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http://tools.researchonresearch.org/dodsg/web/WebDatabaseHTML.php?service=detail&id=64

THIS RESOURCE IS NO LONGER IN SERVICE, documented on Septemeber 02, 2014. Through a collaborative effort with experts in doctor-elderly patient interaction who participated in the development of ADEPT, a database of approximately 435 audio and video tapes of visits of patients age 65 and older (n=46) to their primary physician was established for testing ADEPT and for access by medical educators and researchers. Data associated with each tape include reason for visit, physician characteristics (age, race, gender), patient characteristics (age, race, gender), companion characteristics (age, race, gender), and length of doctor-patient relationship. Through a collaborative effort with experts in doctor-elderly patient interaction who participated in the development of ADEPT, a database of approximately 435 audio and video tapes of visits of patients age 65 and older (n=46) to their primary physician was established for testing ADEPT and for access by medical educators and researchers. Data associated with each tape include reason for visit, physician characteristics (age, race, gender), patient characteristics (age, race, gender), companion characteristics (age, race, gender), and length of doctor-patient relationship. Patient visits to their primary physician were videotaped at four sites: an academic medical center in the Midwest, an academic medical center in the Southwest, a suburban managed care medical group, and an urban group of physicians in independent practice. Repeat visits between the same doctor and patient were taped for 19 patients resulting in 48 tapes of multiple visits. Patients were recruited in the waiting room for a convenience sample. Before the visit, patients provided demographic data and completed a global satisfaction form. Following the visit, patients completed the SF-36, and the ABIM for patient satisfaction. Two weeks following the visit, patients were contacted by telephone and asked about their understanding, compliance and their utilization of health services over the past year. At twelve months, patients were contacted by telephone for administration of the SF-36, the global satisfaction form, and the utilization of health services survey. Data Availability: Archived at the Saint Louis University School of Medicine Library. Interested researchers and medical educators should contact the PI, Mary Ann Cook, JVCRadiology (at) sbcglobal.net * Dates of Study: 1998-2001 * Study Features: Longitudinal, Anthropometric Measures * Sample Size: 46

Proper citation: ADEPT - Assessment of Doctor-Elderly Patient Encounters (RRID:SCR_008901) Copy   

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http://edwardslab.bmcb.georgetown.edu/

The Edwards lab conducts research in various aspects of computational biology and bioinformatics, particularly proteomics and mass spectrometry informatics and DNA and protein based signatures for pathogen detection. Some tools provided by Edwards Lab are the PepArML Meta-Search Engine, PeptideMapper Web-Service, Peptide Sequence Databases, Rapid Microorganism Identification Database (RMIDb), and GlycoPeptideSearch. Our primary area of research is the analysis of mass spectrometry experiments for proteomics. Proteomics, the qualitative and quantitative analysis of the expressed proteins of a cell, makes it possible to detect and compare the protein abundance profiles of different samples. Proteins observed to be under or over expressed in disease samples can lead to diagnostic markers or drug targets. The observation of mutated or alternatively spliced protein isoforms may provide domain experts with clues to the mechanisms by which a disease operates. The detection of proteins by mass spectrometry can even signal the presence of airborne microorganisms, such as anthrax, in the detect-to-protect time-frame. Recent research has focused on the discovery of novel peptides in proteomics datasets, improving the sensitivity and specificity of peptide identification using spectral matching with hidden Markov models, and unsupervised machine-learning based peptide identification result combining. Outside of proteomics, we work on computational tools for the design of highly specific oligonucleotides useful for pathogen signatures and PCR assay design. Recent research has focused on precomputing all human oligos of length 20 that are unique up to 4 string edits; and all bacterial 20-mer oligos that are species specific up to 4 string edits.

Proper citation: Edwards Lab (RRID:SCR_008860) Copy   

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http://hub.ucsf.edu/

Portal to resources, expertise, and best practices for investigators, study staff, participants and partners/affiliates to facilitate efficient, compliant and ethical study conduct and management. This collaborative effort across a number of organizations and administrative units was built to leverage existing resources and create new content where readily accessible resources currently don''''t exist. The goals of the HUB are to: * Promote excellence in the quality of clinical research management through education. * Facilitate effective and timely clinical research initiation by improving institutional processes and providing clinical research protocol, regulatory, budget, and financial tools. * Increase awareness of clinical trials in the community through education and community participant recruitment outreach activities. * Interface with institutional/industry partners to support enhanced clinical research practice.

Proper citation: Clinical Research Resource HUB (RRID:SCR_008979) Copy   

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http://www.cbs.dtu.dk/services/NetOGlyc/

Server that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins.

Proper citation: NetOGlyc (RRID:SCR_009026) Copy   

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https://www.ncbi.nlm.nih.gov/pubmed/18174824

A face-to-face household survey of assessing the prevalence of mental health disorders in a probability sample of 3005 adolescents aged 12-17 years residing in the Mexico City metropolitan area during 2005. The prevalence of mental health disorders and the use of services were assessed with the computer-assisted adolescent version of the World Mental Health Composite International Diagnostic Interview.

Proper citation: Mexican Adolescent Mental Health Survey (RRID:SCR_009654) Copy   

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http://link.springer.com/article/10.1007%2Fs11357-003-0002-y

A database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments.

Proper citation: AgingDB (RRID:SCR_010226) Copy   

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http://purl.bioontology.org/ontology/EHDAA

A structured controlled vocabulary of stage-specific anatomical structures of the human. It has been designed to mesh with the mouse anatomy and incorporates each Carnegie stage of development (CS1-20). The abstract version of the human developmental anatomy ontology compresses all the tissues present over Carnegie stages 1-20 into a single hierarchy. The heart, for example, is present from Carnegie Stage 9 onwards and is thus represented by 12 EHDA IDs (one for each stage). In the abstract mouse, it has a single ID so that the abstract term given as just ''heart'' really means ''heart (CS 9-20)''. Timing details will be added to the abstract version of the ontology in a future release.

Proper citation: Human Developmental Anatomy Ontology abstract version 1 (RRID:SCR_010323) Copy   

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http://purl.bioontology.org/ontology/VSO

An extension of the Ontology for General Medical Science (OGMS) that covers the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. VSO provides also a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.

Proper citation: Vital Sign Ontology (RRID:SCR_010446) Copy   

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http://purl.bioontology.org/ontology/HINO

An Interaction Network Ontology (INO) extension for the domain of human interaction networks. It has currently incoporated Reactome reactions and pathways. Like INO, HINO aligns with BFO. HINO is developed by following the OBO Foundry principles.

Proper citation: Human Interaction Network Ontology (RRID:SCR_010339) Copy   

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http://purl.bioontology.org/ontology/OCRE

Ontology to support systematic description of, and interoperable queries on, human studies and study elements.

Proper citation: Ontology of Clinical Research (RRID:SCR_010392) Copy   

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http://www.loria.fr/~coulet/sopharm2.0_description.php

A domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. It articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables the representation of pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables the representation of a patient and more largely a panel included in trials, and populations. SO-Pharm enables the representation of measured items on patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.

Proper citation: Suggested Ontology for Pharmacogenomics (RRID:SCR_003497) Copy   

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http://www.humanvariomeproject.org/

Project facilitating the establishment and maintenance of standards systems and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The Human Variome Project produces two categories of recommendations: HVP Standards and HVP Guidelines. HVP Standards are those systems, procedures and technologies that the Human Variome Project Consortium has determined should be used by the community. These carry more weight than the less prescriptive HVP Guidelines, which cover those systems, procedures and technologies that the Human Variome Project Consortium has determined would be beneficial for the community to adopt. HVP Standards and Guidelines are central to supporting the work of the Human Variome Project Consortium and cover a wide range of fields and disciplines, from ethics to nomenclature, data transfer protocols to collection protocols from clinics. They can be thought of as both technical manuals and scientific documents, and while the impact of HVP Standards and Guidelines differ, they are both generated in a similar fashion. A document has been generated both as a guide for those collecting and distributing data and for those developing policy. Items should include those generated by HGVS/HVP collaborators as well as those generated by groups of individual Societies and Standards bodies in all relevant fields worldwide.

Proper citation: Human Variome Project (RRID:SCR_003492) Copy   

•   Source: SciCrunch Registry

http://www.humanconnectomeproject.org/

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

Proper citation: MGH-USC Human Connectome Project (RRID:SCR_003490) Copy   

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http://www.i2b2cictr.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies.

Proper citation: i2b2 Cross-Institutional Clinical Translational Research project (RRID:SCR_003367) Copy   

•   Source: SciCrunch Registry

http://www.brainfacts.org/

A web portal that aggregates information and educational materials about the brain and brain diseases. Resources such as videos, key brain concepts, and hands-on activities may be used and shared with the public.

Proper citation: brainfacts.org (RRID:SCR_003514) Copy   

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http://brainarray.mbni.med.umich.edu/Brainarray/Database/ProbeMatchDB/ncbi_probmatch_para_step1.asp

Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms.

Proper citation: ProbeMatchDB 2.0 (RRID:SCR_003433) Copy   

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http://www.pediatricmri.nih.gov/

Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at each time point. Participant recruitment used community based sampling that included hospital venues (e.g., maternity wards and nurseries, satellite physician offices, and well-child clinics), community organizations (e.g., day-care centers, schools, and churches), and siblings of children participating in other research at the Pediatric Study Centers. At timepoint 1, of those enrolled, 114 children had T1 scans that passed quality control checks. Staged data release plan: The first data release included structural MR images and clinical/behavioral data from the first assessments, Visit 1, for Objective 1. A second data release included structural MRI and clinical/behavioral data from the second visit for Objective 1. A third data release included structural MRI data for both Objective 1 and 2 and all time points, as well as preliminary spectroscopy data. A fourth data release added cortical thickness, gyrification and cortical surface data. Yet to be released are longitudinally registered anatomic MRI data and diffusion tensor data. A collaborative effort among the participating centers and NIH resulted in age-appropriate MR protocols and clinical/behavioral batteries of instruments. A summary of this protocol is available as a Protocol release document. Details of the project, such as study design, rationale, recruitment, instrument battery, MRI acquisition details, and quality controls can be found in the study protocol. Also available are the MRI procedure manual and Clinical/Behavioral procedure manuals for Objective 1 and Objective 2.

Proper citation: NIH MRI Study of Normal Brain Development (RRID:SCR_003394) Copy   

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http://www.eyemoviepedia.com/

Archive and access films from the field of Ophthalmology for free on highly secure servers for permanent access and citeability. A citeable identification number (specific addressing using DOI), allows for citation of individual films in journal publications. Films may be commented by the author either in speech, or in text. Key wording provided by the authors at the time of submission, make each film recognizable to internet search machines.

Proper citation: eyeMoviePedia (RRID:SCR_003541) Copy   

•   Source: SciCrunch Registry

https://bioportal.bioontology.org/ontologies/NEMO/?p=summary

Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).

Proper citation: NEMO Ontology (RRID:SCR_003386) Copy   

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http://fcon_1000.projects.nitrc.org/indi/pro/Berlin.html

Dataset consisting of a community sample of individuals ranging in age from 18 to 60 years old with at least two 7.5-minute resting state fMRI scans. During the resting state scan participants were instructed to relax while keeping their eyes open. In part of the sample eye status was randomized between scans. The particular eye status for each scan is indicated in the phenotypic information. No visual stimulus was presented. A subset of participants completed the ICS and PANAS affective behavior scales. The following data are released for every participant: * Scanner Type: Siemens, 3T Trio Tim * 7.5-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * Demographic information, inluding ICS and PANAS scores (included in the release file).

Proper citation: Neuro Bureau - Berlin Mind and Brain Sample (RRID:SCR_003537) Copy   

•   Source: SciCrunch Registry