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The PRIDE database and related tools and resources in 2019: improving support for quantification data

Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher, Enrique Pérez, Julian Uszkoreit (+11 others)
2018 Nucleic Acids Research  
In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016.  ...  Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format.  ...  At last, we would like to thank all data submitters and collaborators for their contributions. FUNDING  ... 
doi:10.1093/nar/gky1106 pmid:30395289 fatcat:rzamufx42bcrnf6a2pcp64aoee

Abstracts from HSG 2019

2019 Neurotherapeutics  
Areas where there are not enough support or resources include care given outside of the clinic, such as in home care, and training non-specialists in how to care for people with Huntington's Disease.  ...  Enhancing resources for both formal and informal care for patients and families should be a central goal for HD organizations.  ...  care in the future, would have the necessary tools and resources.  ... 
doi:10.1007/s13311-019-00788-3 pmid:31595435 pmcid:PMC6985315 fatcat:z36763kxpfabvnn532hxglmvxe

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

2019 Nucleic Acids Research  
Since then, in addition to the four PX existing members at the time (PRIDE, PeptideAtlas including the PASSEL resource, MassIVE and jPOST), two new resources have joined PX: iProX (China) and Panorama  ...  At the end of June 2019, more than 14 100 datasets had been submitted to PX resources since 2012, and from those, more than 9 500 in just the last three years.  ...  ACKNOWLEDGEMENTS The ProteomeXchange partners would like to thank all data submitters and collaborators for their contributions. FUNDING  ... 
doi:10.1093/nar/gkz984 pmid:31686107 pmcid:PMC7145525 fatcat:nvick5so3bgcndkofvl2irwzgy

Western Medical Research Conference 2019 (Formerly Western Regional Meeting) Camel, California, January 24–26 2019

2019 Journal of Investigative Medicine  
Using the low end of the cost range for each antibiotic, the median cost difference in the 25 to <30, 35 to <40, 45 to <50, and 75 to <80 year age groups were significantly greater by $3, $7, $18, and  ...  Using the data collected in our multi-institutional CH-STRONG survey-based study, we examine CHD women's reproductive history, health concerns, and discussions with care providers; assess whether results  ...  The data supported continued efforts to use RESpect in the setting of childhood NHL diagnosis. The work was supported by the St. Baldrick's and Chun Foundations, MD007584 and MD007601.  ... 
doi:10.1136/jim-2018-000939.64 fatcat:cfvir6qxcfghjf6nzfbrgix54q

Correction to: Abstracts for MASCC/ISOO Annual Meeting 2019

Irina Bespalova
2019 Supportive Care in Cancer  
Missing abstracts in the original paper.  ...  Conclusions Preliminary evidence seems to support TCM as supportive therapy to alleviate treatment-related symptoms and improve health status in children with cancer.  ...  , appropriate, specific and timely support for clinicians in the field.  ... 
doi:10.1007/s00520-019-05043-1 pmid:31468193 fatcat:deceaiuyirbvphf4phfy2laxbq

2019 Women in Sport and Exercise Conference Abstracts

2020 Women in Sport & Physical Activity Journal  
educational resource specifically designed for Generation Z on the issues relating to gender equality and equal opportunities in sport.  ...  This Mum Moves (TMM) is a project aiming to support women to be active throughout motherhood by providing health care profressionals with the tools (training and resources) to deliver physical activiry  ... 
doi:10.1123/wspaj.2020-0011 fatcat:edd42t5ucbcc7nl6jvbp2tvmya

Quantifying the impact of public omics data

Yasset Perez-Riverol, Andrey Zorin, Gaurhari Dass, Manh-Tu Vu, Pan Xu, Mihai Glont, Juan Antonio Vizcaíno, Andrew F. Jarnuczak, Robert Petryszak, Peipei Ping, Henning Hermjakob
2019 Nature Communications  
Finally, we propose a set of recommendations for authors, journals and data resources to promote an optimal quantification of the impact of datasets.  ...  In 2016, we released the first version of the Omics Discovery Index (OmicsDI) as a light-weight system to aggregate datasets across multiple public omics data resources.  ...  Finally, we propose a set of recommendations for authors, journals and data resources to promote an optimal quantification of the impact of datasets. Results Omics data reanalysis and citations.  ... 
doi:10.1038/s41467-019-11461-w pmid:31383865 pmcid:PMC6683138 fatcat:gbh7v4yiwnahpfznf2xljmyuka

Integrative Systems Biology Resources and Approaches in Disease Analytics [chapter]

Marco Fernandes, Holger Husi
2019 Systems Biology [Working Title]  
Here, we will describe several database resources, standalone and web-based tools applied in disease analytics workflows based in data-driven integration of outputs of multi-omic detection platforms.  ...  a single database framework, instead of search and fetch a single component at time across a scatter of databases resources.  ...  The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.  ... 
doi:10.5772/intechopen.84834 fatcat:szdavjmg2jbwpnjl2irao6ehty

In Silico Tools and Phosphoproteomic Software Exclusives

Paul, Muthu, Chilukuri, Haga, Chun, Oh
2019 Processes  
For meaningful solutions and deliverables, these tools need to be implemented in clinical studies for obtaining answers to pharmacodynamic questions, saving time, costs and energy.  ...  The gap between development of bioinformatics tools and their implementation in clinical research is highlighted.  ...  Other basic databases for proteins and genes include: UniProt Knowledgebase, Entrez tools such as PANTHER, DAVID, KEGG, and IPA, have been improved for data mapping.  ... 
doi:10.3390/pr7120869 fatcat:cvcyyncprzaexde433uashoco4

Meeting the challenge of developing food crops with improved nutritional quality and food safety: leveraging proteomics and related omics techniques

Shalu Jain, Anjana Rustagi, Deepak Kumar, Mohd Aslam Yusuf, Shashi Shekhar, Neera Bhalla Sarin
2019 Biotechnology Letters  
Food safety is another important issue where proteomics and related platforms can offer solution for absolute quantitation of food allergens and mycotoxins present in the plant-based food.  ...  In this review, we briefly describe how proteomics techniques can potentially be used for improving the nutrient profile of major crops, through high throughput multiplexed assays.  ...  Acknowledgements This work was supported by partial  ... 
doi:10.1007/s10529-019-02655-9 fatcat:pus3s6bmvzbgzevl5okaucnqui

A Primer on Data Analytics in Functional Genomics: How to Move from Data to Insight?

Piotr Grabowski, Juri Rappsilber
2019 TIBS -Trends in Biochemical Sciences. Regular ed  
This is now changing with the appearance of resources to help bench-side biologists become skilled at computational data analysis and handling large omics data sets.  ...  Here, we show an entry route into the field of omics data analytics. We provide information about easily accessible data sources and suggest some first steps for aspiring computational data analysts.  ...  Acknowledgments We would like to thank Francis O'Reilly and Sven Giese for critically reading the manuscript and their helpful suggestions.  ... 
doi:10.1016/j.tibs.2018.10.010 pmid:30522862 pmcid:PMC6318833 fatcat:6sbywhr27zcvfjbr7cmyjxy7hq

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Farhana R. Pinu, David J. Beale, Amy M. Paten, Konstantinos Kouremenos, Sanjay Swarup, Horst J. Schirra, David Wishart
2019 Metabolites  
Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics  ...  As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with  ...  Acknowledgments: The authors would like to thank the organizing committee of ANZMET 2018. Conflicts of Interest: The authors declare no conflict of interest. Metabolites 2019, 9, 76  ... 
doi:10.3390/metabo9040076 pmid:31003499 pmcid:PMC6523452 fatcat:deiwu7rgpnb3tfr7glbewoyar4

piNET: a versatile web platform for downstream analysis and visualization of proteomics data [article]

Behrouz Shamsaei, Szymon Chojnacki, Marcin Pilarczyk, Mehdi Najafabadi, Chuming Chen, Karen Ross, Andrea Matlock, Jeremy Muhlich, Somchai Chutipongtanate, Dusica Vidovic, Vagisha Sharma, Juozas Vasiliauskas (+8 others)
2019 bioRxiv   pre-print
On the other hand, tools for downstream analysis, interpretation and visualization of proteomics data sets, in particular those involving PTMs, require further improvement and integration to accelerate  ...  Computational methods and tools to identify and quantify peptides, proteins and post-translational modifications (PTMs) that are captured in modern mass spectrometers have matured over the years.  ...  of databases, tools and resources for proteomics research (7) .  ... 
doi:10.1101/607432 fatcat:d5yluyxpyfbpzoqksczhun3zwe

Data from differentially expressed proteins in platelet components associated with adverse transfusion reactions

Chaker Aloui, Céline Barlier, Danielle Awounou, Stéphane Claverol, Jocelyne Fagan, Fabrice Cognasse, Olivier Garraud, Sandrine Laradi
2019 Data in Brief  
The reported data herein have been deposited into the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD003510 for the pooled platelet components (PPCs) and PXD008886  ...  The presented dataset was used for the study focused on the search for differentially expressed proteins in blood platelet components (PCs) associated with adverse transfusion reactions (ATRs).  ...  We also thank the blood donors for agreeing to take part in this study.  ... 
doi:10.1016/j.dib.2019.104013 pmid:31297409 pmcid:PMC6598860 fatcat:tochldm3pvg57e36tqa7yi4fym

Quantitative proteome landscape of the NCI-60 cancer cell lines

Tiannan Guo, Augustin Luna, Vinodh N. Rajapakse, Ching Chiek Koh, Zhicheng Wu, Wei Liu, Yaoting Sun, Huanhuan Gao, Michael P. Menden, Chao Xu, Laurence Calzone, Loredana Martignetti (+27 others)
2019 iScience  
In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses.  ...  Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry.  ...  Jerry Collins and Dr. James H. Doroshow) for sharing the drug data and supporting for data acquisition from the DTP to the CellMiner team.  ... 
doi:10.1016/j.isci.2019.10.059 pmid:31733513 pmcid:PMC6889472 fatcat:j4w2gpvfvbhydmhouvykp5quba
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