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PubMed2002

The Protein Information Resource: an integrated public resource of functional annotation of proteins.

The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery. The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence Database (PSD), the major annotated protein sequence database in the public domain, containing about 250 000 proteins. To improve protein annotation and the coverage of experimentally validated data, a bibliography submission system is developed for scientists to submit, categorize and retrieve literature information. Comprehensive protein information is available from iProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well as cross-references to over 40 biological databases. To provide timely and comprehensive protein data with source attribution, we have introduced a non-redundant reference protein database, PIR-NREF. The database consists of about 800 000 proteins collected from PIR-PSD, SWISS-PROT, TrEMBL, GenPept, RefSeq and PDB, with composite protein names and literature data. To promote database interoperability, we provide XML data distribution and open database schema, and adopt common ontologies. The PIR web site (http://pir.georgetown.edu/) features data mining and sequence analysis tools for information retrieval and functional identification of proteins based on both sequence and annotation information. The PIR databases and other files are also available by FTP (ftp://nbrfa.georgetown.edu/pir_databases).

Amino Acid Sequence↗
PubMed2003

Beyond Medline: reducing bias through extended systematic review search.

OBJECTIVE: To evaluate the sensitivity and precision of various extended search methods in identifying randomized controlled trials (RCTs) for systematic reviews. METHOD: Prospective analysis of extended search methods (specialized databases or trial registries, reference lists, hand-searching, personal communication, and Internet) used in two systematic reviews of RCTs. The gold standard was the total number of RCTs identified by major databases (MEDLINE, EMBASE, etc.) and extended search strategies combined. Sensitivity was the proportion of all known RCTs identified by any extended search method. Precision reflected the proportion of all items uncovered by any extended search method that actually were RCTs. RESULTS: The extended search identified 94 additional RCTs for the systematic reviews beyond those identified with the major databases. Specialized databases and trial registries had the highest sensitivity and precision for the lipid-lowering project (13.6% and 52.7%, respectively; p < .05) followed by scanning of reference lists (7.2% sensitivity and 41.9% precision; p <.05). Hand-searching was more effective than personal communication and Internet searching (1.7% sensitivity and 12.2% precision; p < .05). The acupuncture project had slightly different results, with the specialized databases and trial registries tied with the review of reference lists for highest sensitivity (14.2%). The precision followed the same trend as the lipid-lowering project (17.6% specialized databases; 8.3% reference lists; p < .05). A post-hoc analysis showed that 75 of the 94 RCTs were indexed in the major databases but missed by the major database search. CONCLUSIONS: Extended searching identified additional RCTs for the systematic reviews beyond those found in major databases. Specialized databases and trial registries were most effective. An important number of RCTs were missed by the major database search. Timing and accuracy of indexing may explain this finding. The definitive measure, whether there is an association between the method used to uncover RCTs, the quality of the items uncovered and their impact on systematic review results, is yet to be determined.

Humans↗
PubMed1994

Implementation of a relational patient record with integration of educational and reference information.

The clinician must identify pertinent diagnostic information and develop appropriate medical management plans in the context of rapidly changing research information, new therapeutic options and expanding diagnostic modalities. To assist in recognition of patterns relevant to diagnostic or therapeutic interventions, the medical record must be presented in a format that emphasizes important data interrelationships. Reference and educational information specifically pertinent to the case being reviewed must be immediately accessible. A system that presents point of care patient centered clinical information, a summarized patient record, in a relational format with linked reference information has been developed. Data is acquired from the VA patient information database and provided over a PC network. At the time of data transfer, preliminary analysis and reorganization of data is performed such that interrelationships between laboratory, pharmacy and diagnostic information can be rapidly recognized. During data compilation reference and educational information is linked with patient data such that it can be accessed with a mouse click ("hotspot") when the record is subsequently reviewed. The medical record and CD-ROM based reference databases are then made available to users on a PC network in a Windows (tm) environment. Initial experience with the system is very favorable and suggests that evaluation of patient data may be significantly enhanced.

Computer Communication Networks↗
PubMed2005

AGML Central: web based gel proteomic infrastructure.

SUMMARY: AGML Central is a web-based open-source public infrastructure for dissemination of two-dimensional Gel Electrophoresis (2-DE) proteomics data in AGML format (Annotated Gel Markup Language). It includes a growing collection of converters from proprietary formats such as those produced by PDQUEST (BioRad), PHORETIX 2-D (Nonlinear Dynamics) and Melanie (GenBio SA). The resulting unifying AGML formatted entry, with or without the raw gel images, is optionally stored in a database for future reference. AGML Central was developed to provide a common platform for data dissemination and development of 2-DE data analysis tools. This resource responds to an increasing use of AGML for 2-DE public source data representation which requires automated tools for conversion from proprietary formats. Conversion and short-term storage is made publicly available, permanent storage requires prior registering. A JAVA applet visualizer was developed to visualize the AGML data with cross-reference links. In order to facilitate automated access a SOAP web service is also included in the AGML Central infrastructure. AVAILABILITY: http://bioinformatics.musc.edu/agmlcentral.

Database Management Systems↗
PubMed2003

Active Sequences Collection (ASC) database: a new tool to assign functions to protein sequences.

Active Sequences Collection (ASC) is a collection of amino acid sequences, with an unique feature: only short sequences are collected, with a demonstrated biological activity. The current version of ASC consists of three sections: DORRS, a collection of active RGD-containing peptides; TRANSIT, a collection of protein regions active as substrates of transglutaminase enzyme (TGase), and BAC, a collection of short peptides with demonstrated biological activity. Literature references for each entry are reported, as well as cross references to other databases, when available. The current version of ASC includes more than 800 different entries. The main scope of this collection is to offer a new tool to investigate the structural features of protein active sites, additionally to similarity searches against large protein databases or searching for known functional patterns. ASC database is available at the web address http://crisceb.unina2.it/ASC/ which also offers a dedicated query interface to compare user-defined protein sequences with the database, as well as an updating interface to allow contribution of new referenced active sequences.

Amino Acid Sequence↗
PubMed2004

PIRSF: family classification system at the Protein Information Resource.

The Protein Information Resource (PIR) is an integrated public resource of protein informatics. To facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors, PIR has extended its superfamily concept and developed the SuperFamily (PIRSF) classification system. Based on the evolutionary relationships of whole proteins, this classification system allows annotation of both specific biological and generic biochemical functions. The system adopts a network structure for protein classification from superfamily to subfamily levels. Protein family members are homologous (sharing common ancestry) and homeomorphic (sharing full-length sequence similarity with common domain architecture). The PIRSF database consists of two data sets, preliminary clusters and curated families. The curated families include family name, protein membership, parent-child relationship, domain architecture, and optional description and bibliography. PIRSF is accessible from the website at http://pir.georgetown.edu/pirsf/ for report retrieval and sequence classification. The report presents family annotation, membership statistics, cross-references to other databases, graphical display of domain architecture, and links to multiple sequence alignments and phylogenetic trees for curated families. PIRSF can be utilized to analyze phylogenetic profiles, to reveal functional convergence and divergence, and to identify interesting relationships between homeomorphic families, domains and structural classes.

Amino Acid Motifs↗
PubMed1998

PAH Mutation Analysis Consortium Database: 1997. Prototype for relational locus-specific mutation databases.

PAHdb (http://www.mcgill.ca/pahdb ) is a curated relational database (Fig. 1) of nucleotide variation in the human PAH cDNA (GenBank U49897). Among 328 different mutations by state (Fig. 2) the majority are rare mutations causing hyperphenylalaninemia (HPA) (OMIM 261600), the remainder are polymorphic variants without apparent effect on phenotype. PAHdb modules contain mutations, polymorphic haplotypes, genotype-phenotype correlations, expression analysis, sources of information and the reference sequence; the database also contains pages of clinical information and data on three ENU mouse orthologues of human HPA. Only six different mutations account for 60% of human HPA chromosomes worldwide, mutations stratify by population and geographic region, and the Oriental and Caucasian mutation sets are different (Fig. 3). PAHdb provides curated electronic publication and one third of its incoming reports are direct submissions. Each different mutation receives a systematic (nucleotide) name and a unique identifier (UID). Data are accessed both by a Newsletter and a search engine on the website; integrity of the database is ensured by keeping the curated template offline. There have been >6500 online interrogations of the website.

Animals↗
PubMed2006

Management of antiphospholipid antibody syndrome: a systematic review.

CONTEXT: Antiphospholipid antibodies are autoantibodies directed against proteins that bind to phospholipid. Antiphospholipid antibody syndrome (APS) refers to the association between antiphospholipid antibodies and thrombosis risk or pregnancy morbidity. Patients with APS may be at increased risk of recurrent arterial or venous thrombosis or pregnancy loss. OBJECTIVE: To systematically review the evidence for treatment of thrombosis risk in patients with antiphospholipid antibodies or APS. EVIDENCE ACQUISITION: Search of MEDLINE (1966 to November 2005) and Cochrane Library electronic databases (2005) and reference lists for randomized trials, meta-analyses of randomized trials, and prospective cohort studies of the treatment of thrombosis risk in patients with antiphospholipid antibodies or APS. Studies were selected on the basis of clinical relevance. EVIDENCE SYNTHESIS: Among patients with antiphospholipid antibodies, the absolute risk of developing new thrombosis is low (<1% per year) in otherwise healthy patients without prior thrombotic events, may be moderately increased (up to 10% per year) in women with recurrent fetal loss without prior thrombosis, and is highest (>10% in the first year) in patients with a history of venous thrombosis who have discontinued anticoagulant drugs within 6 months. Compared with placebo or untreated control, anticoagulation with moderate-intensity warfarin (adjusted to a target international normalized ratio [INR] of 2.0-3.0) reduces the risk of recurrent venous thrombosis by 80% to 90% irrespective of the presence of antiphospholipid antibodies and may be effective for preventing recurrent arterial thrombosis. No evidence exists that high-intensity warfarin (target INR, >3.0) is more effective than moderate-intensity warfarin. For patients with a single positive antiphospholipid antibody test result and prior stroke, aspirin and moderate-intensity warfarin appear equally effective for preventing recurrent stroke. Treatment issues that have not been addressed in clinical trials, or for which the evidence is conflicting, include the role of antithrombotic prophylaxis in patients with antiphospholipid antibodies without prior thrombosis, the optimal treatment of noncerebrovascular arterial thrombosis, recurrent thrombosis despite warfarin therapy, and treatment of women with antiphospholipid antibodies and recurrent fetal loss. CONCLUSIONS: In patients with APS, moderate-intensity warfarin is effective for preventing recurrent venous thrombosis and perhaps also arterial thrombosis. Aspirin appears to be as effective as moderate-intensity warfarin for preventing recurrent stroke in patients with prior stroke and a single positive test result for antiphospholipid antibody. The optimal treatment of other thrombotic aspects of APS needs to be addressed in well-designed prospective studies.

Antibodies, Antiphospholipid↗
PubMed1998

A database of germline p53 mutations in cancer-prone families.

We created a comprehensive database covering all published cases of germline p53 mutations. The current version lists 580 tumours in 448 individuals belonging to 122 independent pedigrees. The database describes each p53 mutation (type of the mutation, exon and codon affected by the mutation, nucleotide and amino acid change), each family (family history of cancer, diagnosis of Li-Fraumeni syndrome), each affected individual (sex, generation, p53 status, from which parent the mutation was inherited) and each tumour (type, age of onset, p53 status-loss of heterozygosity, immunostaining). Each entry contains the original reference(s). The database is freely available and can be obtained from http://www.lf2.cuni.cz

Computer Communication Networks↗
PubMed2003

[Acute upper respiratory tract infections: outpatient diagnosis and treatment].

OBJECTIVE: To present an updated review of the most common upper respiratory infections (URI) in children seen by the pediatrician in outpatient clinics, for better diagnostic and therapeutic decisions. SOURCES: References from Medline database were reviewed. The most relevant articles were selected. SUMMARY OF THE FINDINGS: Acute rhinopharyngitis, sinusitis, streptococcal tonsillitis and viral croup are presented in a concise and critical view. Differential and etiological diagnosis limitations and the abusive use of antimicrobials in these illnesses are also discussed. CONCLUSIONS: URI are the most common cause of visits to pediatrician clinics. Therefore, update and critical concepts, as well as references are essential for a proper management of these illnesses, decreasing the indication of unnecessary diagnostic tests and avoiding non-effective and harmful treatments.

Acute Disease↗
PubMed2005

ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants.

Genome-wide mapping in the identification of novel candidate genes has always been the standard method in genetics and genomics to correlate a clinically interesting phenotypic trait with a genotype. However, the performance of a mapping experiment using classical microsatellite approaches can be very time consuming. The high-throughput analysis of single-nucleotide polymorphisms (SNPs) has the potential of being the successor of microsatellite analysis routinely used for these mapping approaches, where one of the major obstacles is the design of the appropriate SNP marker set itself. Here we report on ARTS, an advanced retrieval tool for SNPs, which allows researchers to comb freely the public mouse dbSNP database for multiple reference and test strains. Several filters can be applied in order to improve the sensitivity and the specificity of the search results. By employing the panel generator function of this program, it is possible to abbreviate the extraction of reliable sequence data for a large marker panel including several different mouse strains from days to minutes. The concept of ARTS is easily adaptable to other species for which SNP databases are available, making it a versatile tool for the use of SNPs as markers for genotyping. The web interface is accessible at http://andromeda.gsf.de/arts.

Animals↗
PubMed2002

Evaluating DNA tests of motherless cases using a Philippine genetic database.

BACKGROUND: In 5 percent of paternity determination cases, only DNA samples from the alleged father and child pairs are tested. The absence of the mother's DNA increases the probability of false paternity inclusions, which affects laboratories that use a limited number of DNA markers. The effect of coincidental matches between unrelated individuals on DNA tests of motherless cases was determined using the Philippine population genetic database of the National Capital Region (NCR). STUDY DESIGN AND METHODS: Seven short tandem repeat (STR) markers were used, namely HUMvWA, HUMTH01, HUMCSF1PO, HUMFOLP23, D8S306, HUMFES/FPS, and HUMF13A01. Values of the probability of paternity with (W) and without a mother (W(-mother)) were determined using the equation W = cumulative likelihood ratio/cumulative likelihood ratio + 1). These values were determined for 50 volunteer families and compared with values calculated from randomly matched pairs in a reference NCR population database. RESULTS: The W and W(-mother) values of the 50 families range from 96.48 to 99.99 percent and 79.76 to 99.99 percent, respectively. In the NCR database, 195 coincidental matches in seven STR loci out of 5253 possible pairs (3.71%) were detected with W(-mother) values ranging from 12.47 to 99.83 percent. Of these, 53 and 10 random pairs have W(-mother) greater than 95.0 and 99.0 percent, respectively. CONCLUSION: W was higher than W(-mother) in the 50 families. However, the existence of unrelated individuals in the NCR database that randomly matched at seven STR loci and that has W(-mother) values greater than 99.0 percent highlights the need for greater precaution when dealing with motherless cases.

Databases, Genetic↗
PubMed2005

BioThesaurus: a web-based thesaurus of protein and gene names.

UNLABELLED: BioThesaurus is a web-based system designed to map a comprehensive collection of protein and gene names to protein entries in the UniProt Knowledgebase. Currently covering more than two million proteins, BioThesaurus consists of over 2.8 million names extracted from multiple molecular biological databases according to the database cross-references in iProClass. The BioThesaurus web site allows the retrieval of synonymous names of given protein entries and the identification of protein entries sharing the same names. AVAILABILITY: BioThesaurus is accessible for online searching at http://pir.georgetown.edu/iprolink/biothesaurus

Animals↗
PubMed1997

UnCover on the Web: search hints and applications in library environments.

Among the huge maze of resources available on the Internet, UnCoverWeb stands out as a valuable tool for medical libraries. This up-to-date, free-access, multidisciplinary database of periodical references is searched through an easy-to-learn graphical user interface that is a welcome improvement over the telnet version. This article reviews the basic and advanced search techniques for UnCoverWeb, as well as providing information on the document delivery functions and table of contents alerting service called Reveal. UnCover's currency is evaluated and compared with other current awareness resources. System deficiencies are discussed, with the conclusion that although UnCoverWeb lacks the sophisticated features of many commercial database search services, it is nonetheless a useful addition to the repertoire of information sources available in a library.

Computer Communication Networks↗
PubMed2006

IRESite: the database of experimentally verified IRES structures (www.iresite.org).

IRESite is an exhaustive, manually annotated non-redundant relational database focused on the IRES elements (Internal Ribosome Entry Site) and containing information not available in the primary public databases. IRES elements were originally found in eukaryotic viruses hijacking initiation of translation of their host. Later on, they were also discovered in 5'-untranslated regions of some eukaryotic mRNA molecules. Currently, IRESite presents up to 92 biologically relevant aspects of every experiment, e.g. the nature of an IRES element, its functionality/defectivity, origin, size, sequence, structure, its relative position with respect to surrounding protein coding regions, positive/negative controls used in the experiment, the reporter genes used to monitor IRES activity, the measured reporter protein yields/activities, and references to original publications as well as cross-references to other databases, and also comments from submitters and our curators. Furthermore, the site presents the known similarities to rRNA sequences as well as RNA-protein interactions. Special care is given to the annotation of promoter-like regions. The annotated data in IRESite are bound to mostly complete, full-length mRNA, and whenever possible, accompanied by original plasmid vector sequences. New data can be submitted through the publicly available web-based interface at http://www.iresite.org and are curated by a team of lab-experienced biologists.

5' Untranslated Regions↗
PubMed2004

Evaluation of five full-text drug databases by pharmacy students, faculty, and librarians: do the groups agree?

OBJECTIVES: The purpose of this study is to assess the usefulness of five full-text drug databases as evaluated by medical librarians, pharmacy faculty, and pharmacy students at an academic health center. Study findings and recommendations are offered as guidance to librarians responsible for purchasing decisions. METHODS: Four pharmacy students, four pharmacy faculty members, and four medical librarians answered ten drug information questions using the databases AHFS Drug Information (STAT!Ref); DRUGDEX (Micromedex); eFacts (Drug Facts and Comparisons); Lexi-Drugs Online (Lexi-Comp); and the PDR Electronic Library (Micromedex). Participants noted whether each database contained answers to the questions and evaluated each database on ease of navigation, screen readability, overall satisfaction, and product recommendation. RESULTS: While each study group found that DRUGDEX provided the most direct answers to the ten questions, faculty members gave Lexi-Drugs the highest overall rating. Students favored eFacts. The faculty and students found the PDR least useful. Librarians ranked DRUGDEX the highest and AHFS the lowest. The comments of pharmacy faculty and students show that these groups preferred concise, easy-to-use sources; librarians focused on the comprehensiveness, layout, and supporting references of the databases. CONCLUSION: This study demonstrates the importance of consulting with primary clientele before purchasing databases. Although there are many online drug databases to consider, present findings offer strong support for eFacts, Lexi-Drugs, and DRUGDEX.

Academic Medical Centers↗
PubMed2005

A comparative study of six European databases of medically oriented Web resources.

OBJECTIVES: The paper describes six European medically oriented databases of Web resources, pertaining to five quality-controlled subject gateways, and compares their performance. METHOD: The characteristics, coverage, procedure for selecting Web resources, record structure, searching possibilities, and existence of user assistance were described for each database. Performance indicators for each database were obtained by means of searches carried out using the key words, "myocardial infarction." RESULTS: Most of the databases originated in the 1990s in an academic or library context and include all types of Web resources of an international nature. Five databases use Medical Subject Headings. The number of fields per record varies between three and nineteen. The language of the search interfaces is mostly English, and some of them allow searches in other languages. In some databases, the search can be extended to Pubmed. Organizing Medical Networked Information, Catalogue et Index des Sites Médicaux Francophones, and Diseases, Disorders and Related Topics produced the best results. CONCLUSIONS: The usefulness of these databases as quick reference resources is clear. In addition, their lack of content overlap means that, for the user, they complement each other. Their continued survival faces three challenges: the instability of the Internet, maintenance costs, and lack of use in spite of their potential usefulness.

Databases, Bibliographic↗
PubMed2002

A successful cross-training experience of reference service at UCLA.

This paper describes a successful cross-training and reference librarian exchange experience involving two librarians at UCLA, one based at the Louise M. Darling Biomedical Library and the other based at the College Library, which primarily serves undergraduates. The experience has increased the reference skills and expertise of both librarians by introducing them to new sets of reference tools and databases, and has broadened their network of colleagues within the UCLA Library system. The participating libraries have also benefited from the exchange, and the program is expanding to include other UCLA libraries.

Inservice Training↗