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neXtProt, a new knowledgebase on human proteins

Lydie Lane, Lydie Lane
2010 Nature Precedings  
Olivier Evalet, Anne Gleizes, Alain Gateau, Alexandre Masselot (GeneBio) • Research : Guido Bologna, Anne-Lise Veuthey • Project direction : Amos Bairoch, Lydie Lane, Nasri Nahas (Genebio) is developed  ... 
doi:10.1038/npre.2010.5104.1 fatcat:h5tjjfdg4jatjip7exd7rc7mly

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

Michel Schneider, Lydie Lane, Emmanuel Boutet, Damien Lieberherr, Michael Tognolli, Lydie Bougueleret, Amos Bairoch
2009 Journal of Proteomics  
The UniProt knowledgebase, UniProtKB, is the main product of the UniProt consortium. It consists of two sections, UniProtKB/Swiss-Prot, the manually curated section, and UniProtKB/TrEMBL, the computer translation of the EMBL/GenBank/DDBJ nucleotide sequence database. Taken together, these two sections cover all the proteins characterized or inferred from all publicly available nucleotide sequences. The Plant Proteome Annotation Program (PPAP) of UniProtKB/Swiss-Prot focuses on the manual
more » ... ion of plant-specific proteins and protein families. Our major effort is currently directed towards the two model plants Arabidopsis thaliana and Oryza sativa. In UniProtKB/Swiss-Prot, redundancy is minimized by merging all data from different sources in a single entry. The proposed protein sequence is frequently modified after comparison with ESTs, full length transcripts or homologous proteins from other species. The information present in manually curated entries allows the reconstruction of all described isoforms. The annotation also includes proteomics data such as PTM and protein identification MS experimental results. UniProtKB and the other products of the UniProt consortium are accessible online at www.uniprot.org.
doi:10.1016/j.jprot.2008.11.010 pmid:19084081 pmcid:PMC2689360 fatcat:emmux5erffecnl5qjpjth4l5f4

Proteomics Pioneer Award 2013: Professor Amos Bairoch, University of Geneva, Switzerland*

Frederique Lisacek, Lydie Lane
2014 EuPA Open Proteomics  
doi:10.1016/j.euprot.2013.12.002 fatcat:4ykanzbmu5hijp6wirbfgviyv4

Converting neXtProt into Linked Data and nanopublications

Christine Chichester, Oliver Karch, Pascale Gaudet, Lydie Lane, Barend Mons, Amos Bairoch
2015 Semantic Web Journal  
neXtProt provides a comprehensive knowledgebase on human proteins complemented by an extensive cross incorporation of annotations from many databases. With the diversity of published data, provenance information becomes critical to providing reliable and trustworthy services to scientists, thus the tracking of provenance in open, decentralized systems is especially important. Since the nanopublication system addresses many of these challenges, we have developed the neXtProt Linked Data by
more » ... izing in RDF/XML annotations specific to neXtProt and started employing the nanopublication model to give appropriate attribution to all data. Specifically, a use case demonstrates the handling of post-translational modification (PTM) data modeled as nanopublications to illustrate how the different levels of provenance and data quality thresholds can be captured in this model.
doi:10.3233/sw-140149 fatcat:7m4nfnx7srde3j65a4kybowtbq

Devising a Consensus Framework for Validation of Novel Human Coding Loci

Elspeth A. Bruford, Lydie Lane, Jennifer Harrow
2015 Journal of Proteome Research  
Lane and Amos Bairoch (neXtProt 4 )).  ...  participating annotation resources (HAVA-NA, 3 neXtProt, 4 RefSeq, 5 and Swiss-Prot 6 ) prior to the workshop by the organizing committee (Jen Harrow (GENCODE 7 ), Elspeth Bruford (HGNC 8 ), and Lydie  ... 
doi:10.1021/acs.jproteome.5b00688 pmid:26367542 pmcid:PMC4765950 fatcat:qbkoa5dbzbanjnpd73evkqt2qq

The neXtProt peptide uniqueness checker: a tool for the proteomics community

Mathieu Schaeffer, Alain Gateau, Daniel Teixeira, Pierre-André Michel, Monique Zahn-Zabal, Lydie Lane, John Hancock
2017 Bioinformatics  
The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. Availability and implementation: The pepx program is available at https://github.com/calipho-sib/ pepx and can be launched from the command line or through a cgi web interface. Indexing requires a
more » ... nce file in FASTA format. The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/.
doi:10.1093/bioinformatics/btx318 pmid:28520855 pmcid:PMC5860159 fatcat:l3gqnsyllzapxhqj5cddt7nrrq

Querying NeXtProt Nanopublications and Their Value for Insights on Sequence Variants and Tissue Expression

Christine Chichester, Pascale Gaudet, Oliver Karch, Paul Groth, Lydie Lane, Amos Bairoch, Barend Mons, Antonis Loizou
2014 Social Science Research Network  
Understanding how genetic di↵erences between individuals impact the regulation, expression, and ultimately function of proteins is an important step toward realizing the promise of personal medicine. There are several technical barriers hindering the transition of biological knowledge into the applications relevant to precision medicine. One important challenge for data integration is that new biological sequences (proteins, DNA) have multiple issues related to interoperability potentially
more » ... ing a quagmire in the published data, especially when di↵erent data sources do not appear to be in agreement. Thus, there is an urgent need for systems and methodologies to facilitate the integration of information in a uniform manner to allow seamless querying of multiple data types which can illuminate, for example, the relationships between protein modifications and causative genomic variants. Our work demonstrates for the first time how semantic technologies can be used to address these challenges using the nanopublication model applied to the neXtProt data set, a curated knowledgebase of information about human proteins. We have applied the nanopublication model to demonstrate querying over several named graphs, including the provenance information associated with the curated scientific assertions from neXtProt. We show by the way of use cases using sequence variations, post-translational modifications (PTMs) and tissue expression, that querying the neXtProt nanopublication implementation is a credible approach for expanding biological insight.
doi:10.2139/ssrn.3199138 fatcat:qg2k2ldsgzellcg7jt4bvjueiy

Advances in the Chromosome-Centric Human Proteome Project: looking to the future

Young-Ki Paik, Gilbert S. Omenn, William S. Hancock, Lydie Lane, Christopher M. Overall
2017 Espert Review of Proteomics  
Lane.  ...  C-HPP made some efforts to secure a commitment to share raw MS/MS data through PXD and proteome-wide datasets for annotation across the C-HPP teams via neXtProt (led by Lydie Lane), and PeptideAtlas (led  ... 
doi:10.1080/14789450.2017.1394189 pmid:29039980 fatcat:sdejqopphrf73ksrjjp2fg3qjy

DERA is the human deoxyribose phosphate aldolase and is involved in stress response

Lisa Salleron, Giovanni Magistrelli, Camille Mary, Nicolas Fischer, Amos Bairoch, Lydie Lane
2014 BBA - Molecular Cell Research  
Deoxyribose-phosphate aldolase (EC 4.1.2.4), which converts 2-deoxy-D-ribose-5-phosphate into glyceraldehyde-3-phosphate and acetaldehyde, belongs to the core metabolism of living organisms. It was previously shown that human cells harbor deoxyribose phosphate aldolase activity but the protein responsible of this activity has never been formally identified. This study provides the first experimental evidence that DERA, which is mainly expressed in lung, liver and colon, is the human deoxyribose
more » ... phosphate aldolase. Among human cell lines, the highest DERA mRNA level and deoxyribose phosphate aldolase activity were observed in liver-derived Huh-7 cells. DERA was shown to interact with the known stress granule component YBX1 and to be recruited to stress granules after oxidative or mitochondrial stress. In addition, cells in which DERA expression was down-regulated using shRNA formed fewer stress granules and were more prone to apoptosis after clotrimazole stress, suggesting the importance of DERA for stress granule formation. Furthermore, the expression of DERA was shown to permit cells in which mitochondrial ATP production was abolished to make use of extracellular deoxyinosine to maintain ATP levels. This study unraveled a previously undescribed pathway which may allow cells with high deoxyribose-phosphate aldolase activity, such as liver cells, to minimize or delay stress-induced damage by producing energy through deoxynucleoside degradation.
doi:10.1016/j.bbamcr.2014.09.007 pmid:25229427 fatcat:2fu46j6lovf3lg46fbym62yjzi

Protein variety and functional diversity: Swiss-Prot annotation in its biological context

Brigitte Boeckmann, Marie-Claude Blatter, Livia Famiglietti, Ursula Hinz, Lydie Lane, Bernd Roechert, Amos Bairoch
2005 Comptes rendus. Biologies  
We all know that the dogma 'one gene, one protein' is obsolete. A functional protein and, likewise, a protein's ultimate function depend not only on the underlying genetic information but also on the ongoing conditions of the cellular system. Frequently the transcript, like the polypeptide, is processed in multiple ways, but only one or a few out of a multitude of possible variants are produced at a time. An overview on processes that can lead to sequence variety and structural diversity in
more » ... ryotes is given. The UniProtKB/Swiss-Prot protein knowledgebase provides a wealth of information regarding protein variety, function and associated disorders. Examples for such annotation are shown and further ones are available at http://www.expasy.org/sprot/tutorial/examples_CRB. To cite this article: B. Boeckmann et al., C. R. Biologies 328 (2005).  2005 Académie des sciences. Published by Elsevier SAS. All rights reserved. Résumé Un gène, plusieurs protéines : l'annotation de Swiss-Prot dans le contexte biologique. Il est maintenant évident pour tout le monde que le dogme « un gène, une protéine » est obsolète. Au cours de la synthèse d'une protéine fonctionnelle, le transcrit et la chaîne polypeptidique peuvent être modifiés de multiples façons. Ces modifications ont une incidence directe sur la fonction biologique de la protéine et dépendent non seulement de l'information génétique, mais également des conditions dans lesquelles se trouve la cellule : un nombre limité d'isoformes protéiques est produit dans une cellule donnée, à un moment précis. Cet article dresse un bref inventaire des processus biologiques impliqués dans la formation de protéines différentes à partir d'un même gène chez les eucaryotes, ainsi qu'une description des diversités structurelle et fonctionnelle qui en découlent. La banque de connaissances sur les protéines UniProtKB/Swiss-Prot est particulièrement riche en informations décrivant l'origine des différences entre les séquences de protéines dérivées d'un même gène, les modifications post-traductionnelles, ainsi que les conséquences de cette variabilité sur leur(s) fonction(s) et, le cas échéant, les maladies associées. De nombreux exemples
doi:10.1016/j.crvi.2005.06.001 pmid:16286078 fatcat:m72bsba2enfxdm5xue4shdtnua

C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved inbc1Complex Assembly and Supercomplex Stabilization

Marjorie Desmurs, Michelangelo Foti, Etienne Raemy, Frédéric Maxime Vaz, Jean-Claude Martinou, Amos Bairoch, Lydie Lane
2015 Molecular and Cellular Biology  
(D) Mitochondrion-enriched fractions from HeLa cells were digested by proteinase K in the absence (lane 2) or presence (lane 5) of saponin and analyzed by immunoblotting.  ...  Control samples were analyzed in lanes 1, 3, 4, and 6. C11orf83 was only digested by proteinase K in the presence of saponin (lane 5), indicating that C11orf83 is in the IM and faces the IMS.  ... 
doi:10.1128/mcb.01047-14 pmid:25605331 pmcid:PMC4355537 fatcat:ypaaqs35f5gxfeyy344k3nvdxq

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Heinz Stockinger, Adrian M. Altenhoff, Konstantin Arnold, Amos Bairoch, Frederic Bastian, Sven Bergmann, Lydie Bougueleret, Philipp Bucher, Mauro Delorenzi, Lydie Lane, Philippe Le Mercier, Frédérique Lisacek (+12 others)
2014 Nucleic Acids Research  
The SIB Swiss Institute of Bioinformatics (www.isbsib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years.
doi:10.1093/nar/gku380 pmid:24792157 pmcid:PMC4086091 fatcat:ps6txa3xijhpxbpl2radc6dvdi

Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression

Christine Chichester, Pascale Gaudet, Oliver Karch, Paul Groth, Lydie Lane, Amos Bairoch, Barend Mons, Antonis Loizou
2014 Journal of Web Semantics  
Understanding how genetic di↵erences between individuals impact the regulation, expression, and ultimately function of proteins is an important step toward realizing the promise of personal medicine. There are several technical barriers hindering the transition of biological knowledge into the applications relevant to precision medicine. One important challenge for data integration is that new biological sequences (proteins, DNA) have multiple issues related to interoperability potentially
more » ... ing a quagmire in the published data, especially when di↵erent data sources do not appear to be in agreement. Thus, there is an urgent need for systems and methodologies to facilitate the integration of information in a uniform manner to allow seamless querying of multiple data types which can illuminate, for example, the relationships between protein modifications and causative genomic variants. Our work demonstrates for the first time how semantic technologies can be used to address these challenges using the nanopublication model applied to the neXtProt data set, a curated knowledgebase of information about human proteins. We have applied the nanopublication model to demonstrate querying over several named graphs, including the provenance information associated with the curated scientific assertions from neXtProt. We show by the way of use cases using sequence variations, post-translational modifications (PTMs) and tissue expression, that querying the neXtProt nanopublication implementation is a credible approach for expanding biological insight.
doi:10.1016/j.websem.2014.05.001 fatcat:5s7em2vmvbanhfq5fmozvfjfau

Functional Identification of APIP as Human mtnB, a Key Enzyme in the Methionine Salvage Pathway

Camille Mary, Paula Duek, Lisa Salleron, Petra Tienz, Dirk Bumann, Amos Bairoch, Lydie Lane, Ferdinando Di Cunto
2012 PLoS ONE  
All lanes were loaded with 80 mg of cell lysate proteins. Anti a-tubulin (atub) was used as a loading control. The bands present below APIP were nonspecifically stained with the anti-APIP antibody.  ... 
doi:10.1371/journal.pone.0052877 pmid:23285211 pmcid:PMC3532061 fatcat:3awgdnznvnazzi57s6g6pgql7m

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0 [article]

Eric W Deutsch, Lydie Lane, Chris M Overall, Nuno Bandeira, Mark S Baker, Charles Pineau, Robert L Moritz, Fernando Corrales, Sandra Orchard, Jennifer E Van Eyk, Young-Ki Paik, Susan T Weintraub (+2 others)
2019 bioRxiv   pre-print
The Human Proteome Organization's (HUPO) Human Proteome Project (HPP) developed Mass Spectrometry (MS) Data Interpretation Guidelines that have been applied since 2016. These guidelines have helped ensure that the emerging draft of the complete human proteome is highly accurate and with low numbers of false-positive protein identifications. Here, we describe an update to these guidelines based on discussions with the wider HPP community over the past year. The revised Guidelines 3.0 address
more » ... ral major and minor identified gaps. The main checklist has been reorganized under headings and subitems and related guidelines have been grouped. We have added guidelines for emerging data independent acquisition (DIA) MS workflows and for use of the new Universal Spectrum Identifier (USI) system being developed by the HUPO Proteomics Standards Initiative (PSI). In addition, we discuss updates to the standard HPP pipeline for collecting MS evidence for all proteins in the HPP, including refinements to minimum evidence. We present a new plan for incorporating MassIVE-KB into the HPP pipeline for the next (HPP 2020) cycle in order to obtain more comprehensive coverage of public MS data sets. In sum, Version 2.1 of the HPP MS Data Interpretation Guidelines has served well and this timely update version 3.0 will aid the HPP as it approaches its goal of collecting and curating MS evidence of translation and expression for all predicted ~20,000 human proteins encoded by the human genome.
doi:10.1101/733576 fatcat:tge7sztiqbfqfk7zotktdhemjy
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