A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Filters
The Protein Identifier Cross-Reference (PICR) service: reconciling protein identifiers across multiple source databases
2007
BMC Bioinformatics
Preserved Fulltext
Results: We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the ...
This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the ...
Acknowledgements PICR contributors are supported through the BBSRC ISPIDER grant and EU FP6 "Felics" (contract number 021902 (RII3)) grants. RC would like to thank KC for invaluable contributions. ...
doi:10.1186/1471-2105-8-401
pmid:17945017
pmcid:PMC2151082
fatcat:vegtt57cdbaslkka4ekupxyamu
BridgeDb app: unifying identifier mapping services for Cytoscape
2014
F1000Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Côté RG, Jones P, Martens L, et al.: The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC bioinformatics. 2007; 8(1): 401. ...
.: The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC bioinformatics. 2010; 11(1): 5. ...
BioMart 3 , Synergizer 4 , PICR 5 and BridgeDb web services and BridgeDb database files. ...
doi:10.12688/f1000research.4521.1
pmid:25110584
pmcid:PMC4111116
fatcat:zxsxgtu6vbem3jucnwgzj2gkse
IdMapper: A Java Application for ID Mapping across Multiple Cross-referencing Providers
2009
Genomics & Informatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Id mapping across service providers is possible by remapping the resultant ids. ...
It supports three widely used mapping services and can convert many ids from one source database into many target databases at once. ...
Acknowledgments This work was supported by a grant (2007-03983) from the Korea Science and Engineering Foundation funded by the Ministry of Education, Science and Technology of Korea government. ...
doi:10.5808/gi.2009.7.4.208
fatcat:7zdtp6u3ojazbeg6xmtvjr6zsa
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis
2010
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Conclusions: Efficient cross-referencing of metabolite identifiers is a key technology for metabolomics data analysis. ...
Online chemical databases use multiple types of identifiers in parallel but lack a common primary key for reliable database consolidation. ...
Authors' contributions HR initiated the project, designed and implemented the program and wrote the manuscript. MK wrote the manuscript, provided GC-MS data and evaluated the program. ...
doi:10.1186/1471-2105-11-214
pmid:20426876
pmcid:PMC2879285
fatcat:sxefdspssfej5nkqkuuhgikhqu
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
2020
International Journal of Molecular Sciences
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
We conclude with a discussion of how quantitative protein data can be used to reconstruct protein interactions and signaling networks. ...
We first introduce bioinformatics software and tools designed for mass spectrometry-based protein identification and quantification, and then we review the different statistical and machine learning methods ...
PhosphoSitePlus [134] A comprehensive web services for post-translational modifications. PICR [136] Reconciling protein identifiers across multiple source databases. ...
doi:10.3390/ijms21082873
pmid:32326049
pmcid:PMC7216093
fatcat:5zbrkah4xvec3mq3ypal7cxfbu
Methods For Functional Inference In The Proteome And Interactome
2017
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
In Chapters 2 and 3, I describe the construction of a database and web tool to aid in foundational genomics research by providing predictions of interacting protein domains in interactomes and all-by-all ...
3D interfaces of protein interactions by taking into account the evolutionary relationships and biophysical properties of proteins. ...
ACKNOWLEDGEMENTS I am incredibly fortunate to have had the support of many people over the course of my life and studies. There are an awful lot of people to thank. ...
doi:10.7298/x4b27s8t
fatcat:35wbklivsvgc7fbd6ex2sgnm6e