? Resource Informatics Core Pathway Commons (PC) is a convenient single point of access for all publicly accessible pathway information in the standard BioPAX format. The long-term vision is to achieve a complete computable map of the cell across all species and conditions.
We aim to provide for the efficient exchange of pathway data; aggregation and integration into a shared public information store; distribution in a value-added, standardized form; and availability to the end-user in the context of domain-specific portals, such as genomics, model organism and bioinformatics web portals, via state-of-the-art internet web service technology. This Resource Informatics Core supports the Resource Project and is supported by the Management, Dissemination, and Training Core. The Resource Informatics Core aims to produce and disseminate PC as a high quality, accessible and stable informatics resource over time. We also aim to develop novel ways to increase efficiency and promote sustainability and maintainability beyond the award. Specific outputs include the PC website for querying pathway data and analyzing user data, web service, download site, the BioPAX standard and associated software libraries and tools. Twelve major pathway and molecular interaction databases will be supported in the upcoming PC release and over twenty additional databases are scheduled for inclusion in this proposal. Our informatics core specific aims are to 1) provide next-generation user-centric access to the PC resource and continuously aggregate, validate, and integrate pathways from major available sources; 2) work with data and tool providers and users to disseminate and improve the resource; and 3) work towards increased efficiency and sustainability of Pathway Commons and the pathway resource ecosystem.
| Ebhardt, H Alexander; Root, Alex; Liu, Yansheng et al. (2018) Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer. NPJ Syst Biol Appl 4:26 |
| Liyanage, Sanduni U; Hurren, Rose; Voisin, Veronique et al. (2017) Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML. Blood 129:2657-2666 |
| Michailidou, Kyriaki (see original citation for additional authors) (2017) Association analysis identifies 65 new breast cancer risk loci. Nature 551:92-94 |
| Milne, Roger L (see original citation for additional authors) (2017) Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer. Nat Genet 49:1767-1778 |
| Tong, Jiefei; Helmy, Mohamed; Cavalli, Florence M G et al. (2017) Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome, and tyrosine-phosphatome in acute myeloid leukemia. Proteomics 17: |
| Helmy, Mohamed; Crits-Christoph, Alexander; Bader, Gary D (2016) Ten Simple Rules for Developing Public Biological Databases. PLoS Comput Biol 12:e1005128 |
| Kusebauch, Ulrike; Campbell, David S; Deutsch, Eric W et al. (2016) Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell 166:766-778 |
| Luna, Augustin; Babur, Özgün; Aksoy, Bülent Arman et al. (2016) PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinformatics 32:1262-4 |
| Jones, Robert A; Robinson, Tyler J; Liu, Jeff C et al. (2016) RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation. J Clin Invest 126:3739-3757 |
| Kucera, Mike; Isserlin, Ruth; Arkhangorodsky, Arkady et al. (2016) AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations. F1000Res 5:1717 |
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