Archive for the ‘E-Science’ Category
The 22nd annual edition of the Nucleic Acids Research Database Issue features nine free full-text papers from NCBI staff that present recent updates to the databases, including GenBank, Gene, and RefSeq. These papers describe the state of NCBI databases as well as future plans to improve their use, from new reference resources created to improve the usability of viral sequence data to in-house curation efforts in the Conserved Domain Database, and much more. The articles are all available from PubMed.
The National Institutes of Health (NIH) launched two more funding opportunities to support NIH Big Data to Knowledge (BD2K) Initiative Research Education for developing educational resources for information professionals.
This funding announcement seeks applications for the development of a Massive Open Online Course (MOOC) that covers a comprehensive set of topics related to the management of biomedical Big Data. The primary audience for this course is librarians and information specialists, who could use these materials as the basis of training and services to graduate students, faculty, research staff and administrators at their organizations. However, the resource should also be usable by any of these audiences for self-instruction. The application due date is March 17, 2015.
This funding announcement seeks applications for the development of curriculum modules that can be used by librarians and other information specialists to prepare researchers, graduate students and research staff to be full participants in the global community that maintains and accesses digitally-stored biomedical Big Data. The application due date is March 17, 2015.
The National Library of Medicine’s (NLM) ChemIDplus resource is a dictionary of over 400,000 chemicals (names, synonyms, and structures). It includes links to NLM and to other databases and resources, including ones to federal, state and international agencies. You can draw a chemical structure and search for similar substances using the ChemIDplus Advanced search interface. This feature also performs similarity and substructure searches. A four-minute tutorial is available for using the drawing feature of ChemIDplus. The ChemIDplus Lite interface is designed for simple searching on name or registry number.
The NIH has issued a Request for Information (RFI) on the NIH Big Data to Knowledge (BD2K) Initiative Resources for Teaching and Learning Biomedical Big Data Management and Data Science, with a submission deadline of December 31, 2014. As part of its Big Data to Knowledge (BD2K) Initiative, NIH wishes to help the broader scientific community update knowledge and skills in the important areas of the science, storage, management and sharing of biomedical big data, and wants to identify the array of timely, high quality courses and online learning materials already available on data science and data management topics for biomedical big data. With this RFI Notice, the NIH invites interested and knowledgeable persons to inform NIH about existing learning resources covering Biomedical Big Data management and data science topics. All responses must be submitted electronically by December 31, 2014, in the form of an email, using the subject “data management.” PPT files or other curriculum materials should not be attached to responses. Responses are welcome from associations and professional organizations as well as individual stakeholders.
The HIV-1, human interaction database has been updated and is now on an improved page. The improved interface includes help documentation and supports structured queries against Gene, as well as browsing, filtering and downloading the protein and replication interaction data sets. The most recent data release (June 2014) includes 12,785 HIV-1, human protein-protein interactions for 3,142 human genes and 1,316 replication interactions for 1,250 human genes. The HIV-1, human interactions project, collates published reports of two types of interactions – HIV-1, human protein interactions, and human gene knock-downs that affect virus replication which are reported as “replication interactions.”
September 16, 2004 is a special day in the history of PubChem. It marks the beginning of PubChem as an on-line resource! Now fast forward ten years. PubChem provides information daily to many tens of thousands of users. Despite the passage of time, PubChem’s primary mission remains the same: providing comprehensive information on the biological activities of chemical substances.
Providing chemical information to researchers in the biomedical science community is a key part of PubChem’s purpose. Over the years, PubChem introduced and incrementally developed several interfaces, each with its own distinct purpose and set of use cases. Primary to these is the Entrez search interface, where PubChem is organized as three distinct databases: Substance, Compound, and BioAssay. Substance provides substance descriptions (accession number: SID), Compound provides the unique small-molecule chemical content of Substance (accession number: CID), and BioAssay provides biological experiment results for substances (accession number: AID). Each of these databases has an advanced search interface and contain numerous indexes and filters, which can be combined to construct elaborate queries. Additional interfaces exist to search and analyze information in PubChem, including the ability to analyze bioactivity information, download chemical and assay data, search by chemical structure or protein sequence, navigate using integrated classifications, visualize chemical 3-D information, and more.
PubChem continues to evolve the way it provides on-line content. External search engines (like Google, Bing, and others) are now a key way in which researchers locate data. In addition, programmatic interfaces now account for a significant portion of PubChem’s overall usage (+50%). Key programmatic interfaces to PubChem include Entrez Utilities and PUG/REST.
The full RefSeq release 67 is now available on the NCBI FTP site with over 61 million records describing 45,166,402 proteins; 8,163,775 RNAs; and sequences from 41,913 different NCBI TaxIDs. More details about the RefSeq release 67 are included in the release statistics and release notes. In addition, reports indicating the accessions included in the release and the files installed are available.
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The National Institutes of Health (NIH) has issued a Request for Information (RFI) seeking comments and ideas to inform the creation of an NIH Standards Information Resource (NSIR) that would collect, organize, and make available to the public trusted, systematically organized, and curated information about data-related standards. This resource would focus on those standards that are widely used in biomedical research and related activities. The main purpose of the NSIR would be to help a variety of biomedical users such as researchers, clinicians, data curators, and informaticians, among others, identify and choose data-related standards that are best suited to their needs.
NIH seeks responses to the RFI from biomedical researchers, librarians and information scientists, bioinformaticians, publishers, and other interested individuals. All responses must be submitted electronically to BD2K_NSIR_RFI@mail.nih.gov by September 30, 2014. Please include the Notice number NOT-CA-14-053 in the subject line. Responses to this RFI Notice are voluntary. The submitted information will be reviewed by the NIH staff. Submitted information will be considered confidential.
Genomic research advances our understanding of factors that influence health and disease, and sharing genomic data provides opportunities to accelerate that research through the power of combining large and information-rich datasets. To promote sharing of human and non-human genomic data and to provide appropriate protections for research involving human data, the National Institutes of Health (NIH) issued the Genomic Data Sharing (GDS) Policy on August 27, 2014. The GDS Policy takes effect for grant applications with due dates on or after January 25, 2015, for contracts submitted on or after January 25, 2015, and for intramural research projects generating genomic data on or after January 25, 2015. NIH has also issued a press release regarding the GDS Policy. A publication describing the use and impact of the NIH database for Genotypes and Phenotypes (dbGaP) data under the Policy for Sharing of Data Obtained in NIH Supported or Conducted Genome-Wide Association Studies, from 2007 through 2013, has been published in Nature Genetics.
At this month’s Library Assessment Conference held in Seattle, one panel featured assessment librarians presenting data dashboards they created using Tableau software, Tableau Unleashed: Visualizing Library Data. This presentation includes views of dashboards from University of British Columbia Library (by presenter Jeremy Buhler), UMass Amherst Libraries (by Rachel Lewellen), and Ohio State Libraries (by Sarah Murphy). All of the presenters used Tableau software to produce their dashboards.
Tableau may be the most popular software for creating dashboards right now and the company offers a free version that has a great deal of functionality. In fact, at least one presenter (Sarah Murphy) included dashboards she created using Tableau Public. However, users must be cautioned that any data entered into Tableau Public become public information. That means anyone can see and download your raw data. So, if you use it, be sure all identifying information about individuals is stripped from your files and that you are comfortable with other people downloading your raw data. The presenters also mentioned tips for dashboard design. For additional design guidance, check out the freely downloadable resource A Guide to Creating Dashboards People Love to Use by Juice Analytics.