dkNET community events and announcements in August, 2020

Dear dkNET Community,

dkNET provides updates on activities of interest to the NIDDK-supported community. You could keep up to date on these activities through our Twitter feed @dkNET_info, through our Community Calendar, or through dkNET e-mail list. If you have an event or funding opportunities you'd like to advertise, please contact us info_at_dknet.org.

dkNET News

• Congratulations to Dr. Chun-Nan Hsu and co-authors from the dkNET team, RRID team, FAIR Data Informatics Lab at University of California San Diego, and collaborators at National Central University in Taiwan on publishing a new preprint "Antibody Watch: Text Mining Antibody Specificity from the Literature"! The preprint can be downloaded at https://arxiv.org/abs/2008.01937

• dkNET Webinar series: The slides of the dkNET's webinar "Live Demo of the dkNET Signaling Pathways Project", presented by Dr. Neil McKenna, can be downloaded at dkNET SlideShare. Hypothesis generation using SPP coronavirus infection consensomes tutorial is also available at https://youtu.be/jqyvHsORCZ0.

• Signaling Pathways Project (SPP) team has updated the preprint (4th version) "A transcriptional regulatory atlas of coronavirus infection of human cells" on bioRXiv. SPP has also collaborated with the NDEx project to make the coronavirus transcriptional networks available as Cytoscape-style networks.

• Congratulations to dkNET principal investigator Dr. Maryann Martone and all the authors on publishing a new National Academy of Sciences report " Life Cycle Decisions for Biomedical Data: The Challenge of Forecasting Costs". You can read it online or download the prepublication version now.

• The slides of the Research Data Alliance (RDA) webinar "What do you really know about that antibody? Ask dkNET", presented by Dr. Maryann Martone, are now available at dkNET SlideShare.

• New Resources added to dkNET

• • Pancreatlas (RRID:SCR_018567) contains a collection of human pancreas data and images. It is a platform to share data from human pancreas samples. It houses reference datasets from human pancreas samples, achieved through the generosity of organ donors and their families.

• • Nanotomy (RRID:SCR_018565) contains large scale electron microscopy datasets for Human Type 1 Diabetes.

• • Alberta Diabetes Institute IsletCore database (RRID:SCR_018566) contains a collection of data from all pancreatic islet isolations.

• • piNET (RRID:SCR_018693) is a web platform for downstream analysis and visualization of proteomics data. It server that facilitates integrated annotation, analysis, and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. The primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.

• • Signaling Pathways Project (RRID:SCR_018412) is a web multi-omics knowledgebase based upon the public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes, and transcription factors. It is an integrated omics knowledgebase for mammalian cellular signaling pathways. The web browser interface was designed to accommodate numerous routine data mining strategies. Its datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available.

• • METAGENOTE (RRID:SCR_018494) provides a quick and intuitive way to annotate data from genomics studies including microbiome. It is a project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. It contains collection of METAdata of GEnomics studies on web-based NOTEbook. The metadata is stored in a centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via the NCBI Sequence Read Archive (SRA) repository.

Events in August, 2020

Funding opportunities information and deadlines in August, 2020