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Improvements in the protein identifier cross-reference service

Samuel P. Wein, Richard G. Côté, Marine Dumousseau, Florian Reisinger, Henning Hermjakob, Juan A. Vizcaíno
2012 Nucleic Acids Research  
as logical cross-references in the PICR data model.  ...  The Protein Identifier Cross-Reference (PICR) service was originally developed in 2007 at the European Bioinformatics Institute (EBI) to address the shortcomings described above (10) .  ... 
doi:10.1093/nar/gks338 pmid:22544604 pmcid:PMC3394263 fatcat:ikcrg43hazdfrgy5sk6hfrzjum

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

Sameer Velankar, José M. Dana, Julius Jacobsen, Glen van Ginkel, Paul J. Gane, Jie Luo, Thomas J. Oldfield, Claire O'Donovan, Maria-Jesus Martin, Gerard J. Kleywegt
2012 Nucleic Acids Research  
The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database  ...  Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.  ...  We are grateful to the InterPro team and David Binns, Craig McAnulla and Phil Jones in particular, for help with the InterPro mapping process.  ... 
doi:10.1093/nar/gks1258 pmid:23203869 pmcid:PMC3531078 fatcat:rnyow6huf5grfp5fz4oyien7zm

E-MSD: an integrated data resource for bioinformatics

S. Velankar
2004 Nucleic Acids Research  
The Macromolecular Structure Database (MSD) group  ...  ACKNOWLEDGEMENTS Special thanks go to Dr John Tate for help during the preparation of this manuscript. E-MSD gratefully acknowledges the  ...  MSD components are in white, external database components in yellow and the cross-reference components in green.  ... 
doi:10.1093/nar/gki058 pmid:15608192 pmcid:PMC540012 fatcat:z5numsmaibhbxbkxzh7w5vyd7m

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  ...  Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge.  ...  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

A Guide to UniProt for Protein Scientists [chapter]

Claire O'Donovan, Rolf Apweiler
2010 Msphere  
One of the essential requirements of the proteomics community is a high quality annotated nonredundant protein sequence database with stable identifiers and an archival service to enable protein identification  ...  focus on exploiting the knowledge captured in the UniProt databases, the services provided and the availability of complete proteomes.  ...  The Gene Ontology Consortium and UniProt Cross-references to External Sources Nonredundant Complete UniProt Proteome Sets The UniProt consortium released its new improved unified website in 2009: a  ... 
doi:10.1007/978-1-60761-977-2_2 pmid:21082425 fatcat:a547fe36zfeq3f4csfvnrtjog4

Activities at the Universal Protein Resource (UniProt)

2013 Nucleic Acids Research  
Extensive cross-references allow UniProt to provide a service to map different types of identifiers (IDs) across resources that have unique IDs.  ...  As new resources with unique IDs are added as cross-references, they are also added to the mapping service.  ... 
doi:10.1093/nar/gkt1140 pmid:24253303 pmcid:PMC3965022 fatcat:ymvqbpyhizafba7upcn222a6ty

InterPro in 2011: new developments in the family and domain prediction database

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+45 others)
2012 Nucleic Acids Research  
InterPro has utility in the large-scale analysis of whole genomes and metagenomes, as well as in characterizing individual protein sequences.  ...  interfaces and services.  ...  NEW CROSS-REFERENCES New cross-references have been added, linking InterPro entries to related enzyme and pathway information in the PRIAM (21), Reactome (22) , KEGG (23), MetaCyc (24) and UniPathway  ... 
doi:10.1093/nar/gks456 pmcid:PMC3378909 fatcat:oqmafftblfcmdgh4a3i4nzqpzu

InterPro in 2011: new developments in the family and domain prediction database

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+38 others)
2011 Nucleic Acids Research  
NEW CROSS-REFERENCES New cross-references have been added, linking InterPro entries to related enzyme and pathway information in the PRIAM (21), Reactome (22) , KEGG (23), MetaCyc (24) and UniPathway  ...  The existing cross-references to InterPro entries and GO annotations are also provided, as in the current version of InterProScan.  ... 
doi:10.1093/nar/gkr948 pmid:22096229 pmcid:PMC3245097 fatcat:awtdl7qobjhnveofe7jxno6ju4

PDBe: Protein Data Bank in Europe

S. Velankar, Y. Alhroub, A. Alili, C. Best, H. C. Boutselakis, S. Caboche, M. J. Conroy, J. M. Dana, G. van Ginkel, A. Golovin, S. P. Gore, A. Gutmanas (+21 others)
2010 Nucleic Acids Research  
The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank  ...  In addition, the information available for structures determined by means of NMR spectroscopy has been expanded.  ...  depositing their structures and experimental data in the PDB and EMDB.  ... 
doi:10.1093/nar/gkq985 pmid:21045060 pmcid:PMC3013808 fatcat:732ckrjoq5afnk3jt2i7jwjcvy

The PIR-International Protein Sequence Database

D. George
1996 Nucleic Acids Research  
Since 1988 it has been maintained collaboratively by the PIR-International, an association of data collection centers engaged in international cooperation for the development of this research resource  ...  controlled, and well-organized protein sequence database.  ...  This publication was supported in part by grant number P41 LM05798 from the National Library of Medicine.  ... 
doi:10.1093/nar/24.1.17 pmid:8594572 pmcid:PMC145575 fatcat:x24ghg3fnzd55cluciiwo33hbm

Reactome pathway analysis: a high-performance in-memory approach

Antonio Fabregat, Konstantinos Sidiropoulos, Guilherme Viteri, Oscar Forner, Pablo Marin-Garcia, Vicente Arnau, Peter D'Eustachio, Lincoln Stein, Henning Hermjakob
2017 BMC Bioinformatics  
The first step, finding out whether an identifier in the user's sample corresponds to an entity in Reactome, is addressed using a radix tree as a lookup table.  ...  The second step, modelling the proteins, chemicals, their orthologous in other species and their composition in complexes and sets, is addressed with a graph.  ...  GV developed the input parser. OF offered technical support and developed the part of the service related to data storage and management.  ... 
doi:10.1186/s12859-017-1559-2 pmid:28249561 pmcid:PMC5333408 fatcat:b5h3jwolbvepjfiwp4dyecfi3a

DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

Brad T Sherman, Da Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki
2007 BMC Bioinformatics  
The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively  ...  Description: The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources  ...  Acknowledgements The authors are grateful to the referees for their constructive comments and thank David Bryant in the ABCC group for web server support.  ... 
doi:10.1186/1471-2105-8-426 pmid:17980028 pmcid:PMC2186358 fatcat:c4prreos5nhfbhkeiwn62zuxym

Fast and efficient searching of biological data resources--using EB-eye

F. Valentin, S. Squizzato, M. Goujon, H. McWilliam, J. Paern, R. Lopez
2010 Briefings in Bioinformatics  
The data resources represented in the EB-eye include: nucleotide and protein sequences at both the genomic and proteomic levels, structures ranging from chemicals to macro-molecular complexes, gene-expression  ...  He specialises in the development and implementation of Web Services technologies and programmatic interface design and testing.  ...  In addition, the cross-references are checked against the know cross-references for the data resource.  ... 
doi:10.1093/bib/bbp065 pmid:20150321 pmcid:PMC2905521 fatcat:qebowfm43fauvno5ncgtxe5dom

The PIR-International Protein Sequence Database

W. Barker
1998 Nucleic Acids Research  
Since 1988 it has been maintained collaboratively by the PIR-International, an association of data collection centers engaged in international cooperation for the development of this research resource  ...  controlled, and well-organized protein sequence database.  ...  This publication was supported in part by grant number P41 LM05798 from the National Library of Medicine.  ... 
doi:10.1093/nar/26.1.27 pmid:9399794 pmcid:PMC147240 fatcat:mpbgtbyxa5bvvobxtyg2euuk6y

CRONOS: the cross-reference navigation server

Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, H.-Werner Mewes, Andreas Ruepp
2008 Computer applications in the biosciences : CABIOS  
In total, up to 18 different identifier types can be used for identification of cross-references.  ...  The quality of the mapping could be improved substantially by exclusion of ambiguous gene and protein names which were manually validated.  ...  In the past different approaches like calculating sequence identity or molecule names were used to cross-reference identifiers.  ... 
doi:10.1093/bioinformatics/btn590 pmid:19010804 pmcid:PMC2638938 fatcat:asaoknrz6nc2ndfcsltmyv7isi
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