Normalized names for clinical drugs: RxNorm at 6 years

OBJECTIVE

In the 6 years since the National Library of Medicine began monthly releases of RxNorm, RxNorm has become a central resource for communicating about clinical drugs and supporting interoperation between drug vocabularies.

MATERIALS AND METHODS

Built on the idea of a normalized name for a medication at a given level of abstraction, RxNorm provides a set of names and relationships based on 11 different external source vocabularies. The standard model enables decision support to take place for a variety of uses at the appropriate level of abstraction. With the incorporation of National Drug File Reference Terminology (NDF-RT) from the Veterans Administration, even more sophisticated decision support has become possible.

DISCUSSION

While related products such as RxTerms, RxNav, MyMedicationList, and MyRxPad have been recognized as helpful for various uses, tasks such as identifying exactly what is and is not on the market remain a challenge.

Advanced networks and computing in healthcare

As computing and network capabilities continue to rise, it becomes increasingly important to understand the varied applications for using them to provide healthcare. The objective of this review is to identify key characteristics and attributes of healthcare applications involving the use of advanced computing and communication technologies, drawing upon 45 research and development projects in telemedicine and other aspects of healthcare funded by the National Library of Medicine over the past 12 years. Only projects publishing in the professional literature were included in the review. Four projects did not publish beyond their final reports. In addition, the authors drew on their first-hand experience as project officers, reviewers and monitors of the work. Major themes in the corpus of work were identified, characterizing key attributes of advanced computing and network applications in healthcare. Advanced computing and network applications are relevant to a range of healthcare settings and specialties, but they are most appropriate for solving a narrower range of problems in each. Healthcare projects undertaken primarily to explore potential have also demonstrated effectiveness and depend on the quality of network service as much as bandwidth. Many applications are enabling, making it possible to provide service or conduct research that previously was not possible or to achieve outcomes in addition to those for which projects were undertaken. Most notable are advances in imaging and visualization, collaboration and sense of presence, and mobility in communication and information-resource use.

Risk factors for bladder cancer: challenges of conducting a literature search using PubMed

The objective of this study was to assess the risk factors for bladder cancer using PubMed articles from January 2000 to December 2009. The study also aimed to describe the challenges encountered in the methodology of a literature search for bladder cancer risk factors using PubMed. Twenty-six categories of risk factors for bladder cancer were identified using the National Cancer Institute Web site and the Medical Subject Headings (MeSH) Web site. A total of 1,338 PubMed searches were run using the term "urinary bladder cancer" and a risk factor term (e.g., "cigarette smoking") and were screened to identify 260 articles for final analysis. The search strategy had an overall precision of 3.42 percent, relative recall of 12.64 percent, and an F-measure of 5.39 percent. Although search terms derived from MeSH had the highest overall precision and recall, the differences did not reach significance, which indicates that for generalized, free-text searches of the PubMed database, the searchers' own terms are generally as effective as MeSH terms.

Implications of SNOMED CT versioning

PURPOSE

To determine the changes each Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) release undergoes and the implications of those changes.

METHODS

(1) We reviewed the SNOMED CT Component History documentation and analyzed the Component History table in detail. (2) We outlined a list of semantic changes that are made to SNOMED CT concepts that are not recorded as part of the Component History mechanism. (3) We reviewed the SNOMED CT Concept Model mechanism and how it has changed since the July 2006 release. We applied the above methods to determine the impact they had on the Clinical Observations Recording and Encoding (CORE) Problem List published by the United States National Library of Medicine National Institutes of Health.

RESULTS

Of the 5182 concepts in the problem list subset, 2135 (41.2%) underwent some form of change in the form of (1) fully specified name and preferred term; (2) concept status; (3) primitive/fully defined status, defining attributes and normal forms; and/or (4) position in hierarchy (top-level hierarchy, supertypes and subtypes).

CONCLUSIONS

In this paper, we have identified four types of changes that occur over time as new SNOMED CT releases are introduced. Keeping track of these changes is important as they are not well published and have an impact in patient case queries and the accuracy of patient records.

MEDRank: using graph-based concept ranking to index biomedical texts

BACKGROUND

As the volume of biomedical text increases exponentially, automatic indexing becomes increasingly important. However, existing approaches do not distinguish central (or core) concepts from concepts that were mentioned in passing. We focus on the problem of indexing MEDLINE records, a process that is currently performed by highly trained humans at the National Library of Medicine (NLM). NLM indexers are assisted by a system called the Medical Text Indexer (MTI) that suggests candidate indexing terms.

OBJECTIVE

To improve the ability of MTI to select the core terms in MEDLINE abstracts. These core concepts are deemed to be most important and are designated as "major headings" by MEDLINE indexers. We introduce and evaluate a graph-based indexing methodology called MEDRank that generates concept graphs from biomedical text and then ranks the concepts within these graphs to identify the most important ones.

METHODS

We insert a MEDRank step into the MTI and compare MTI's output with and without MEDRank to the MEDLINE indexers' selected terms for a sample of 11,803 PubMed Central articles. We also tested whether human raters prefer terms generated by the MEDLINE indexers, MTI without MEDRank, and MTI with MEDRank for a sample of 36 PubMed Central articles.

RESULTS

MEDRank improved recall of major headings designated by 30% over MTI without MEDRank (0.489 vs. 0.376). Overall recall was only slightly (6.5%) higher (0.490 vs. 0.460) as was F(2) (3%, 0.408 vs. 0.396). However, overall precision was 3.9% lower (0.268 vs. 0.279). Human raters preferred terms generated by MTI with MEDRank over terms generated by MTI without MEDRank (by an average of 1.00 more term per article), and preferred terms generated by MTI with MEDRank and the MEDLINE indexers at the same rate.

CONCLUSIONS

The addition of MEDRank to MTI significantly improved the retrieval of core concepts in MEDLINE abstracts and more closely matched human expectations compared to MTI without MEDRank. In addition, MEDRank slightly improved overall recall and F(2).

The ClinicalTrials.gov results database--update and key issues

BACKGROUND

The ClinicalTrials.gov trial registry was expanded in 2008 to include a database for reporting summary results. We summarize the structure and contents of the results database, provide an update of relevant policies, and show how the data can be used to gain insight into the state of clinical research.

METHODS

We analyzed ClinicalTrials.gov data that were publicly available between September 2009 and September 2010.

RESULTS

As of September 27, 2010, ClinicalTrials.gov received approximately 330 new and 2000 revised registrations each week, along with 30 new and 80 revised results submissions. We characterized the 79,413 registry and 2178 results of trial records available as of September 2010. From a sample cohort of results records, 78 of 150 (52%) had associated publications within 2 years after posting. Of results records available publicly, 20% reported more than two primary outcome measures and 5% reported more than five. Of a sample of 100 registry record outcome measures, 61% lacked specificity in describing the metric used in the planned analysis. In a sample of 700 results records, the mean number of different analysis populations per study group was 2.5 (median, 1; range, 1 to 25). Of these trials, 24% reported results for 90% or less of their participants.

CONCLUSIONS

ClinicalTrials.gov provides access to study results not otherwise available to the public. Although the database allows examination of various aspects of ongoing and completed clinical trials, its ultimate usefulness depends on the research community to submit accurate, informative data.

Informed consent elements. Final rule

The Food and Drug Administration (FDA) is amending the current informed consent regulations to require that informed consent documents and processes for applicable drug (including biological products) and device clinical trials include a specific statement that clinical trial information will be entered into a databank. The databank referred to in this final rule is the clinical trial registry databank maintained by the National Institutes of Health/National Library of Medicine (NIH/NLM) which was created by statute. The submission of clinical trial information to this data bank also is required by statute. This amendment to the informed consent regulations is required by the Food and Drug Administration Amendments Act of 2007 (FDAAA) and is designed to promote transparency of clinical research to participants and patients.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Medical knowledge evolution query constraining aspects

In this paper we present a first analysis towards better understanding of the query constraining aspects of knowledge, as expressed in the most used public medical bibliographic database MEDLINE. Our results indicate, possibly not surprising, that new terms occur, but also that traditional terms are replaced by more specific ones or even go out of use as they become common knowledge. Hence, as knowledge evolve over time, search methods may benefit from becoming more sensitive to knowledge expression, to enable finding new, as well as older, relevant database contents.

BIOSPIDA: A Relational Database Translator for NCBI

As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time.

Disaster Information Specialist Pilot Project: NLM/DIMRC

Medical librarians have often been overlooked as important contributors to hospital disaster preparedness. Recognizing the importance of medical libraries and their potential in disaster planning and management, the National Library of Medicine (NLM), Disaster Information Management Research Center (DIMRC), formed a pilot Disaster Information Specialist Project. This paper describes the preliminary activities of Bishopric Medical Library's Director, Patricia Reynolds, at Sarasota Memorial Health Care System, as a disaster information specialist in the hospital's disaster planning and preparedness.

Outcome reporting among drug trials registered in ClinicalTrials.gov

BACKGROUND

Clinical trial registries are in widespread use to promote transparency around trials and their results.

OBJECTIVE

To describe characteristics of drug trials listed in ClinicalTrials.gov and examine whether the funding source of these trials is associated with favorable published outcomes.

DESIGN

An observational study of safety and efficacy trials for anticholesteremics, antidepressants, antipsychotics, proton-pump inhibitors, and vasodilators conducted between 2000 and 2006.

SETTING

ClinicalTrials.gov, a Web-based registry of clinical trials launched in 1999.

MEASUREMENTS

Publications resulting from the trials for the 5 drug categories of interest were identified, and data were abstracted on the trial record and publication, including timing of registration, elements of the study design, funding source, publication date, and study outcomes. Assessments were based on the primary funding categories of industry, government agencies, and nonprofit or nonfederal organizations.

RESULTS

Among 546 drug trials, 346 (63%) were primarily funded by industry, 74 (14%) by government sources, and 126 (23%) by nonprofit or nonfederal organizations. Trials funded by industry were more likely to be phase 3 or 4 trials (88.7%; P < 0.001 across groups), to use an active comparator in controlled trials (36.8%; P = 0.010 across groups), to be multicenter (89.0%; P < 0.001 across groups), and to enroll more participants (median sample size, 306 participants; P < 0.001 across groups). Overall, 362 (66.3%) trials had published results. Industry-funded trials reported positive outcomes in 85.4% of publications, compared with 50.0% for government-funded trials and 71.9% for nonprofit or nonfederal organization-funded trials (P < 0.001). Trials funded by nonprofit or nonfederal sources with industry contributions were also more likely to report positive outcomes than those without industry funding (85.0% vs. 61.2%; P = 0.013). Rates of trial publication within 24 months of study completion ranged from 32.4% among industry-funded trials to 56.2% among nonprofit or nonfederal organization-funded trials without industry contributions (P = 0.005 across groups).

LIMITATIONS

The publication status of a trial could not always be confirmed, which could result in misclassification. Additional information on study protocols and comprehensive trial results were not available to further explore underlying factors for the association between funding source and outcome reporting.

CONCLUSION

In this sample of registered drug trials, those funded by industry were less likely to be published within 2 years of study completion and were more likely to report positive outcomes than were trials funded by other sources.

PRIMARY FUNDING SOURCE

National Library of Medicine and National Institute of Child Health and Human Development, National Institutes of Health.

Using the NCBI map viewer to browse genomic sequence data

This unit includes a Basic Protocol with an introduction to the Map Viewer, describing how to perform a simple text-based search of genome annotations to view the genomic context of a gene, navigate along a chromosome, zoom in and out, and change the displayed maps to hide and show information. It also describes some of NCBI's sequence-analysis tools, which are provided as links from the Map Viewer. The Alternate Protocols describe different ways to query the genome sequence, and also illustrate additional features of the Map Viewer. Alternate Protocol 1 shows how to perform and interpret the results of a BLAST search against the human genome. Alternate Protocol 2 demonstrates how to retrieve a list of all genes between two STS markers. Finally, Alternate Protocol 3 shows how to find all annotated members of a gene family.

A PubMed-wide associational study of infectious diseases

BACKGROUND

Computational discovery is playing an ever-greater role in supporting the processes of knowledge synthesis. A significant proportion of the more than 18 million manuscripts indexed in the PubMed database describe infectious disease syndromes and various infectious agents. This study is the first attempt to integrate online repositories of text-based publications and microbial genome databases in order to explore the dynamics of relationships between pathogens and infectious diseases.

METHODOLOGY/PRINCIPAL FINDINGS

Herein we demonstrate how the knowledge space of infectious diseases can be computationally represented and quantified, and tracked over time. The knowledge space is explored by mapping of the infectious disease literature, looking at dynamics of literature deposition, zooming in from pathogen to genome level and searching for new associations. Syndromic signatures for different pathogens can be created to enable a new and clinically focussed reclassification of the microbial world. Examples of syndrome and pathogen networks illustrate how multilevel network representations of the relationships between infectious syndromes, pathogens and pathogen genomes can illuminate unexpected biological similarities in disease pathogenesis and epidemiology.

CONCLUSIONS/SIGNIFICANCE

This new approach based on text and data mining can support the discovery of previously hidden associations between diseases and microbial pathogens, clinically relevant reclassification of pathogenic microorganisms and accelerate the translational research enterprise.

Genomic databases and resources at the National Center for Biotechnology Information

The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI Web site. Entrez, a text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Customized genomic BLAST enables sequence similarity searches against a special collection of organism-specific sequence data and viewing the resulting alignments within a genomic context using NCBI's genome browser, Map Viewer.Comparative genome analysis tools lead to further understanding of evolutionary processes, quickening the pace of discovery.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

GenBank

GenBank is a comprehensive database that contains publicly available nucleotide sequences for more than 300,000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Molecular Biology Laboratory Nucleotide Sequence Database in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bi-monthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI homepage: www.ncbi.nlm.nih.gov.

Modular representation of the guideline text: an approach for maintaining and updating the content of medical education

One of the principal challenges in the medical practice is the update of their knowledge. One of the prime roles of the Continuing Medical Education is to train the medical practitioners with the latest advances in health care, specialized to their needs. Online courses and classroom teaching with computer-based representations have become an established mode of delivering medical education. This paper deals with the modularized representation of a medical text concerning clinical practice guidelines. The proposed system takes into consideration the semantics of the Unified Medical Language System and is based upon the marking up and display of the knowledge using the XML and XSLT languages. This modularization of the concepts leads to the determination of the context of a portion or the whole document. Thus, after marking up using our system, the text components can be exchanged, modified or reconstructed, which, in turn, would help to maintain the updates in medical knowledge.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Cataloguing the HIV type 1 human protein interaction network

Although many interactions between HIV-1 and human proteins have been reported in the scientific literature, no publicly accessible source for efficiently reviewing this information was available. Therefore, a project was initiated in an attempt to catalogue all published interactions between HIV-1 and human proteins. HIV-related articles in PubMed were used to develop a database containing names, Entrez GeneIDs, and RefSeq protein accession numbers of interacting proteins. Furthermore, brief descriptions of the interactions, PubMed identification numbers of articles describing the interactions, and keywords for searching the interactions were incorporated. Over 100,000 articles were reviewed, resulting in the identification of 1448 human proteins that interact with HIV-1 comprising 2589 unique HIV-1-to-human protein interactions. Preliminary analysis of the extracted data indicates 32% were direct physical interactions (e.g., binding) and 68% were indirect interactions (e.g., upregulation through activation of signaling pathways). Interestingly, 37% of human proteins in the database were found to interact with more than one HIV-1 protein. For example, the signaling protein mitogen-activated protein kinase 1 has a surprising range of interactions with 10 different HIV-1 proteins. Moreover, large numbers of interactions were published for the HIV-1 regulatory protein Tat and envelope proteins: 30% and 33% of total interactions identified, respectively. The database is accessible at http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/ and is cross-linked to other National Center for Biotechnology Information databases and programs via Entrez Gene. This database represents a unique and continuously updated scientific resource for understanding HIV-1 replication and pathogenesis to assist in accelerating the development of effective therapeutic and vaccine interventions.

A prototype system to support evidence-based practice

Translating evidence into clinical practice is a complex process that depends on the availability of evidence, the environment into which the research evidence is translated, and the system that facilitates the translation. This paper presents InfoBot, a system designed for automatic delivery of patient-specific information from evidence-based resources. A prototype system has been implemented to support development of individualized patient care plans. The prototype explores possibilities to automatically extract patients problems from the interdisciplinary team notes and query evidence-based resources using the extracted terms. Using 4,335 de-identified interdisciplinary team notes for 525 patients, the system automatically extracted biomedical terminology from 4,219 notes and linked resources to 260 patient records. Sixty of those records (15 each for Pediatrics, Oncology & Hematology, Medical & Surgical, and Behavioral Health units) have been selected for an ongoing evaluation of the quality of automatically proactively delivered evidence and its usefulness in development of care plans.

Web screening of US nursing homes by location and quality

To assist American families who will one day need to find a nursing home for a loved one, NLM is developing a Web 2.0 interface to important evaluative information about nursing homes in the US. Currently in prototype form, our Nursing Home Screener locates homes on a Google Map. It allows nursing home quality, indicated by map icons, to be surveyed in any of four major categories: staffing, fire safety deficiencies, healthcare deficiencies, and quality of care inferred from residents health. Within each category, options can be tailored to user preferences. Furthermore, home attributes can be used to selectively hide home markers of less interest. The goal is to offer the public a timely, easy to use site for the rapid location and comparison of nursing homes, thus identifying those worth further review or a personal visit.

A scientific collaboration tool built on the facebook platform

We describe an application ("Medline Publications")written for the Facebook platform that allows users to maintain and publish a list of their own Medline-indexed publications, as well as easily access their contacts lists. The system is semi-automatic in that it interfaces directly with the National Library of Medicine's PubMed database to find and retrieve citation data. Furthermore, the system has the capability to present the user with sets of other users with similar publication profiles. As of July 2008,Medline Publications has attracted approximately 759 users, 624 of which have listed a total of 5,193 unique publications.

Searching the NCBI databases using Entrez

One of the most widely-used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two Basic Protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An Alternate Protocol builds upon the first Basic Protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The Support Protocol reviews how to save frequently-issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

SNOMED CT survey: an assessment of implementation in EMR/EHR applications

A descriptive study of health information technology (HIT) vendors was conducted to identify which EMR/EHR vendors currently work or anticipate working with SNOMED CT, determine the prevalence of SNOMED CT integration in electronic medical record (EMR) and electronic health record (EHR) products, identify the available and potential future applications for SNOMED CT in EMR/EHR systems, and learn what prompts vendors to include SNOMED CT in EMR/EHR systems. The Web-based survey consisting of 25 questions was fielded in November-December 2006. Seventy-two responses were received. The results from this survey on SNOMED CT show a mixed message from respondents with regard to the prevalence of SNOMED CT integration in EMR/EHR products. Those with plans for implementation cited strategic reasons most often. However, HIT vendors who have not yet obtained a SNOMED CT license are waiting for market forces to drive deployment in their systems. Finally, survey respondents currently working with SNOMED CT indicated an expected increase over the next three years in EMR/EHR applications where SNOMED CT will be implemented.

A virtual computer lab for distance biomedical technology education

BACKGROUND

The National Library of Medicine's National Center for Biotechnology Information offers mini-courses which entail applying concepts in biochemistry and genetics to search genomics databases and other information sources. They are highly interactive and involve use of 3D molecular visualization software that can be computationally taxing.

METHODS

Methods were devised to offer the courses at a distance so as to provide as much functionality of a computer lab as possible, the venue where they are normally taught. The methods, which can be employed with varied videoconferencing technology and desktop sharing software, were used to deliver mini-courses at a distance in pilot applications where students could see demonstrations by the instructor and the instructor could observe and interact with students working at their remote desktops.

RESULTS

Student ratings of the learning experience and comments to open ended questions were similar to those when the courses are offered face to face. The real time interaction and the instructor's ability to access student desktops from a distance in order to provide individual assistance and feedback were considered invaluable.

CONCLUSION

The technologies and methods mimic much of the functionality of computer labs and may be usefully applied in any context where content changes frequently, training needs to be offered on complex computer applications at a distance in real time, and where it is necessary for the instructor to monitor students as they work.

[Advanced online search techniques and dedicated search engines for physicians]

In recent years search engines have become an essential tool in the work of physicians. This article will review advanced search techniques from the world of information specialists, as well as some advanced search engine operators that may help physicians improve their online search capabilities, and maximize the yield of their searches. This article also reviews popular dedicated scientific and biomedical literature search engines.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

CPDB: Carcinogenic Potency Database

The Carcinogenic Potency Database reports analyses of animal cancer tests on 1,547 chemicals. These tests are used in support of cancer risk assessments for humans. Results are searchable and are made available via the National Library of Medicine's (NLM) TOXNET system. This column will provide background information on the database, as well as present search basics.

HIV/AIDS information outreach: a community-based approach

OBJECTIVE

The paper provides an overview of the National Library of Medicine's (NLM's) AIDS Community Information Outreach Program during the years 1994 to 2005, discusses the impact of previously funded projects, and explores future implications for HIV/AIDS information outreach to communities in need.

METHODS

A qualitative assessment was conducted to provide information on the impact of projects funded by the AIDS Community Information Outreach Program during fiscal year 2002. Interviews were conducted and final reports were analyzed, resulting in themes based on roles and responsibilities of participants and the impact of the projects in the communities.

RESULTS

Results from the assessment suggest that access to HIV/AIDS information led to improved communication between patients and their health care providers and encouraged better health care decision making. Feedback from reports and interviews included examples of impact such as an increase in services provided to communities, national and global recognition of HIV/AIDS services, sustainability of projects, and improved communication.

CONCLUSION

Community-based health information outreach projects may empower the HIV/AIDS community to become more involved in health care and improve communication with providers. NLM will continue to promote the AIDS Community Information Outreach Program to encourage community organizations to design local projects for their specific communities.

Online resources for SNP analysis: a review and route map

The major online single nucleotide polymorphism (SNP) databases freely available as research tools for genetic analysis are explained, reviewed, and compared. An outline is given of the search strategies that can be used with the most extensive current SNP databases: National Centre for Biotechnology Information (NCBI) dbSNP and HapMap to help the user secure the most appropriate data for the research needs of clinical genetics and population genetics research. A range of online tools that can be useful in designing SNP genotyping assays are also detailed.

The development of the Medical Literature Analysis and Retrieval System (MEDLARS)

OBJECTIVE

The research provides a chronology of the US National Library of Medicine's (NLM's) contribution to access to the world's biomedical literature through its computerization of biomedical indexes, particularly the Medical Literature Analysis and Retrieval System (MEDLARS).

METHOD

Using material gathered from NLM's archives and from personal interviews with people associated with developing MEDLARS and its associated systems, the author discusses key events in the history of MEDLARS.

DISCUSSION

From the development of the early mechanized bibliographic retrieval systems of the 1940s and to the beginnings of online, interactive computerized bibliographic search systems of the early 1970s chronicled here, NLM's contributions to automation and bibliographic retrieval have been extensive.

CONCLUSION

As NLM's technological experience and expertise grew, innovative bibliographic storage and retrieval systems emerged. NLM's accomplishments regarding MEDLARS were cutting edge, placing the library at the forefront of incorporating mechanization and technologies into medical information systems.