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      Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines

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          Abstract

          Protein quantification at proteome‐wide scale is an important aim, enabling insights into fundamental cellular biology and serving to constrain experiments and theoretical models. While proteome‐wide quantification is not yet fully routine, many datasets approaching proteome‐wide coverage are becoming available through biophysical and MS techniques. Data of this type can be accessed via a variety of sources, including publication supplements and online data repositories. However, access to the data is still fragmentary, and comparisons across experiments and organisms are not straightforward. Here, we describe recent updates to our database resource “PaxDb” (Protein Abundances Across Organisms). PaxDb focuses on protein abundance information at proteome‐wide scope, irrespective of the underlying measurement technique. Quantification data is reprocessed, unified, and quality‐scored, and then integrated to build a meta‐resource. PaxDb also allows evolutionary comparisons through precomputed gene orthology relations. Recently, we have expanded the scope of the database to include cell‐line samples, and more systematically scan the literature for suitable datasets. We report that a significant fraction of published experiments cannot readily be accessed and/or parsed for quantitative information, requiring additional steps and efforts. The current update brings PaxDb to 414 datasets in 53 organisms, with (semi‐) quantitative abundance information covering more than 300 000 proteins.

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          The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

          The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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            Activities at the Universal Protein Resource (UniProt)

            The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequences and functional annotation. It integrates, interprets and standardizes data from literature and numerous resources to achieve the most comprehensive catalog possible of protein information. The central activities are the biocuration of the UniProt Knowledgebase and the dissemination of these data through our Web site and web services. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.
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              Uberon, an integrative multi-species anatomy ontology

              We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org
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                Author and article information

                Contributors
                mering@imls.uzh.ch
                Journal
                Proteomics
                Proteomics
                10.1002/(ISSN)1615-9861
                PMIC
                Proteomics
                John Wiley and Sons Inc. (Hoboken )
                1615-9853
                1615-9861
                12 March 2015
                September 2015
                : 15
                : 18 , Focus on Quantitative Proteomics ( doiID: 10.1002/pmic.v15.18 )
                : 3163-3168
                Affiliations
                [ 1 ] Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics University of Zurich Switzerland
                Author notes
                [*] [* ] Correspondence: Dr. Christian von Mering, Institute of Molecular Life Sciences and Swiss, Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland

                E‐mail: mering@ 123456imls.uzh.ch

                [†]

                These authors contributed equally.

                Article
                PMIC8073
                10.1002/pmic.201400441
                6680238
                25656970
                eb9850cb-16e4-47d8-aeb0-364570285cf2
                © 2015 The Authors. PROTEOMICS published by Wiley‐VCH Verlag GmbH & Co. KGaA, Weinheim.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 17 September 2014
                : 20 December 2014
                : 30 January 2015
                Page count
                Figures: 3, Tables: 0, Pages: 6, Words: 3740
                Categories
                Technical Brief
                Technical Brief
                Technical Brief
                Custom metadata
                2.0
                pmic8073
                September 2015
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.7 mode:remove_FC converted:05.08.2019

                Molecular biology
                absolute protein abundance,bioinformatics,evolution,spectral counting
                Molecular biology
                absolute protein abundance, bioinformatics, evolution, spectral counting

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