ArticleBMC bioinformatics2007
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
54 citing papers in PubMed.
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- Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis.International journal of molecular sciences · 2020Review
- Evolving knowledge graph similarity for supervised learning in complex biomedical domains.BMC bioinformatics · 2020Article
- Reactome pathway analysis: a high-performance in-memory approach.BMC bioinformatics · 2017Article
- Data integration in biological research: an overview.Journal of biological research (Thessalonike, Greece) · 2015Review
- Tools for visualization and analysis of molecular networks, pathways, and -omics data.Advances and applications in bioinformatics and chemistry : AABC · 2015Review
- State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.Journal of proteome research · 2014Article
- G-Links: a gene-centric link acquisition service.F1000Research · 2014Article
- Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning--a word of caution.PloS one · 2014Article
- BridgeDb app: unifying identifier mapping services for Cytoscape.F1000Research · 2014Article
- A genomic-scale artificial microRNA library as a tool to investigate the functionally redundant gene space in Arabidopsis.The Plant cell · 2013Article
- UniChem: a unified chemical structure cross-referencing and identifier tracking system.Journal of cheminformatics · 2013Article
- Article
- Interactome3D: adding structural details to protein networks.Nature methods · 2013Article
- Design and application of a data-independent precursor and product ion repository.Journal of the American Society for Mass Spectrometry · 2012Article
- AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities.BMC bioinformatics · 2012Article
- Improvements in the Protein Identifier Cross-Reference service.Nucleic acids research · 2012Article
- The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools.BMC bioinformatics · 2012Article
- Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome.Journal of clinical bioinformatics · 2012Article
- MRMaid: The SRM Assay Design Tool for Arabidopsis and Other Species.Frontiers in plant science · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEach major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. 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 source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs.
resultsWe 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 UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface.
conclusionWe offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.