SEARCH · PubMed Health

Results for “Data Files”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources

PubMed1990

Data file standard for flow cytometry. Data File Standards Committee of the Society for Analytical Cytology.

This data file standard for flow cytometry (FCS) provides a detailed description of a data file structure designed such that the file can include all of the information necessary to describe fully: 1) the instrument used to obtain the data; 2) the sample measured; 3) the data obtained; and 4) the results of analysis of the data. The file may contain one or more data sets. Each data set includes data from a single sample or acquisition run. Each data set consists of a minimum of four parts--HEADER, TEXT, DATA, and ANALYSIS--all of which are required. The file is structured such that the parts of a data set do not have to be in any particular order, except for the HEADER, which must always be first. The HEADER contains pointers to the beginning and end of each of the other three parts. The file is written as a continuous byte stream, with no line or page formating. The HEADER, TEXT, and ANALYSIS parts are written in ASCII format and the DATA part can be written in ASCII, binary integer or floating point. This Standard, noted as FCS2.0, is based on a standard proposed by Murphy and Chused (Cytometry 5:553-555, 1984). Data written utilizing their proposed format (FCS1.0) is compatible with the format described here. Future versions of the standard will maintain compatibility with older versions.

Flow Cytometry↗

PubMed1988

Use of a computer data file for storage of heat resistance data on bacterial spores.

The use of a computer data file to compile published heat resistance data on bacterial spores is described. Information relating to sporulation, heating and recovery of the spores, in addition to decimal reduction times at different temperatures has been stored. The data file was constructed using Minitab and an indexer program on a VAX 11/750 computer operating on VMS. Storage of the data in this way enables rapid manipulation and analysis of large quantities of information relating to heat resistance of bacterial spores.

Clostridium↗

PubMed2003

Formats of image data files that can be used for routine digital light micrography. Part one.

Failing to open computer files that describe image data is not the most frustrating experience that the user of a computer can suffer, but it is high on list of possible aggravations. To ameliorate this, the structure of uncompressed image data files is described here. The various ways in which information that describes a picture can be recorded are related, and a primary distinction between raster or bitmap based and vector or object based image data files is drawn. Bitmap based image data files are the more useful of the two formats for recording complicated images such as digital light micrographs, whereas object based files are better for recording illustrations and cartoons. Computer software for opening a very large variety of different formats of digital image data is recommended, and if these fail, ways are described for opening bitmap based digital image data files whose format is unknown.

Computer Graphics↗

PubMed1990

Introduction to flow cytometry data file standard.

The Data File Standards Committee of the Society for Analytical Cytology presents a Standard to be used for the storage of data associated with flow cytometric measurements. The Standard specifies a format that provides for the inclusion of all information necessary to fully describe: 1) the instrument used for the measurement; 2) the sample measured; 3) the data obtained; and 4) the results of analysis of the data. The Committee and the Society for Analytical Cytology point out that the use of this Standard by all those individuals and companies that generate or use data taken with flow cytometers or generate methods of analysis for the data will encourage the sharing of such data and methods of analysis.

Flow Cytometry↗

PubMed2000

OTS: a program for converting Noldus Observer data files to SDIS files.

A program for converting Noldus Observer data files (ODF) to sequential data interchange standard (SDIS) files is described. Observer users who convert their data files can then take advantage of various flexible and powerful data modification and computational procedures available in the Generalized Sequential Querier, a program that assumes SDIS-formatted files.

Behavior↗

PubMed1984

A proposal for a flow cytometric data file standard.

The increasing complexity of multiparameter data collection and analysis in flow cytometry and the development of relatively inexpensive arc-lamp-based flow cytometers, which increases the probability that laboratories or institutions may have more than one type of instrument, creates a need for shareable analysis programs and for the transport of flow cytometric data files within an installation or from one institution to another. To address this need, we propose a standard file format to be used for all flow cytometric data. The general principles of this proposal are: (1) The data file will contain a minimum of three segments, TEXT, DATA, and ANALYSIS; (2) The TEXT and ANALYSIS segments consist of KEYWORDS, which are the names of data fields, and their values; (3) All TEXT is encoded in ASCII; (4) KEYWORDS and their values may be of any length; (5) Certain KEYWORDS will be standard, i.e., having specified formats to be recognized by all programs. The structure of the DATA segment will be uniquely defined by the values of KEYWORDS in the TEXT area. It may be in any bit resolution, facilitating compatibility between machines with different word length and/or allowing bit compression of the data. The structured nature of the TEXT area should facilitate management of flow cytometric data using existing data base management systems. The proposed file format has been implemented on VAX, PDP-11, and HP9920 based flow cytometry data acquisition systems.

Computers↗

PubMedDate not supplied

Sharing digital micrographs and other data files between computers.

It ought to be easy to exchange digital micrographs and other computer data files with a colleague even on another continent. In practice, this often is not the case. The advantages and disadvantages of various methods that are available for exchanging data files between computers are discussed. When possible, data should be transferred through computer networking. When data are to be exchanged locally between computers with similar operating systems, the use of a local area network is recommended. For computers in commercial or academic environments that have dissimilar operating systems or are more widely spaced, the use of FTPs is recommended. Failing this, posting the data on a website and transferring by hypertext transfer protocol is suggested. If peer to peer exchange between computers in domestic environments is needed, the use of Messenger services such as Microsoft Messenger or Yahoo Messenger is the method of choice. When it is not possible to transfer the data files over the internet, single use, writable CD ROMs are the best media for transferring data. If for some reason this is not possible, DVD-R/RW, DVD+R/RW, 100 MB ZIP disks and USB flash media are potentially useful media for exchanging data files.

Computer Communication Networks↗

PubMedDate not supplied

Archive of mass spectral data files on recordable CD-ROMs and creation and maintenance of a searchable computerized database.

A database containing names of mass spectral data files generated in a forensic toxicology laboratory and two Microsoft Visual Basic programs to maintain and search this database is described. The data files (approximately 0.5 KB/each) were collected from six mass spectrometers during routine casework. Data files were archived on 650 MB (74 min) recordable CD-ROMs. Each recordable CD-ROM was given a unique name, and its list of data file names was placed into the database. The present manuscript describes the use of search and maintenance programs for searching and routine upkeep of the database and creation of CD-ROMs for archiving of data files.

CD-ROM↗

PubMed2001

[Required procedure for nominal data files processing in biomedical research].

To date, biomedical research using nominal data files for the data collection, data acquisition or data processing has had to comply with 2 French laws (Law of December, 20, 1988, modified, relating to the protection of patients participating in biomedical research, and the Law of January, 6, 1978, completed by the Law of July 1, 1994 n degrees 94-548, chapter V bis). This later law dictates rules not only for the establishment of nominal data files, but also confer individual rights to filed persons. These regulations concern epidemiological research, clinical trials, drug watch studies and economic health research. In this note, we describe the obligations and specific general and simplified procedure required for conducting biomedical research. Included in the requirements are an information and authorization procedure with the local and national consultative committees on data processing in biomedical research (CCTIRS, Comité Consultatif sur le Traitement de l'Information en Recherche Biomédicale, and CNIL, Commission Nationale Informatique et Libertés).

Clinical Trials as Topic↗

PubMed2001

Use and validation of public data files for identification of the diabetic population in a Danish county.

INTRODUCTION: This study aims to describe the process of identifying people known to have diabetes through public data files, to validate this method, and to describe models for optimization of such identification processes. PATIENTS AND METHODS: In a study population of 303,250 citizens, the diabetics were identified by combining information from public data files with information from general practitioners. Data validity was checked by comparing the results of data searches in public data files against information from general practitioners and a random sample of diabetics. Two models were defined to optimize the use of public data files for identification of diabetics. In model A the minimum number of parameters needed to obtain a sensitivity as high as possible was identified. In model B the optimal combination of parameters needed to obtain a high positive predictive value combined with a high sensitivity was identified. RESULTS: A total of 5449 diabetics were identified. Of those 4438 (81%) were classified as Type 2 diabetics and 1011 (19%) were classified as Type 1 diabetics. The data validation revealed that one person was misclassified as a diabetic and 93 persons were misclassified as non-diabetics. In model A the identification parameters included: "prescription", "HbA1c", "chiropodist service" and "glucose service". In model B the optimal combination of parameters was identified as: minimum two HbA1c measurements, minimum one visit to a chiropodist, minimum one prescription or minimum one abnormal HbA1c during one year. CONCLUSION: Public data files are suitable for identification of both Type 1 and Type 2 diabetics. Models have been developed to identify diabetics and to promote the possibilities of long-term follow-up and quality assessment in an unselected diabetic population in a region.

Adult↗

PubMed2003

NCL: a C++ class library for interpreting data files in NEXUS format.

UNLABELLED: The NEXUS Class Library (NCL) is a collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses. The NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored therein. Because users are not required to reformat the data file for each program, use of the NEXUS format prevents cut-and-paste errors as well as the proliferation of copies of the original data file. The purpose of making the NCL available is to encourage the use of the NEXUS format by making it relatively easy for programmers to add the ability to interpret NEXUS files in newly developed software. AVAILABILITY: The NCL is freely available under the GNU General Public License from http://hydrodictyon.eeb.uconn.edu/ncl/ SUPPLEMENTARY INFORMATION: Documentation for the NCL (general information and source code documentation) is available in HTML format at http://hydrodictyon.eeb.uconn.edu/ncl/

Databases, Bibliographic↗

PubMed1983

Microcomputers in surgery: a data file and analysis program.

A microcomputer based patient data file and analysis system is both feasible and useful. One such system is described in this paper. The advantages and disadvantages of the system are discussed. It may be used in many patient-related specialties and will enable practitioners not only to file their data but more importantly to analyse it so that they can improve their performance and cost-effectiveness. It is the author's belief that few realize the potential of the microcomputer in clinical practice and many are put off computing and computerized recording and data analysis because of the size and the difficulties that most experience with larger minicomputer-based facilities.

Colonoscopy↗

PubMed1989

A proposed standard data file format for hyperthermia treatments.

One of the most critical areas of research essential to improve the clinical use of hyperthermia in cancer therapy is the determination and evaluation of temperature during therapy. In order to improve the dissemination of newly developed thermometry measurement and analysis programs and facilitate the transport of hyperthermia data files between computers for both intra- and inter- institutional use, we propose a standard file format, the Hyperthermia Data Standard (HDS), which can be used for all hyperthermia data. This data file consists of segments of which nine have been defined. The first is an initial /VERSION segment which identifies the file standard. This is followed by eight major segments: 2) a /IDENT segment which contains file and patient identification information; 3) a /TEXT segment containing additional miscellaneous documentation; 4) a /TUMOR segment which provides tumor and treatment site information; 5) a /HSETUP segment which contains treatment setup information; 6) a /FORMAT segment which defines the data segment structure; 7) a /DATA segment containing the actual thermometry data; 8) a /FOLLOWUP segment for documenting patient response; and 9) an /ANALYSIS segment containing summary information. All segments begin and end with a specified delimiter and, except for the first two (/VERSION and /IDENT), may be repeated more than once. For ease in debugging and verifying adherence to the standard, all information in the file is encoded in printable ASCII characters. All segments consist solely of records containing KEYWORDS and KEYWORD VALUES which identify specified information. Certain KEYWORDS are standard, i.e., having specified names and information formats as defined in this document. The /DATA segment consists of ASCII encoded chronological treatment thermometry and other data whose format and structure is identified in the /FORMAT segment. The /ANALYSIS segment provides the flexibility to store the results of any analysis program along with the actual data file for ease of data management. This thermometry data file standard is designed to provide both flexibility and extendability for all possible forms of hyperthermia treatment data. Furthermore, it is designed to provide a simple format which may be easily read by higher level languages. This document is intended for commercial manufacturers and others who are writing programs to document clinical hyperthermia treatments with the intention that they either use this format for their data storage or provide a means to convert their data into this format.(ABSTRACT TRUNCATED AT 400 WORDS)

Body Temperature↗

PubMed1999

Building quantitative stereology data files with scion image, a public domain image processing and analysis software.

Two-dimensional data obtained from a histological cross-section of a tissue can be utilized to obtain three-dimensional information by the methods of quantitative stereology. The resulting quantitative information is useful in both experimental studies and whole-animal investigations for regulatory and safety purposes. Quantitative stereologic analysis requires considerable data collection and calculation and is thus practical only through the use of computer hardware and software. We have previously reported the development of a program, STEREO, which compiles data from carcinogenesis experiments, recording information from tissue sections for the estimation of the number of altered hepatic foci (AHF) per liver and the volume fraction of AHF in liver on a three-dimensional basis. The data file itself was built by measuring tissue and focal transections through a slide-reading process that involved the manual use of a digitizer. In order to increase the speed and efficiency of the analytical process, we have integrated the STEREO program with a public domain software, Scion Image. This software integration involves two portions: the building macros and the interface. Macros for quantitative stereology used in Scion Image were written to customize and simplify the measurement and to generate data needed for building each of the data files. An interface program, BuildFi.exe, was developed to receive data generated from Scion Image and to align sequential tissue plots from up to four serial sections stained with different markers. As a result, the user can store data on a disk in the format of the STEREO data files. By combining STEREO with Scion Image, the slide-reading process is simplified and can be performed automatically. It has proven to be more objective, time saving, and efficient than all earlier versions.

Animals↗

PubMed1997

Proposed new data file standard for flow cytometry, version FCS 3.0.

In 1984, the first flow cytometry data file format was proposed as Flow Cytometry Standard 1.0 (FCS1.0). FCS 1.0 provided a uniform file format allowing data acquired on one computer to be correctly read and interpreted on other computers running a variety of operating systems. That standard was modified in 1990 and adopted by the Society of Analytical Cytology as FCS 2.0. Here, we report on an update of the FCS 2.0 standard which we propose to designate FCS 3.0. We have retained the basic four segment structure of earlier versions (HEADER, TEXT, DATA and ANALYSIS) in order to maintain analysis software compatibility, where possible. The changes described in this proposal include a method to collect files larger than 100 megabytes (not possible in earlier versions of the standard), the inclusion of international characters in the TEXT portions of the file, a method of verifying data integrity using a 16-bit cyclic redundancy check, and increased keyword support for cluster analysis and time acquisition. This report summarizes the work of the ISAC Data File Standards Committee. The complete and detailed FCS 3.0 standard is available through the ISAC office [Sherwood Group, 60 Revere Drive, Ste 500, Northbrook, IL 60062, phone: (847) 480-9080 ext. 231, fax: (847) 480-9282, E-mail: isac@sherwood-group.com] or through the internet at the ISAC WWW site, http://nucleus.immunol.washington.edu/ISAC.ht ml.

Database Management Systems↗

PubMed1996

Quantitative comparison of planar and SPECT normal data files of thallium-201, technetium-99m-sestamibi, technetium-99m-tetrofosmin and technetium-99m-furifosmin.

UNLABELLED: In recent years, several of 99mTc-labeled myocardial perfusion imaging agents have been developed, such as 99mTc-sestamibi, 99mTc-tetrofosmin and 99mTc-furifosmin. Although images obtained with these new tracers have a general similar appearance, there are differences in the myocardial kinetics, body distribution, general quality of images and imaging protocols. The aim of this study was to quantitatively compare normal exercise planar and SPECT data files obtained with 201TI and 99mTc-labeled agents. METHODS: Lower-limit-of-normal curves were generated for each specific radiopharmaceutical from normal subjects with low (< 3%) pretest likelihood of coronary artery disease using circumferential count distribution profiles from planar and SPECT exercise images. Lower-limit-of-normal curves were statistically compared using the nonparametric Kruskall-Wallis and Wilcoxon tests. RESULTS: Planar and SPECT lower-limit-of-normal curves generated for each radiopharmaceutical showed general similarities. Statistically significant differences among the lower-limit-of-normal curves were found in the planar left anterior oblique view and in the planar left lateral view (p < 0.05 for each). No statistically significant differences existed between lower-limit-of-normal curves of various radiopharmaceuticals on the planar anterior view and on SPECT imaging. CONCLUSION: For quantitative analysis of planar images, radiopharmaceutical-specific normal data files are mandatory. Although SPECT normal data files of various radiopharmaceuticals are not statistically different, they are not identical. It appears, nevertheless, prudent to use radiopharmaceutical-specific normal data files for quantitative analysis of SPECT images.

Adult↗

PubMed2006

Method to assess identifiability in electronic data files.

The authors developed the Record Uniqueness (RU) software program to assess electronic data files for risk of confidentiality breach based on unique combinations of key variables. The underlying methodology utilized by the RU program generates a frequency distribution for every variable selected for analysis and for all combinations of the variables selected. In addition, the program provides the regression coefficient that designates the relative contribution of each variable to the unique records on the data file. The authors used RU to evaluate a North American Association of Central Cancer Registries research data set with 4.67 million cases from 34 population-based cancer registries for 1995-2001. To illustrate the process and utility of RU, they describe the evaluation process of the confidentiality risk of adding a county-based socioeconomic measure to the research file. The RU method enables one to be assured of record confidentiality, provides flexibility to adjust record uniqueness thresholds for different users or purposes of data release, and facilitates good stewardship of confidential data balanced with maximum use and release of information for research. RU is a useful data tool that can quantify the risk of confidentiality breach of electronic health databases, including reidentifiability of cases through triangulation of information or linkage with other electronic databases.

Confidentiality↗

PubMed2003

Formats of image data files that can be used in routine digital light micrography. Part two.

This is part two of an article that describes the properties of the image data files that are encountered routinely in digital light micrography. In the current part of the article, the differences between saving image data as large intact files and smaller files that have had some information removed, i.e., using lossy compression, are related first. Subsequently, appropriate ways of configuring computers to deal with the large intact image data files are suggested. The structures of the image data files used for recording dynamic sequences and kinematic animations of series of digital light micrographs, i.e., movie formats, are then described. Finally, some information is supplied about choosing file formats for compressing both static and dynamic image data sets.

Computer Graphics↗