Archive for the ‘E-Science’ Category
Both versions of TOXMAP, classic and beta, now include the Toxics Release Inventory (TRI) 2013 National Analysis data, as well as recent cancer and disease mortality data from NCI SEER. This is the first version of the TOXMAP beta with health data, whereas mortality data in TOXMAP classic has been updated. To view national county-level cancer and disease mortality data from 2007-2011 in TOXMAP beta, bring up the US Census & Health Data window and navigate to the Mortality tab. Two sub-tabs list cancer and disease mortality layers that can be overlaid on the map (one at a time).
TOXMAP maps the TRI chemicals reported to the EPA, as required by the Emergency Planning and Community Right to Know Act (EPCRA). A complete list of TRI chemicals required to be reported to the EPA can be found on the Toxics Release Inventory (TRI) Program website.
Fifty years ago, Marshall W. Nirenberg, PhD, deciphered the genetic code. It led to a Nobel Prize—the first for a scientist at the National Institutes of Health. Dr. Nirenberg’s family recently donated his Nobel Prize medal to the National Library of Medicine to be added to the papers and other items that chronicle his contributions to science. NLM’s History of Medicine Division hosted the first of three events at NIH that will celebrate the legacy of Marshall Nirenberg, who died in 2010, and the fiftieth anniversary of his deciphering of the genetic code. Subsequent events will be announced by the NIH Office of Intramural Research.
A Tribute to Marshall Nirenberg was filled with personal stories from his wife; from a scientist in his lab; and from a historian who helped develop NLM’s Nirenberg collection. The event, held March 17, was recorded and can be viewed on demand. One of the most significant pieces in the Nirenberg collection is the chart that is the first summary of the genetic code. Dated January 18, 1965, when more than half of the code had been deciphered, the document, with curatorial notes provided by Serlin, was recently added to NLM’s Turning the Pages project, which is available online and as an iPad app. Dr. Nirenberg won the Nobel Prize for Physiology or Medicine in 1968. He shared the award with Har Gobind Khorana of the University of Wisconsin and Robert W. Holley of the Salk Institute.
A new Big Data to Knowledge (BD2K) funding opportunity is available, Supplements to Support Interoperability of NIH Funded Biomedical Data Repositories, with an April 20 application due date. NIH is accepting administrative supplement requests to support projects that will establish or improve interoperability among NIH funded biomedical data repositories. Improved interoperability is expected to lead to increased efficiency of repositories’ operations and cost reductions, which are significant factors of the NIH’s long-term sustainability plans for the biomedical data repositories. Each supplement request should be associated to a collaborative project consisting of a biomedical data repository supported by an active NIH-funded parent grant, and one or more collaborating sites that together implement the interoperability goals of this FOA. The collaborating sites may be other biomedical data repositories, or may provide computational tools and data standards, or perform other activities that facilitate interoperability among data repositories. Supplement requests will only be accepted from active NIH-funded parent grants that primarily support biomedical data repositories with an overall annual budget above $500,000 in direct costs.
Valentina di Francesca (NHGRI) will be organizing an administrative review panel for these supplements as a group. Administrative review is expected to occur in May 2015, and completed by August 24, 2015. Awards are expected to be made in August/September 2015.
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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