National Institutes of Health, National Library of Medicine (September, 1993). Factsheet. Bethesda, Maryland, U.S.A.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....article s original URL. vehicle accident [5] Record linkage (originally known as medical record linkage ) is now widely used in research in October 2002, a search of the biomedical literature via PubMed for medical record linkage as a Medical Subject Heading returned over 1,300 references [6]. The process of record linkage is trivial where the records that relate to the same entity or event all share a common, unique key or identifier an SQL equijoin operation, or its equivalent in other data management environments, can be used to link records. However, often there is no unique ....

National Center for Biotechnology Information PubMed Overview. Bethesda, MA, U.S. National Library of Medicine 2002,

.... structure ENTREZSVR This module provides access to GenBank using tools from the Entrez package developed at the National Center for Biotechnology Information [12] This is a complex data source, where an average entry has over 12 levels of nesting and over 150 subobjects, in the ASN.1 format [13]. The implementation of this module is really a wrapper around a C program, asncpl, developed by Kyle Hart at the University of Pennsylvania Human Genome Center for Chromosome 22. val SelectLab : labno val LevelLab : labno val NameLab : labno val ArgsLab : labno val PathLab : labno val ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN. 1 Specification, 1992. Revision 2.0.

....over the World Wide Web, is becoming the standard data interchange format for electronic business transactions. MIMAS have worked with two publishers to format their article metadata for supply to ingenta [16] and also with a publisher to deliver metadata to PubMed (National Library of Medicine) [17]. 3.1 A Common DTD Where a publisher has data produced by several typesetters, different journals may have article metadata which conforms to different DTDs. Some journals may have the article header information only in SGML, with the full articles in another format such as PDF, whereas others ....

....quality checking and possible repeat. This probably follows tasks such as initial, preflight quality checking, and some valuing adding, for instance including links from the bibliographic references in the articles to the corresponding full text articles or to abstracting services such as Medline [17]. Some of the steps in the process may be performed automatically, but some, such as quality checking, will be manual operations. This process must usually be done within a tight timescale to ensure that journal issues are published electronically in a timely fashion. As the production process ....

National Center for Biotechnology Information, National Library of Medicine, PubMed and Medline. http://www.ncbi.nlm.gov/PubMed/

....of run time errors if the inferred type and the actual structure are not compatible. This is an important feature because most of our data sources do not have explicit schemas, while a few have extremely large schemas that take many pages to write down for example, the ASN.1 schema of Entrez [22] making it impractical to have any form of declaration. We now come to the fourth requirement. A data exchange format is an agreement on how to lay out data in a data stream or message when the data is exchanged between two systems. In our case, it is the format for exchanging data between ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

....the capabilities of new data sources. This is also not found in traditional relational optimizer since their data model is very homogeneous and their systems are usually inextensible. ffl The data sources have complex structures. For example, one of our most important genetic database is GenBank [17]. A sequence record in this database typically has over 12 levels of nesting and 150 subobjects. Therefore, the optimizer has deal with queries that are considerably more complex than those supported by relational databases. ffl The schemas and statistics of the data sources can be nonexistence ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

....if the inferred type and the actual structure are not compatible. This is an important feature because most of our data sources do not have explicit schemas, while a few have extremely big explicit schemas that run into tens of pages an example big complex schema is the ASN.1 schema of Entrez [20] making it impractical to have any form of declaration. We now come to the fourth requirement. A data exchange format is an agreement on how to lay out data in a data stream or message when the data is exchanged between two systems. In our case, it is the format for exchanging data between ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

....list fjj jjg sequence of set f g set of record [l 1 : 1 ; l n : n ] sequence (labeled fields) variant l 1 : 1 ; l n : n choice (tagged union) Figure 1: Sample complex type typical of ASN.1 data sources. which indexing is provided for efficient retrieval (ASN.1 [31, 33]) binary files that can be interpreted textually or graphically via special purpose interfaces (ACeDB [44] and image databases of molecular and chemical structures. These formats have been adopted in preference to database management systems for several reasons, chief among which is that the ....

....a CPL module which caches relational metadata locally, allowing the system to typecheck user specified SQL statements prior to passing them to the drivers. The ASN.1 Entrez driver is used to connect to ASN.1 GenBank [33] We have developed a similar driver to access BLAST servers. These drivers [33, 31] are significantly more complicated than the Sybase one because there is no real query language interface for ASN.1. The selection of ASN.1 values from Entrez is accomplished through pre computed indexes in the style of information retrieval systems, i.e. one whose syntax simply uses boolean ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

....Programming Language, CPL, has been built on top of Kleisli and serves as its high level query language. The openness of Kleisli allows us to easily connect it to several genetic databases and their associated tools. A partial list of these databases and tools include GDB [8] NCBI ASN.1 [7], Sortez [4] Entrez [6] and BLAST [1] These can then be freely combined in any CPL queries. In Spring 1993, the Department of Energy published a report [3] which listed 12 impossible genomic data retrieval problems. These were thought to be impossible because they involve the integration of ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

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U.S. National Institutes of Health, National Library of Medicine. Medical Subject Headings (MeSH). [Online] Available at http://www.nlm.nih.gov/mesh/meshhome.html. Accessed June 25, 2004.

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U.S. National Institutes of Health, National Library of Medicine. PubMed. [Online] Available at http://www.ncbi.nlm.nih.gov. PubMed. Accessed June 25, 2004.

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U.S. National Institutes of Health, National Library of Medicine. ClinicalTrials.gov. [Online] Available at http://clinicaltrials. gov/. Accessed June 25, 2004.

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U.S. National Institutes of Health, National Library of Medicine. MEDLINEplus. [Online] Available at http://www.medlineplus. gov. Accessed June 25, 2004.

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U.S. National Institutes of Health, National Library of Medicine. Genetics Home Reference. [Online] Available at http://ghr. nlm.nih.gov. Accessed June 25, 2004.

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National Library of Medicine (U.S.). Proceedings of the Second Visible Human Project Conference. R. A. Banvard and P. Cerveri, eds. October 1-2, 1998.

....associated with 3 dimensional images from sensor probes and symbolic textbook labelling. Until recently the construction of the template itself seemed to be the major obstacle for the successful application of these methods. It was therefore a welcome surprise to learn of the The Visible Human [10] project undertaken by the National Medical Library (NML) in which digital anatomical templates are being constructed for two complete human beings. We quote from the NML: This Visible Human project would include digital images derived from computerized tomography, magnetic resonance imagery, and ....

U.S. National Library of Medicine Board of Regents (1987) National Library of Medicine, Long Range Plan: ELECTRONIC IMAGING (U.S. Dept. of Health and Human Services, Public Health Service, National Institutes of Health, Bethesda, MD).

....repetitive DNA repeats 1 monomer, clone alpha RI(680) 22 73 I 1. Querying a Non relational Data Source We have implemented a general C program for accessing the Entrez family of databases provided by the National Center Biotechnology for Information [17] This data is stored in ASN.1 format [18] which contains data structures such as sets and records, and also has lists and variants [13] which are not commonly seen in traditional database models. The liberal use of nested data types make this database decidedly non relational, but it is easily represented with the native data ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

....schema and instance level. For example, the variety and quantity of information contained in an entry from databases such as Hart is supported by NFS grant BIR 9413215. The work began under grant P50 HG0045 of the National Center for Human Genome Research, National Insitute of Health. GenBank [19] is immense. The schema for the ASN.1 version of GenBank describes over 160 individual structures. A typical instance has 12 or more levels of nesting and over 150 branches, and the database itself is a homogeneous collection of these instances. The dominant requirement for querying this type of ....

....and discuss related work. 2 Types, Paths, and Branches In order to describe querying with path and branch expressions, we shall first describe the type system and a fragment of the GenBank schema. The types we propose for data exchange formats are similar to the restricted form of ASN.1[19] used by the National Center for Biotechnology Information (NCBI) Types are created by recursive application of record (called sequence in ASN.1) variant (called choice in ASN.1) and set (called set of in ASN.1) constructors over a collection of base types. The grammar is given below. The ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

....of format and limited information retrieval facilities pose a fundamental barrier to creating the Biomatrix. Biomedical data sources include conventional relational databases with SQL or OPM [17] interfaces, formatted text files on top of which indexing is provided for efficient retrieval (ASN.1 [38, 40]) binary files that can be interpreted textually or graphically via special purpose interfaces (ACeDB [52] and image databases of molecular and chemical structures. These formats have been adopted in preference to database management systems for several reasons, chief among which is that the ....

....a CPL module which caches relational metadata locally, allowing the system to typecheck userspecified SQL statements prior to passing them to the drivers. The ASN.1 Entrez driver is used to connect to ASN.1GenBank [40] We have developed a similar driver to access BLAST servers. These drivers [40, 38] are significantly more complicated than the Sybase one because there is no real query language interface for ASN.1. The selection of ASN.1 values from Entrez is accomplished through pre computed indexes in the style of information retrieval systems, i.e. one whose syntax simply uses boolean ....

National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Specification, 1992. Revision 2.0.

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National Institutes of Health, National Library of Medicine (September, 1993). Factsheet. Bethesda, Maryland, U.S.A.

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National Library of Medicine (US) (ed) (2003) Genes and disease. Bethesda, MD

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National Center for Biotechnology Information. Data bases. National Library of Medicine. [Web site] 2003; URL: http://www.ncbi.nlm.nih.gov/Database/index.html

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National Center for Biotechnology Information: PubMed Overview. Bethesda, MA, U.S. National Library of Medicine 2002

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National Center for Biotechnology Information: PubMed Overview. Bethesda, MA, U.S. National Library of Medicine 2002

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National Center for Biotechnology Information, National Library of Medicine. Unigene Web site. Available at: http://www.ncbi.nlm.nih.gov/UniGene /index.html. Accessed September 2000.

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National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD. NCBI ASN.1 Speci#cation, 1992. Revision 2.0.

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