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PubMed2004

[Construction of directory for biomedical databases on INTERNET].

OBJECTIVE: To construct a global directory of biomedical databases(DBD), which can be used free of charge on INTERNET. It will be convenient for researchers to find out related databases quickly, easily and accurately by using DBD since there are not enough useful tools for database retrieval. Biomedical databases will be an accelerator in development of biomedicine with the help of DBD. METHODS: PubMed and Google were main tools for searching related databases. Proper search strategy with rigorous indexing rules helped us to filter databases. The database management system was Microsoft SQL-Server 2000. The web pages of DBD were designed with Macromedia Dreamwaver MX. ASP (active server pages) technology was used to deal with the key words and scores sent by users. RESULTS: There were 66 subjects and 1 258 databases in DBD at this time. We released the Chinese and English versions of DBD on the INTERNET at the same time http://cmbi.bjmu.edu.cn/DBList/index.htm http://cmbi.bjmu.edu.cn/DBList/index_en.htm . Score system was also established to evaluate the content of the indexed databases. Users can search DBD by subjects key words and alphabetic databases' names easily. CONCLUSION: DBD has laid the primary foundation for further core biomedical database evaluation system. DBD, as a useful tool for biomedical database retrieval, will be of great aid to users since databases have played a more and more important role in the biomedical research.

Databases as Topic↗

PubMedDate not supplied

Icelandic. Decision of the Supreme Court on the protection of privacy with regard to the processing of Health Sector Databases. Attorney at Law vs The State of Iceland.

Mr. R appealed for a decision by the Court to overturn the refusal of the Medical Director of Health to her request that health information in medical records pertaining to herdeceased father should not be entered into the Health Sector Database. Furthermore, she called for recognition of her right to prohibit the transfer of such information into a database. Article 8 of Act No 139/1998 on a Health Sector Database provides for the right of patients to refuse permission, by notification to the Medical Director of Health, for information concerning them to be entered into the Health Sector Database. The Court concluded that R could not exercise this right acting as a substitute of her deceased father, but it was recognised that she might, on the basis of her right to protection of privacy, have an interest in preventing the transfer of health data concerning her father into the database, as information could be inferred from such data relating to the hereditary characteristics of her father which might also apply to herself. It was revealed in the course of proceedings that extensive information concerning people's health is entered into medical records, e.g. medical treatment, life-style and social conditions, employment and family circumstances, together with a detailed identification of the person that the information concerns. It was recognised as unequivocal that the provisions of Paragraph 1 of Article 71 of the Constitution applied to such information and guaranteed to every person the right to protection of privacy in this respect. The Court concluded that the opinion of the District Court, which, inter alia, was based on the opinion of an assessor, to the effect that so-called one-way encryption could be carried out in such a secure manner that it would be virtually impossible to read the encrypted data, had not been refuted. It was noted, however, that Act No. 139/1998 provides no details as to what information from medical records is required to be encrypted in this manner prior to transfer into the database or whether certain information contained in the medical records will not be transferred into the database. The documents of the case indicate that only the identity number of the patient would be encrypted in the database, and that names, both those of the patient and his relatives, as well as the precise address, would be omitted. It is obvious that information on these items is not the only information appearing in the medical records which could, in certain cases, unequivocally identify the person concerned. Act No. 139/1998 also provides for authorisation to the licensee to process information from the medical records transferred into the database. The Act stipulates that certain specified public entities must approve procedures and process methods and monitor all queries and processing of information in the database. However, there is no clear definition of what type of queries will be directed to the database or in what form the replies to such queries will appear. The Court concluded that even though individual provisions of Act No 139/1998 repeatedly stipulate that health information in the Health Sector Database should be non-personally identifiable, it is far from adequately ensured under statutory law that this stated objective will be achieved. In light of the obligations imposed on the legislature by Paragraph 1 of Article 71 of the Constitution, the Court concluded that various forms of monitoring of the creation and, operation of the database are no substitute in this respect without foundation in definite statutory norms. In light of these circumstances, and taking into account the principles of Icelandic law concerning the confidentiality and protection of privacy, the Court concluded that the right of R in this matter must be recognised, and her court claims, therefore, upheld.

Databases, Factual↗

PubMed2003

SEMEDA: ontology based semantic integration of biological databases.

MOTIVATION: Many molecular biological databases are implemented on relational Database Management Systems, which provide standard interfaces like JDBC and ODBC for data and metadata exchange. By using these interfaces, many technical problems of database integration vanish and issues related to semantics remain, e.g. the use of different terms for the same things, different names for equivalent database attributes and missing links between relevant entries in different databases. RESULTS: In this publication, principles and methods that were used to implement SEMEDA (Semantic Meta Database) are described. Database owners can use SEMEDA to provide semantically integrated access to their databases as well as to collaboratively edit and maintain ontologies and controlled vocabularies. Biologists can use SEMEDA to query the integrated databases in real time without having to know the structure or any technical details of the underlying databases. AVAILABILITY: SEMEDA is available at http://www-bm.ipk-gatersleben.de/semeda/. Database providers who intend to grant access to their databases via SEMEDA are encouraged to contact the authors.

Computational Biology↗

PubMed2026

Published Database Resources for Traditional, Complementary, and Integrative Medicine: Update of a Systematic Review.

BACKGROUND: Traditional, Complementary, and Integrative Medicine (TCIM) has been established in the academic context of universities. In recent years, strategies have been developed worldwide to strengthen the role of TCIM in supporting the health of the population. Online databases are a common way for obtaining evidence-based information. This article is an update of a former systematic review from 2010 on published databases resources for TCIM. METHODS: The databases CINAHL, CAMbase, Web of Science, MEDLINE/PubMed, and Google Scholar search engine were searched for databases related to TCIM published in peer-reviewed journals between 2010 and November 2024. All included databases were visited online, and information on the origin, content, and scope of the database was extracted. RESULTS: A total of 6579 articles were identified through the literature search. After exclusion of irrelevant articles, full-text screening of 127 articles yielded 37 new databases. Together with 16 still available old databases, these mainly contained information on herbal therapies (n = 15) and Traditional Chinese Medicine (n = 11) from 18 different countries. Newly identified medicinal plant databases offer various scientific resources such as crude drugs, indigenous plants, and structures for natural and phytochemical components with molecular biological content. CONCLUSIONS: This literature review illustrates the dynamic development in the database landscape over the last 15 years. While the number of bibliographic databases is shrinking, databases in the field of medical plants/herbal therapy content are on the rise, which might be due to advances in plant genomics and molecular biology.

Humans↗

PubMed1993

Validity of rheumatoid arthritis diagnoses listed in the Saskatchewan Hospital Separations Database.

A Saskatchewan hospital separations database was compared to abstracted hospital records to determine the reliability of the database (i.e. accuracy with which the computer data reflect the charts from which they were coded) and the validity of classifying rheumatoid arthritis status with the database (i.e. the extent to which rheumatoid arthritis mentioned in the database reflected the condition of the patient). A sample of hospitalized subjects fell into three categories: 144 who never had a database diagnosis of any arthritis, 146 who had a database diagnosis of osteoarthritis, and 142 who had a database diagnosis of rheumatoid arthritis. These 432 people experienced 1717 hospitalizations eligible to match a hospital database listing by date, and 1618 matched. Of the remaining 99, 35 were relatively recent and probably had not yet been entered into the database, 39 were possibly entered incorrectly, and 25 could not be matched in any way. Of 150 hospitalizations with a database diagnosis of rheumatoid arthritis, this diagnosis was in the hospital record for 125. Chart documentation of rheumatoid arthritis status was greatest for subjects who, according to the database, were hospitalized by a rheumatologist: of 73 subjects in this category, abstractions showed 69.9% met > or = 5 American Rheumatism Association criteria, 15.1% met < 5 criteria but had a rheumatologist's diagnosis of rheumatoid arthritis, 1.3% met < 5 criteria and had a rheumatoid arthritis diagnosis by a non-rheumatologist, and 13.7% had no mention of rheumatoid arthritis or its symptoms in any medical record abstracted. In summary, reliability of the database was excellent, but validity depended on the source of diagnosis.

Arthritis, Rheumatoid↗

PubMed1999

Can cardiovascular clinical characteristics be identified and outcome models be developed from an in-patient claims database?

The objective of this study was to assess whether administrative (claims) databases can be used to assess clinical variables and predict outcome. Although administrative databases are useful for assessing resource utilization, their utility for assessing clinical information is less certain. Prospectively gathered clinical databases, however, are expensive and not widely available. The UB92 formulation of the hospital bill was used as an administrative source of data and compared with the clinical cardiovascular database at Emory University. The claims database was compared with the clinical database for 11 variables. Outcome models were developed with multivariate methods. A total of 11,883 patients who underwent catheterization (5,255 underwent percutaneous transluminal coronary angioplasty [PTCA] and 3,794 underwent coronary artery bypass surgery [CABG]) between 1991 and 1995 were included. For some variables, the claims database correlated well (diabetes, sensitivity 87%, specificity 99%), whereas for others the claims database was less accurate (peripheral vascular disease, sensitivity 20%, specificity 99%). Uncertain coding in the claims database, which can result in the same code being used for co-morbid states and severity of disease, as well as complications, limited the ability of claims to predict outcome. Clinical databases may also be limited by lack of objectivity and missing data. The utility of claims databases to assess severity of disease and co-morbid states is limited, and outcome modeling and risk assessment from claims databases may be inappropriate and spurious. Developing better data standards and less expensive methods for acquisition of clinical data is necessary for improved outcome assessment.

Cardiovascular Diseases↗

PubMed1998

Assessment of bibliographic databases performance in information retrieval for occupational and environmental toxicology.

OBJECTIVE: To determine the efficiency of the major bibliographic databases by assessing the percentage of references among the total literature available that can be retrieved from each database. We also evaluated the best database combinations to carry out an exhaustive search. METHODS: BIOSIS, EMBASE, MEDLINE, NIOSH-TIC, and TOXLINE were searched on two topics: allergy to latex and asbestos and mesothelioma, in the title, abstract, or keywords (textwords). This search was performed for the years 1994 and 1995. All the records were classified by journal and author's name and were verified for each record whether or not it was indexed in each database. Statistical analysis was performed with chi 2 test. RESULTS: 777 articles in 510 issues were found. The efficiency of each database (percentage of articles recovered) and of combinations varied between 11% and 63% for one database and between 42% and 86% for a combination of two databases. The reasons why these differences exist between databases, and within a database, between two different subjects or two different years are reported. CONCLUSION: Firstly, it is not advisable to assert that a bibliography is complete when only one database is searched. Secondly, the efficiency of the databases may be quite different. Finally, it is suggested that the best way to be as exhaustive as possible is to search two or more databases-for example, in EMBASE and TOXLINE, or to a lesser extent EMBASE and MEDLINE. This seems to be the best compromise solution between time consumed for searching and efficiency.

Asbestos↗

PubMed2003

Generic design of Web-based clinical databases.

BACKGROUND: The complexity and the rapid evolution and expansion of the domain of clinical information make development and maintenance of clinical databases difficult. Whenever new data types are introduced or existing types are modified in a conventional relational database system, the physical design of the database must be changed accordingly. For this reason, it is desirable that a clinical database be flexible and allow for modifications and for addition of new types of data without having to change the physical database schema. The ideal clinical database would therefore implement a highly-detailed logical database schema in a completely-generic physical schema that stores the wide variety of clinical data in a small and constant number of tables. OBJECTIVE: The objective was to review the medical literature regarding generic design of clinical databases. METHODS: A search strategy was devised for PubMed and Google to get the best match of peer-reviewed articles and free Web resources on the subject. RESULTS: Eight peer reviewed articles and a Web tutorial were found. All the resources described the so-called Entity-Attribute-Value (EAV) design as a means of simplifying the physical layout of data tables in a clinical database. In Entity-Attribute-Value design all data can be stored in a single generic table with conceptually 3 columns: 1 for entity (eg, patient identification), 1 for attribute (eg, name), and 1 for value (eg, "Jens Hansen"). To add more descriptive fields to the entity class, all that is necessary is to add attribute values to be stored in the attribute field. The main advantages of the Entity-Attribute-Value design are flexibility and effective entity-centered data retrieval. The main disadvantages are complicated front-end programming needed to display data in a conventional layout that the user understands and less-efficient attribute-centered queries. The Internet offers unique opportunities for database deployment, eliminating problems of user-interface deployment. Furthermore, Web forms may be generated in a completely-generic fashion during run time from metadata describing the semantic structure of clinical information stored in the database. CONCLUSIONS: The Entity-Attribute-Value model is useful for generic design of clinical databases. Depending on the specific requirements of the application, more or less complex metadata models may be applied.

Databases, Factual↗

PubMed1994

SORTEZ: a relational translator for NCBI's ASN.1 database.

The National Center for Biotechnology Information (NCBI) has created a database collection that includes several protein and nucleic acid sequence databases, a biosequence-specific subset of MEDLINE, as well as value-added information such as links between similar sequences. Information in the NCBI database is modeled in Abstract Syntax Notation 1 (ASN.1) an Open Systems Interconnection protocol designed for the purpose of exchanging structured data between software applications rather than as a data model for database systems. While the NCBI database is distributed with an easy-to-use information retrieval system, ENTREZ, the ASN.1 data model currently lacks an ad hoc query language for general-purpose data access. For that reason, we have developed a software package, SORTEZ, that transforms the ASN.1 database (or other databases with nested data structures) to a relational data model and subsequently to a relational database management system (Sybase) where information can be accessed through the relational query language, SQL. Because the need to transform data from one data model and schema to another arises naturally in several important contexts, including efficient execution of specific applications, access to multiple databases and adaptation to database evolution this work also serves as a practical study of the issues involved in the various stages of database transformation. We show that transformation from the ASN.1 data model to a relational data model can be largely automated, but that schema transformation and data conversion require considerable domain expertise and would greatly benefit from additional support tools.

Algorithms↗

PubMed1992

Human HPRT mutant database: software for data entry and retrieval.

We have developed a computer database containing information on over 1,000 human hypoxanthine guanine phosphoribosyl transferase (HPRT) mutants. Both published and unpublished data are present. The database itself is maintained in a dBASE format (.DBF) and we provide a set of programs to examine and extract information from the database. A program to input information into the database is also supplied. The database and programs are available directly from us or via remote FTP (file transfer protocol) using BITNET/INTERNET. All programs require an IBM-compatible computer, the MS-DOS operating system (version 3.3 or greater), and a hard disk with about 5 megabytes of free disk space. The purpose of the database is 1) to allow investigators to contribute their HPRT mutants directly to the database in a standardized fashion, and 2) to allow access to the entire database with a set of programs that allows manipulation and extraction of data. For example, using our programs it is possible to i) order the database by base pair position, ii) examine only information regarding mutagenesis by a particular agent, iii) search for a particular author, iv) create a report which contains selected portions of the database, the report can be printed or saved as a file. The database will be updated every several months and distributed.

Databases, Bibliographic↗

PubMed2004

Web-accessible proteome databases for microbial research.

The analysis of proteomes of biological organisms represents a major challenge of the post-genome era. Classical proteomics combines two-dimensional electrophoresis (2-DE) and mass spectrometry (MS) for the identification of proteins. Novel technologies such as isotope coded affinity tag (ICAT)-liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations. The vast amount and diverse types of proteomic data require adequate web-accessible computational and database technologies for storage, integration, dissemination, analysis and visualization. A proteome database system (http://www.mpiib-berlin.mpg.de/2D-PAGE) for microbial research has been constructed which integrates 2-DE/MS, ICAT-LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources. The two-dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification. The ICAT-LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs. H37Rv. By formulating complex queries within a functional protein classification database "FUNC_CLASS" for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways. The use of the R language in the database architecture allows high-level data analysis and visualization to be performed "on-the-fly". The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data. The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. Currently, the database system includes proteome information for six strains of microorganisms.

Bacterial Proteins↗

PubMed1996

An inequality for 3D database searching and its use in evaluating the treatment of conformational flexibility.

A mathematical formula is introduced for predicting the number of hits that should be observed in a flexible 3D database search, based on the results of a set of related queries. The projected number of hits is always greater than or equal to the actual number of hits, the discrepancy being due to imperfect treatment of conformational flexibility of the molecules. Hence, the difference between the projected and actual number of hits, delta, serves to measure how well conformational flexibility is being treated, in a manner that is objective, easy for a user to quickly verify, and independent of the particular algorithm for flexible 3D database search. It is shown that delta is a function both of how well conformational flexibility is treated and of the precision of the query. When the distance constraint is defined only to a precision of +/- 2.0 A, in a single-conformer database of drug-like molecules delta values of only 0.03 are found, while in a single-conformer database of di- and tripeptides, delta is 0.15. At increased precision, a flexible 3D database search becomes critical. For a single-conformer database, using a query of precision +/- 0.2 A, applied to a database of drug-like molecules, delta is 0.97; applied to a database of di- and tripeptides, delta is 2.21. By contrast, treating conformational flexibility by storing up to 100 conformers per molecule, at this precision, applied to a database of drug-like molecules, delta is 0.002; applied to a database of di- and tripeptides, delta is 0.07. This inequality, and hence delta, is defined only for database queries containing a single distance constraint; how the inequality may generalize to higher-dimensional queries is still unclear.

Algorithms↗

PubMed2002

Social benefits of non-criminal genetic databases: missing persons and human remains identification.

A Missing Persons Genetic Identification Program (Phoenix Program) was implemented in Spain in order to try to identify cadavers and human remains that could not be identified using traditional forensic approaches; to our knowledge, this is the first database ever implemented and in function in the world. Two separate mitochondrial DNA (mtDNA) databases have been generated and comparisons can be made automatically to match identical or similar sequences contained in both databases. One database is called the Reference Database (RD), which contains mtDNA sequences from maternal relatives of missing persons that provide the samples voluntarily after informed consent. The other database is called the Questioned Database (QD) and is comprised of mtDNA data on unknown remains and cadavers that could not be unequivocally identified. The combined database is a civil database designed solely for human identification and because of the informed consent and voluntary donation of reference samples is different from other databases now used to solve criminal cases. It is timely and incumbent on other willing countries to begin an international collaboration so compatibility and full utility can be enjoyed with this kind of non-criminal database.

Cadaver↗

PubMed2004

Automated linking of free-text complaints to reason-for-visit categories and International Classification of Diseases diagnoses in emergency department patient record databases.

STUDY OBJECTIVE: The use of the International Classification of Diseases system to describe emergency department (ED) case mix has disadvantages. We therefore developed computer algorithms that recognize a combination of words, word fragments, and word patterns to link free-text complaint fields to 20 reason-for-visit categories. We examine the feasibility and reliability of applying these reason-for-visit categories to ED patient-visit databases. METHODS: We analyzed a database (containing complaints and International Classification of Diseases diagnoses for 1 year's visits to a single ED) using a 3-step process (create initial terms, maximize sensitivity, maximize specificity) to define inclusion and exclusion terms for 20 reason-for-visit categories. To assess the reliability of the reason-for-visit assignment algorithm, we repeated the final 2 steps on a second database, composed of visits sampled from 21 EDs. For each database, we determined the prevalence of complaints that link to each reason-for-visit category and the distributions of International Classification of Diseases, Ninth Revision diagnoses that resulted for all patients and patients stratified by age. RESULTS: The 20 reason-for-visit categories capture 77% of all patients in database 1 (mean age 33.5 years) and 67% of all patients in database 2 (mean age 38.9 years). The percentage of visits captured by the 20 reason-for-visit categories, by age range, for databases 1 and 2 are (respectively) 0 to 2 years (84% and 76%), 3 to 10 years (82% and 74%), 11 to 65 years (76% and 68%), and 66 years or older (69% and 60%). The proportions of all complaints that link to each reason-for-visit category are largely similar between databases. Every complaint field that is linked to each reason-for-visit category includes at least 1 term that relates it to the category title, and the most frequently assigned diagnoses in each reason-for-visit category are those that one would expect to be associated with the reason-for-visit category complaints. CONCLUSION: The method by which free-text complaint fields are parsed into reason-for-visit categories is feasible and reasonably reliable; the finalized database 1 reason-for-visit category inclusion/exclusion terms lists required only modest changes to work well in database 2. The reason-for-visit categories used here are broadly defined to maximize the proportion of visits that they capture; more narrowly defined reason-for-visit categories will require more extensive revision of their inclusion/exclusion terms lists when used in different databases. A prospective, reason-for-visit-based ED classification system could have several useful applications (including syndromic surveillance), although content validity analysis will be necessary to investigate this hypothesis.

Adolescent↗

PubMedDate not supplied

Evaluation of consumer drug information databases.

OBJECTIVES: To evaluate prescription drug information contained in six consumer drug information databases available on CD-ROM, and to make health care professionals aware of the information provided, so that they may appropriately recommend these databases for use by their patients. DESIGN: Observational study of six consumer drug information databases: The Corner Drug Store, Home Medical Advisor, Mayo Clinic Family Pharmacist, Medical Drug Reference, Mosby's Medical Encyclopedia, and PharmAssist. SETTING: Not applicable. PATIENTS OR OTHER PARTICIPANTS: Not applicable. INTERVENTIONS: Information on 20 frequently prescribed drugs was evaluated in each database. The databases were ranked using a point-scale system based on primary and secondary assessment criteria. MAIN OUTCOME MEASURES: For the primary assessment, 20 categories of information based on those included in the 1998 edition of the USP DI Volume II, Advice for the Patient: Drug Information in Lay Language were evaluated for each of the 20 drugs, and each database could earn up to 400 points (for example, 1 point was awarded if the database mentioned a drug's mechanism of action). For the secondary assessment, the inclusion of 8 additional features that could enhance the utility of the databases was evaluated (for example, 1 point was awarded if the database contained a picture of the drug), and each database could earn up to 8 points. RESULTS: The results of the primary and secondary assessments, listed in order of highest to lowest number of points earned, are as follows: Primary assessment--Mayo Clinic Family Pharmacist (379), Medical Drug Reference (251), PharmAssist (176), Home Medical Advisor (113.5), The Corner Drug Store (98), and Mosby's Medical Encyclopedia (18.5); secondary assessment--The Mayo Clinic Family Pharmacist (8), The Corner Drug Store (5), Mosby's Medical Encyclopedia (5), Home Medical Advisor (4), Medical Drug Reference (4), and PharmAssist (3). CONCLUSION: The Mayo Clinic Family Pharmacist was the most accurate and complete source of prescription drug information based on the USP DI Volume II and would be an appropriate database for health care professionals to recommend to patients.

CD-I↗

PubMed2000

The quest to deduce protein function from sequence: the role of pattern databases.

In the wake of the numerous now-fruitful genome projects, we have witnessed a 'tsunami' of sequence data and with it the birth of the field of bioinformatics. Bioinformatics involves the application of information technology to the management and analysis of biological data. For many of us, this means that databases and their search tools have become an essential part of the research environment. However, the rate of sequence generation and the haphazard proliferation of databases have made it difficult to keep pace with developments, even for the cognoscenti. Moreover, increasing amounts of sequence information do not necessarily equate with an increase in knowledge, and in the panic to automate the route from raw data to biological insight, we may be generating and propagating innumerable errors in our precious databases. In the genome era upon us, researchers want rapid, easy-to-use, reliable tools for functional characterisation of newly determined sequences. For the pharmaceutical industry in particular, the Pandora's box of bioinformatics harbours an information-rich nugget, ripe with potential drug targets and possible new avenues for the development of therapeutic agents. This review outlines the current status of the major pattern databases now used routinely in the analysis of protein sequences. The review is divided into three main sections. In the first, commonly used terms are defined and the methods behind the databases are briefly described; in the second, the structure and content of the principal pattern databases are discussed; and in the final part, several alignment databases, which are frequently confused with pattern databases, are mentioned. For the new-comer, the array of resources, the range of methods behind them and the different tools required to search them can be confusing. The review therefore also briefly mentions a current international endeavour to integrate the diverse databases, which effort should facilitate sequence analysis in the future. This is particularly important for target-discovery programmes, where the challenge is to rationalise the enormous numbers of potential targets generated by sequence database searches. This problem may be addressed, at least in part, by reducing search outputs to the more focused and manageable subsets suggested by searches of integrated groups of family-specific pattern databases.

Amino Acid Motifs↗

PubMed1999

The PIR-International Protein Sequence Database.

The Protein Information Resource (PIR; http://www-nbrf.georgetown. edu/pir/) supports research on molecular evolution, functional genomics, and computational biology by maintaining a comprehensive, non-redundant, well-organized and freely available protein sequence database. Since 1988 the database has been maintained collaboratively by PIR-International, an international association of data collection centers cooperating to develop this resource during a period of explosive growth in new sequence data and new computer technologies. The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available. Full-scale family classification supports comparative genomics research, aids sequence annotation, assists database organization and improves database integrity. The PIR WWW server supports direct on-line sequence similarity searches, information retrieval, and knowledge discovery by providing the Protein Sequence Database and other supplementary databases. Sequence entries are extensively cross-referenced and hypertext-linked to major nucleic acid, literature, genome, structure, sequence alignment and family databases. The weekly release of the Protein Sequence Database can be accessed through the PIR Web site. The quarterly release of the database is freely available from our anonymous FTP server and is also available on CD-ROM with the accompanying ATLAS database search program.

Amino Acid Sequence↗

PubMed2005

[The use of bibliographic databases by Spanish-speaking Latin American biomedical researchers: a cross-sectional study].

OBJECTIVE: To describe how Spanish-speaking biomedical professionals in Latin America access and utilize bibliographic databases. METHODS: Based on a MEDLINE search, 2 515 articles published between August 2002 and August 2003 were identified that dealt with and/or had authors from 16 countries: Argentina, Bolivia, Chile, Colombia, Costa Rica, Cuba, Ecuador, Guatemala, Honduras, Mexico, Nicaragua, Panama, Paraguay, Peru, Uruguay, and Venezuela. The search was limited to references to basic science, clinical science, or social medicine. A survey was sent by e-mail to researchers who lived in 15 of the 16 countries (the exception being Nicaragua). The survey asked about the researcher's area of work (basic science, clinical science, or public health), the level of skill in using databases, the frequency and type of access to the databases most utilized, the impact from not having access to the full text of articles when preparing a manuscript, and how the respondent usually obtained the full-text version of articles. RESULTS: A total of 586 e-mail messages with the survey were sent out, and 185 responses were received (32%). The databases most utilized to obtain biomedical information were MEDLINE (34.1%), general search engines (Google, Yahoo!, and AltaVista) (15.9%), on-line journals (9.8%), BIREME-LILACS (6.0%), BioMedNet (5.4%), the databases of the Centers for Disease Control and Prevention of the United States of America (5.2%), and the Cochrane Library (4.9%). Of the respondents, 64% said they had average or advanced abilities in using MEDLINE. However, 71% of the respondents did not use or were not aware of the MEDLINE Medical Subject Headings (MeSH), a controlled vocabulary established by the National Library of Medicine of the United States of America for indexing articles. The frequency of accessing the databases was similar in all the countries studied, without significant differences in terms of the type of access (authorized access to commercial databases, unauthorized access to those databases, or access to databases available for free) or the level of abilities. Of the respondents, 87% said they had not included important references in the articles that they had published because they had not had access to the full text of those items, and 56% said they had cited articles that they had not read in full. In addition, 7.6% of the respondents admitted to unauthorized use of limited-access databases, such as through borrowed passwords or copied disks. More than two-thirds of the respondents said they obtained the full text of articles through photocopies or directly from the authors. CONCLUSIONS: In order to encourage scientific output by Latin American researchers, more of them need to be trained in the use of the most frequently used databases, especially MEDLINE. Those researchers also need to have expanded access to the biomedical literature.

Biomedical Research↗