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https://medicine.ouhsc.edu/

College of Medicine is the largest component of the University of Oklahoma Health Sciences Center and is at the center of OU Health. OU College of Medicine offers Physician Associate Program and MD/PhD dual degree program to meet unique interests of medical students. The college also offers students the option to take MPH coursework.

Proper citation: University of Oklahoma College of Medicine; Oklahoma; USA (RRID:SCR_006249) Copy   

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http://www.ctalearning.com/

A searchable, keyword-indexed bibliography on conditioned taste aversion learning, the avoidance of fluids and foods previously associated with the aversive effects of a variety of drugs. The database includes articles as early as 1951, and papers just published given that the database is ongoing and constantly updated. In the mid 1950''s, John Garcia and his colleagues at the Radiological Defense Laboratory at Hunters Point in San Francisco assessed the effects of ionizing radiation on a myriad of behaviors in the laboratory rat. One of their behavioral findings was that radiated rats avoided consumption of solutions that had been present during radiation, presumably due to the association of the taste of the solution with the aversive effects of the radiation. These results were published in Science and introduced to the literature the phenomenon of conditioned taste aversion learning (or the Garcia Effect). Subsequently, Garcia and his colleagues demonstrated that such learning appeared unique in a number of respects, including the fact that these aversions were acquired often in a single conditioning trial, selectively to gustatory stimuli and even when long delays were imposed between access to the solution and administration of the aversive agent. Together, these unique characteristics appeared to violate the basic tenets of traditional learning theory and along with a number of other behavioral phenomena (e.g., bird song learning, species-specific defense reactions, tonic immobility and schedule-induced polydipsia) introduced the concept of biological constraints on learning that forced a reconceptualization of the role evolution played in the acquisition of behavior (Garcia and Ervin, 1968; Revusky and Garcia, 1970; Rozin and Kalat, 1971). Although the initial investigations into conditioned taste aversion learning focused on these biological and evolutionary issues and their relation to learning, research in this area soon assessed the basic generality of the phenomenon, specifically, under what conditions such learning did or did not occur. With such research, a wide variety of gustatory stimuli were reported as effective conditioned stimuli and an extensive list of drugs with diverse consequences were reported as effective aversion-inducing agents. Aversions were established in a range of strains and species and under many experimental conditions. Research in this area continues to extend the conditions under which such learning occurs and to demonstrate its biological, neurochemical and anatomical substrates. Although the conditions under which aversion learning are reported to occur appear to generalize from the specific conditions under which they were originally reported, a number of factors including sex, age, training and testing procedures, deprivation level and drug history, all affect the rate of its acquisition and its terminal strength (Riley, 1998). In addition to these experimental demonstrations and assessments of generality, research on conditioned taste aversions has expanded to include investigations into its research and clinical applications (Braveman and Bronstein, 1985). In so doing, taste aversion learning has been applied to the characterization and classification of drug toxicity, the demonstration of the stimulus properties of abused drugs, the management of wildlife predation, the assessment of the etiology and treatment of cancer anorexia, the study of the biochemistry and molecular biology of learning, the etiology and control of alcohol use and abuse, the receptor characterization of the motivational effects of drugs, the occurrence of drug interactions, the characterization of drug withdrawal, the determination of taste psychophysics, the treatment of autoimmune diseases and the evaluation of the role of malaise in drug-induced satiety and drug-induced behavioral deficits. The speed with which aversions are acquired and the relative robustness of this preparation have made conditioned taste aversion learning a widely used, highly replicable and sensitive tool. In 1976, we published the first of three bibliographies on conditioned taste aversion learning. In this initial publication (see Riley and Baril, 1976), we listed and annotated 403 papers in this field. Subsequent lists published in 1977 (Riley and Clarke, 1977) and 1985 (Riley and Tuck, 1985) listed 632 and 1373 papers, respectively. Since that time, we have maintained a bibliography on taste aversion learning utilizing a variety of journal and on-line searches as well as benefiting from the generous contribution of preprints, reprints and pdf files from many colleagues. To date, the number of papers on conditioned taste aversion learning is approaching 3000. The present database lists these papers and provides a mechanism for searching the articles according to a number of search functions. Specifically, it was constructed to provide the reader access to these articles via a variety of search terms, including Author(s), Key Words, Date, Article Title and Journal. One can search for single or multiple items within any specific category. Further, one can search a single or combination of categories. The database is constantly being updated, and any feedback and suggestions are welcome and can be sent to CTALearning (at) american.edu.

Proper citation: Conditioned Taste Aversion: An Annotated Bibliography (RRID:SCR_005953) Copy   

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http://dataver.net/

DataVer is the premier data management verification service for scientific data. DataVer''s data management plan (DMP) Compliance Review and the companion Star Ratings will bring transparency to the investigator''s compliance with data management and sharing guidelines on a grant by grant basis. DataVer will accomplish this through 1) open publication of its review standards and procedures that it applies to all submitted grants and 2) openly report the results of its findings through its web portal so anyone can look up the compliance history of an investigator or lab. The Data Management Plan. The NIH and the NSF typically require a DMP detailing data types and quantity, its storage duration, and plans for making the data accessible to fellow scientists. The DMP is supposed to meet their published guidelines outlining the data management and sharing requirements to which the PI must agree as a condition of funding. The compliance record to date is less than ideal.. Institutional funders may not require a specific DMP as such but many have specific requirements for data management and post-grant data availability. While a specific DMP as such may not be produced for these grants, the data management and sharing is expected to comport with the funders'' guidelines. To date, there are no standardized or uniform means to track or assess the compliance of the investigator with the DMP or published guidelines. While individual institutions have tasked program managers with monitoring the compliance, the process is not uniform and the data stays within the specific institute, unavailable for other granting institutes or foundations. What DataVer does. DataVer offers two services with variations. First, it offers a DMP (or funder guideline) compliance review. For this DataVer compares the actual data management and data sharing of the grant funded data to the approved DMP and with the guidelines its funding agency(s). Second, DataVer rates the actual usability and accessibility of the data based on its own published standards on a three star rating scale. This indicates at a glance how well the data is organized and whether it''s available for reuse by an outside investigator. These procedures give the funders and the scientific community accurate, standardized and timely reports on an investigators'' data storage and data sharing in a publicly available database. We at DataVer believe this light, cast on actual data openness, will further encourage increased care in data management and archiving as well as increased data sharing. This openness and transparency will be a positive means to increase data management plan and guideline compliance, and will stimulate increased attention to the accessibility and usability of the data, so important to its reuse. We will offer a means by which universities, investigators, research facilities, and data repositories can obtain a compliance certification for consistently setting a high standard of data accessibility and usability across multiple grants. This certification is a means by which these stakeholders can demonstrate their achievement in support of data sharing. Grantors will be able to see an institution or facility''s pattern of compliance when deciding where to spend their limited resources.

Proper citation: DataVer (RRID:SCR_005954) Copy   

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http://idi.fundacionctic.org/tabels/

A tool to bridge the gap between tabular formats and linked data by transforming data tables to RDF datasets, it is able to process spreadsheets, csv files, but also other tabular formats: statistical oriented ones (PC-Axis), analysis tool formats, shapefiles (GIS) and so on. The aim is to provide means to discover and to surface the data structures hidden in tables, and to enable users to combine data over and above the limits of files and formats. By transforming data tables to RDF datasets, the information integration achieves a new dimension. Raw data transcends into a world of linked resources brimming with enrichment and entity reconciliation opportunities. Tabels is not a mere transformation tool, but it facilitates end-user exploitation of data by supplying front-end interactive mechanisms. Moreover, Tabels offers the possibility to disambiguate terms extracted from the input files against online datasets such as DBPedia, publishing and relating information from offline sources to the Linked Data cloud. Furthermore, the RDF datasets generated by Tabels can be extended or manipulated by means of declarative directives (based on the Jena rules engine and the SPARQL 1.1 interface). Tabels is more than a transformation tool and it is geared with data-sensitive front-end widgets to facilitate end users the exploitation and exploration of data: namely, chart views, faceted views, interactive charts and maps and sparql endpoint.

Proper citation: Tabels (RRID:SCR_006123) Copy   

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http://isaac.bioapps.biozentrum.uni-wuerzburg.de/isaac/modules/genome/species.xhtml

Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups.

Proper citation: InterSpecies Analysing Application using Containers (RRID:SCR_006243) Copy   

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

Ontology for knowledge representation related to computer-based decision support in rehabilitation; concepts and relationships in the rehabilitation domain, integrating clinical practice, the ICD (specifically its 11th revision), the clinical investigator record ontology, the ICF and SNOMED CT.

Proper citation: Physical Medicine and Rehabilitation (RRID:SCR_005948) Copy   

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http://unice.fr/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2021.University of Nice Sophia Antipolis was university located in Nice, France and neighboring areas. It was founded in 1965 and was organized in eight faculties, two autonomous institutes and engineering school. It was merged in 2019 into the University of C�te d'Azur.

Proper citation: University of Nice Sophia Antipolis; Nice; France (RRID:SCR_006114) Copy   

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http://kronos.biol.uoa.gr/~mariak/dbDNA.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An annotated and searchable collection of protein sequences for the families of DNA-binding proteins. DnaProt maximizes family information retrieval and helps reveal the relationships within the various functional binding classes. This classification system, implemented in an web-based management resource, is available for online DNA-binding pattern search and specific DNA-binding record retrieval. The database contains 3238 full-length sequences (retrieved from the SWISS-PROT database, release 38) that include, at least, a DNA-binding domain. Sequence entries are organized into families defined by PROSITE patterns, PRINTS motifs and de novo excised signatures. Combining global similarities and functional motifs into a single classification scheme, DNA-binding proteins are classified into 33 unique classes, which helps to reveal comprehensive family relationships. To maximize family information retrieval, DnaProt contains a collection of multiple alignments for each DNA-binding family while the recognized motifs can be used as diagnostically functional fingerprints. All available structural class representatives have been referenced. The resource was developed as a Web-based management system for online free access of customized data sets. Entries are fully hyperlinked to facilitate easy retrieval of the original records from the source databases while functional and phylogenetic annotation will be applied to newly sequenced genomes.

Proper citation: DnaProt (RRID:SCR_006230) Copy   

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http://www.univ-brest.fr/GB

French university, located in Brest, in the Academy of Rennes.

Proper citation: University of Western Brittany; Brest; France (RRID:SCR_006232) Copy   

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http://open-biomed.sourceforge.net/opmv/ns.html

A lightweight provenance vocabulary to provide terms to enable practitioners of data publishing to publish their data responsibly. It is closely based on the community provenance data model, the Open Provenance Model (OPM). Since release 1.0 OPMV becomes a profile of OPM. OPMV can be used together with other provenance-related RDF/OWL vocabularies/ontologies, such as Dublin Core, FOAF, the Changeset Vocabulary, and the Provenance Vocabulary. As being grounded on OPM, the OPMV aims to assist the interoperability between provenance information on the Semantic Web. The Open Provenance Model Vocabulary is defined as an OWL-DL ontology and it is partitioned into a core ontology and supplementary modules. In order to avoid making the core ontology too complex, the core module only implements structures defined in OPM and the supplementary modules provide less frequently used terms and a broad range of specializations of the core terms. * Classes: Agent, Artifact, Process * Properties: used, wasControlledBy, wasDerivedFrom, wasEncodedBy, wasEndedAt, wasGeneratedAt, wasGeneratedBy, wasPerformedAt, wasPerformedBy, wasStartedAt, wasTriggeredBy, wasUsedAt

Proper citation: Open Provenance Model Vocabulary (RRID:SCR_005937) Copy   

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http://nanopub.org/wordpress/

Format for creating, finding, using and citing nanopublications. A nanopublication has two basic elements: * The Assertion: An assertion is a minimal unit of thought, expressing a relationship between two concepts (called the Subject and the Object) using a third concept (called the Predicate). * The Provenance: This is metadata providing some context about the assertion. Provenance means, ''''how this came to be'''' and includes Supporting metadata (like methods) and Attribution metadata (such as authors, institutions, time-stamps, grants, links to DOIs, URLs). Nanopublications can be serialized using existing ontologies and RDF, allowing nanopublications to be machine readable and opening the door to universal interoperability. In turn, this allows extremely large, heterogeneous and decentralized data to be analyzed for the discovery of new associations that would otherwise be beyond the capacity of human reasoning. Nanopublication infrastructure is administered by the Concept Web Alliance, and are based on open standards. They anticipate the community-driven evolution of nanopublication formats to fit the changing needs of authors and publishers.

Proper citation: Nanopub.org (RRID:SCR_005933) Copy   

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http://www.nitrc.org/projects/nyu_trt/

EPI-images of 25 participants gathered during rest as well as anonymized anatomical images of the same participants. The resting-state fMRI images were collected on several occasions: # the first resting-state scan in a scan session # 5-11 months after the first resting-state scan # about 30 (< 45) minutes after 2. Each scan occasion is released as a new version release of the resource. ---Caution: Participants here are part of the NewYork_a contribution to the 1000 Functional Connectomes Project. DO NOT combine datasets.

Proper citation: NYU CSC TestRetest (RRID:SCR_005975) Copy   

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http://www.mouseimaging.ca/

A unique resource and comprehensive imaging facility combining the latest state-of-the-art digital medical imaging technologies for the characterization of mouse functional genomics. The goals of the Mouse Imaging Centre are: * To provide a variety of medical imaging technologies adapted to studying genetically modified mice. These technologies include magnetic resonance (MR) imaging, micro computed tomography (micro-CT), ultrasound biomicroscopy (UBM), and optical projection tomography (OPT). * To screen large numbers of mice for models of human diseases. * To image an individual mouse over time to observe development, disease progression and responses to experimental treatment. * To develop an exciting team of investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. * To work by collaboration with researchers throughout the world. When we look for human diseases in the human population, we make extensive use of medical imaging. Therefore, it makes sense to have available the same imaging capabilities as we investigate mice for models of human disease. The Mouse Imaging Centre (MICe) has developed high field magnetic resonance imaging microscopy, ultrasound biomicroscopy, micro computed tomography, and optical techniques. With these imaging tools, MICe is screening randomly mutagenized mice to look for phenotypes that represent human diseases and is taking established human disease models in mice and using imaging to follow the progression of disease and response to treatment over time. It is clear that imaging has a major contribution to make to phenotyping genetic variants and to characterizing mouse models. MICe is staffed by an exciting new team of about 30 investigators with expertise in imaging techniques, computer science, engineering, imaging processing, developmental biology and mouse pathology. The Mouse Imaging Centre (MICe) is not a fee-for-service facility but works through collaborations. Services include: * Projects involving MicroCT are available as a fee for service. * We will eventually move to the same model above with MRI. * Ultrasound Biomicroscopy is used for cardiac, embryo and cancer studies and is available as fee for service at $100 per study or in some cases on a collaborative basis. * Optical Projection Tomography has only limited availability on a collaborative basis. Mouse Atlas As our images are inherently three-dimensional, we will be able to make quantitative measures of size and volume. With this in mind, we are developing a mouse atlas showing the normal deviation of organ sizes. This atlas is an important resource for biologists as it has the potential to eliminate the need to sacrifice as many controls when making comparisons with mutants. Mouse Atlas Examples: * Variational Mouse Brain Atlas * Cerebral Vascular Atlas of the CBA Mouse * Neuroanatomy Atlas of the C57Bl/6j Mouse * Vascular Atlas of the Developing Mouse Embryo * Micro-CT E15.5 Mouse Embryo Atlas

Proper citation: MICe - Mouse Imaging Centre (RRID:SCR_006145) Copy   

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http://oligogenome.stanford.edu/

The Stanford Human OligoGenome Project hosts a database of capture oligonucleotides for conducting high-throughput targeted resequencing of the human genome. This set of capture oligonucleotides covers over 92% of the human genome for build 37 / hg19 and over 99% of the coding regions defined by the Consensus Coding Sequence (CCDS). The capture reaction uses a highly multiplexed approach for selectively circularizing and capturing multiple genomic regions using the in-solution method developed in Natsoulis et al, PLoS One 2011. Combined pools of capture oligonucleotides selectively circularize the genomic DNA target, followed by specific PCR amplification of regions of interest using a universal primer pair common to all of the capture oligonucleotides. Unlike multiplexed PCR methods, selective genomic circularization is capable of efficiently amplifying hundreds of genomic regions simultaneously in multiplex without requiring extensive PCR optimization or producing unwanted side reaction products. Benefits of the selective genomic circularization method are the relative robustness of the technique and low costs of synthesizing standard capture oligonucleotide for selecting genomic targets.

Proper citation: OligoGenome (RRID:SCR_006025) Copy   

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https://www.quidel.com/

An Antibody supplier

Proper citation: Quidel (RRID:SCR_006146) Copy   

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http://db-mml.sjtu.edu.cn/ICEberg/

ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community.

Proper citation: ICEberg (RRID:SCR_006026) Copy   

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http://www.uwmedicine.org/

Public medical school in the northwest United States, located in Seattle and affiliated with the University of Washington.

Proper citation: University of Washington School of Medicine; Washington; USA (RRID:SCR_006147) Copy   

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http://martinos.org/mne/

Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics.

Proper citation: MNE software (RRID:SCR_005972) Copy   

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http://www.uoregon.edu/

Public flagship research university in Eugene, Oregon, United States.

Proper citation: University of Oregon; Oregon; USA (RRID:SCR_006269) Copy   

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http://www.actrec.gov.in/

The Advanced Centre for Treatment, Research and Education in Cancer (ACTREC) is the new state-of-the-art R&D satellite of the Tata Memorial Centre (TMC), which also includes under its umbrella the Tata Memorial Hospital (TMH), the largest cancer hospital in Asia. ACTREC has the mandate to function as a national centre for treatment, research and education in cancer. TMC is an autonomous grant-in-aid institution of the Department of Atomic Energy (DAE), Government of India. It is registered under the Societies Registration Act (1860) and the Bombay Public Trust Act (1950). Its Governing Council is headed by the Chairman, Atomic Energy Commission, Government of India. ACTREC comprises of 2 arms - one for basic research and another for clinical research. The basic research building was inaugurated in March 2002 at the new site of ACTREC in Kharghar, Navi Mumbai. In August 2002, the Cancer Research Institute (CRI) shifted in toto from its Parel campus in Mumbai to serve as the basic research arm of ACTREC. The clinical research arm of ACTREC comprising of the Clinical Research Centre (CRC) has become functional from March 2005. ACTREC also has a 50-bed hospital fully equipped with state-of-the-art diagnostic and therapeutic facilities. Research investigations at CRI currently focus on molecular mechanisms responsible for causation of major human cancers relevant to India. It is envisaged that in the future, ACTREC will play a greater role in drug development and emerging therapies for treatment and prevention of cancer.

Proper citation: ACTREC - Advanced Centre for Treatment Research and Education in Cancer (RRID:SCR_006021) Copy   

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