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The Protein Identifier Cross-Reference (PICR) service: reconciling protein identifiers across multiple source databases

Richard G Cote, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob
2007 BMC Bioinformatics  
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

Jianjiong Gao, Chao Zhang, Martijn van Iersel, Li Zhang, Dong Xu, Nikolaus Schultz, Alexander R. Pico
2014 F1000Research  
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

Hoo-Keun Lee, Hyeon-Jin Kim, Ung-Sik Yu
2009 Genomics & Informatics  
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

Henning Redestig, Miyako Kusano, Atsushi Fukushima, Fumio Matsuda, Kazuki Saito, Masanori Arita
2010 BMC Bioinformatics  
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

Chen Chen, Jie Hou, John J Tanner, Jianlin Cheng
2020 International Journal of Molecular Sciences  
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

Michael Joseph Meyer
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