to search for complexes and proteins matching a client's search term.
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Figure 3: Description of the complex matching algorithm used to search for complexes and proteins matching a client's search term.

Mentions: Figure 3 illustrates the complex matching algorithm whereby GRIP searches for protein complexes containing the search term entered using the GUI. The PHP algorithm firstly determines if the search criteria entered by the user is a complex id or complex name. The search criteria are inserted into an SQL query to obtain complex information related to the search term. For each of the protein complexes obtained, proteins within the complex are also extracted. All these data are output to the GUI.


GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction.

Browne F, Wang H, Zheng H, Azuaje F - Source Code Biol Med (2009)

Description of the complex matching algorithm used to search for complexes and proteins matching a client's search term.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2636808&req=5

Figure 3: Description of the complex matching algorithm used to search for complexes and proteins matching a client's search term.
Mentions: Figure 3 illustrates the complex matching algorithm whereby GRIP searches for protein complexes containing the search term entered using the GUI. The PHP algorithm firstly determines if the search criteria entered by the user is a complex id or complex name. The search criteria are inserted into an SQL query to obtain complex information related to the search term. For each of the protein complexes obtained, proteins within the complex are also extracted. All these data are output to the GUI.

Bottom Line: Extraction of these data can be both complex and time consuming.A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae.Manual construction of reference datasets can be a time consuming process requiring programming knowledge.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Computing and Mathematics, University of Ulster at Jordanstown, Northern Ireland, UK. hy.wang@ulster.ac.uk.

ABSTRACT

Background: Information about protein interaction networks is fundamental to understanding protein function and cellular processes. Interaction patterns among proteins can suggest new drug targets and aid in the design of new therapeutic interventions. Efforts have been made to map interactions on a proteomic-wide scale using both experimental and computational techniques. Reference datasets that contain known interacting proteins (positive cases) and non-interacting proteins (negative cases) are essential to support computational prediction and validation of protein-protein interactions. Information on known interacting and non interacting proteins are usually stored within databases. Extraction of these data can be both complex and time consuming. Although, the automatic construction of reference datasets for classification is a useful resource for researchers no public resource currently exists to perform this task.

Results: GRIP (Gold Reference dataset constructor from Information on Protein complexes) is a web-based system that provides researchers with the functionality to create reference datasets for protein-protein interaction prediction in Saccharomyces cerevisiae. Both positive and negative cases for a reference dataset can be extracted, organised and downloaded by the user. GRIP also provides an upload facility whereby users can submit proteins to determine protein complex membership. A search facility is provided where a user can search for protein complex information in Saccharomyces cerevisiae.

Conclusion: GRIP is developed to retrieve information on protein complex, cellular localisation, and physical and genetic interactions in Saccharomyces cerevisiae. Manual construction of reference datasets can be a time consuming process requiring programming knowledge. GRIP simplifies and speeds up this process by allowing users to automatically construct reference datasets. GRIP is free to access at http://rosalind.infj.ulst.ac.uk/GRIP/.

No MeSH data available.


Related in: MedlinePlus