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http://clinicaltrials.gov/show/NCT01211678

A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise.

Proper citation: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations (RRID:SCR_004019) Copy   

•   Source: SciCrunch Registry

http://dermatlas.med.jhmi.edu/derm/

Database of dermatology cases and browsable by diagnosis, category or body site with 12,176 images, 583 contributors and dermatology links. You may retrieve images using any diagnosis, disease category, body site, pigmentation, image contributor, patient age, image name, and/or key words. You are welcome submit images or to download images for lectures and other teaching purposes - or with permission for other uses. Additionally, you may search DermAtlas from your website. Add YOUR Link On the DermAtlas'''' Add a Link Page you can associate your link with as many diagnoses as you like. Case submission If you have a high quality image that you would like to submit to DermAtlas, submit the requested information, and upload the image. The data and image will automatically be sent to the editors for review. You will be notified within one week of submission of images. In order for an image to be considered for inclusion into this collection, consent must be obtained from the patient or his/her legal guardian. Contributors are solely responsible for obtaining consent.

Proper citation: DermAtlas. (RRID:SCR_004977) Copy   

•   Source: SciCrunch Registry

http://knhi.de/en/network/

Association of physicians, scientists, academics, research institutes and self-help groups that provides and nurtures interdisciplinary cooperation between research and primary, secondary and tertiary health care. Many internationally renowned heart failure researchers and working groups live and work in Germany. Nevertheless, there is insufficient cooperation of the respective working groups and research projects in this area. In order to remain internationally competitive in the heart failure research community, excellent implementation of large scale clinical and genetic trials is indispensable. Further, deficits in the effective presentation and transfer of research findings into clinical practice need to be addressed. An adequate translation of guidelines into practical, tangible instructions can facilitate clinical practice both in primary and tertiary care fundamentally. The need for action to address the research-practice-gap is obvious.

Proper citation: Competence Network Heart Failure (RRID:SCR_004979) Copy   

•   Source: SciCrunch Registry

http://glioblastoma.alleninstitute.org/

Platform for exploring the anatomic and genetic basis of glioblastoma at the cellular and molecular levels that includes two interactive databases linked together by de-identified tumor specimen numbers to facilitate comparisons across data modalities: * The open public image database, here, providing in situ hybridization data mapping gene expression across the anatomic structures inherent in glioblastoma, as well as associated histological data suitable for neuropathological examination * A companion database (Ivy GAP Clinical and Genomic Database) offering detailed clinical, genomic, and expression array data sets that are designed to elucidate the pathways involved in glioblastoma development and progression. This database requires registration for access. The hope is that researchers all over the world will mine these data and identify trends, correlations, and interesting leads for further studies with significant translational and clinical outcomes. The Ivy Glioblastoma Atlas Project is a collaborative partnership between the Ben and Catherine Ivy Foundation, the Allen Institute for Brain Science and the Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment.

Proper citation: Ivy Glioblastoma Atlas Project (RRID:SCR_005044) Copy   

•   Source: SciCrunch Registry

http://health.usf.edu/byrd/adrc/index.htm

A statewide consortium dedicated to Alzheimer's disease research to better understand the disease and related memory disorders. It includes Alzheimer's researchers and clinicians from institutions across Florida such as USF Health, Mayo Clinic Jacksonville, and Mount Sinai Medical Center. The purpose of the ADRC is to assist institutions in developing an infrastructure (cores) that can be used for various research projects with the goal of better understanding Alzheimer's disease and related disorders. The Florida ADRC is comprised of six cores, three projects and three pilot projects among other collaborations that utilize these cores.

Proper citation: Florida Alzheimer's Disease Research Center (RRID:SCR_004940) Copy   

•   Source: SciCrunch Registry

http://www.bioportfolio.com/

BioPortfolio is a leading news, information and knowledge resource covering the global life science industries impacted on by biotechnology. The site aims to provide the lay person, the researcher and the management executive with a single location to source core information on specific bio-related topics, to collate relevant data associated with each topic and to point the user to relevant knowledge resources. We publish up to the minute news (see biotechnology news categories) and regularly update content across our information databases. BioPortfolio promotes and sells market research and management reports from 30+ publishers. In addition our unique corporate database lists 40,000+ companies and organizations. BioPortfolio aims to bring together high quality information about marketed drugs - medication and relevant clinical trials, research papers and recent news from PubMed, ClinicalTrials.gov, and DailyMed. Additionally, resources include biotech, pharma and medical job listings. When the BioPortfolio site was launched in February 1997 the company aimed to provide a global free-to-use resource with defined aims and mission statement: to meet the increasing demand of consumers, scientists, investors, commerce and government for timely, accurate and commercially useful information and intelligence on biotechnology companies, technologies and products world-wide. Driven by the success of the site we have made major investments and improvements to enhance our content and to apply the latest web technologies to improve functionality and site utility. We believe this unique depth and breadth of content is supporting individuals, organizations and policy-makers to become more aware of the role of biotechnology on the global economy. With 97,000 users visiting the site more than once per month we are confident that we are providing information our users need. We hope you the users find the site of value for both personal and professional reasons. Please enjoy this free resource and email your comments!

Proper citation: BioPortfolio (RRID:SCR_005230) Copy   

•   Source: SciCrunch Registry

http://ctsaconnect.org/

THIS RESOURCE IS NO LONGER IS SERVICE. Documented on December 5th, 2022. Semantic framework to integrate information about research activities, clinical activities, and scientific resources to facilitate the production and consumption of Linked Open Data about investigators, physicians, biomedical research resources, services, and clinical activities. The goal is to enable software to consume data from multiple sources and allow the broadest possible representation of researchers'''' and clinicians'''' activities and research products. Current research tracking and networking systems rely largely on publications, but clinical encounters, reagents, techniques, specimens, model organisms, etc., are equally valuable for representing expertise. CTSAConnect will provide linkage between semantic representations of a wide range of clinical and research data using controlled vocabularies mapped to the Unified Medical Language System (UMLS) as a bridge between the two subject areas. The data sources include data from Medicaid, hospital billing systems, CTSAShareCenter, and other CTSA resource data, eagle-i and VIVO. It allows institutions to leverage existing tools and data sources by making the information they contain more discoverable and easier to integrate. For instance, with the ISF, researchers can be characterized by organizational affiliations, grant and project participation, research resources that they have generated, and publications that they have (co)-authored. Clinicians can be characterized by training and credentials, by clinical research topic, and by the kinds of procedures and specialization that can be inferred from encounter data. LOD refers to data that has been given a specific Uniform Resource Identifier (URI), for the purpose of sharing and linking data and information on the Semantic Web. While a large amount of data is published as LOD, there remains a significant gap in the representation of research resources and clinical expertise. Researchers can be characterized by the organization to which they belong, the grants and research in which they have participated, the research topics and research resources (reagents, biospecimens, animal models) they have generated, as well as the publications they have (co)-authored. Clinician profiles on the other hand, can be defined by their credentials, clinical research topics, and the kinds of procedures and specialization that can be inferred from clinical encounter data. They believe that integrating and relating this diversity of information sources and platforms requires addressing the overlap between research resources and the attributes and activities of researchers and clinicians. CTSAconnect aims to promote integration and discovery of research activities, resources, and clinical expertise. To this end, they will publish their ontologies and LOD via their website, which will also illustrate repeatable methods and examples of how to extract, consume, and utilize this valuable new LOD using freely available tools like VIVO, eagle-i, and Google APIs. CTSAconnect is a collaboration between Oregon Health & Science University, Stony Brook University, Cornell University, Harvard University, University at Buffalo, and the University of Florida, and leverages the work of eagle-i (eagle-i.net), VIVO (vivoweb.org), and ShareCenter (ctsasharecenter.org).

Proper citation: CTSAconnect (RRID:SCR_005225) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/gtr/

Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests.

Proper citation: Genetic Testing Registry (RRID:SCR_005565) Copy   

•   Source: SciCrunch Registry

http://toc.lbg.ac.at/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project.

Proper citation: Ludwig Boltzmann Cluster Translationale Onkologie (RRID:SCR_000020) Copy   

•   Source: SciCrunch Registry

http://www.epilepsygenetics.eu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EPIGEN (RRID:SCR_000093) Copy   

•   Source: SciCrunch Registry

http://www.aetionomy.eu/

Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery.

Proper citation: AETIONOMY (RRID:SCR_000232) Copy   

•   Source: SciCrunch Registry

http://www.cdisc.org/

A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.

Proper citation: Clinical Data Interchange Standards Consortium (RRID:SCR_000219) Copy   

•   Source: SciCrunch Registry

http://knightadrc.wustl.edu/

The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.

Proper citation: Washington University School of Medicine Knight Alzheimers Disease Research Center (RRID:SCR_000210) Copy   

•   Source: SciCrunch Registry

https://www.qcif.edu.au/

Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services.

Proper citation: Queensland Cyber Infrastructure Foundation Ltd (RRID:SCR_000208) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/services/genomes/uwe25/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK.

Proper citation: Protochlamydia amoebophila UWE25 (RRID:SCR_008222) Copy   

•   Source: SciCrunch Registry

http://dtp.nci.nih.gov/docs/3d_database/dis3d.html

The NCI DIS 3D database is a collection of 3D structures for over 400,000 drugs. The database is an extension of the NCI Drug Information System. The structural information stored in the DIS is only the connection table for each drug. The connection table is just a list of which atoms are connected and how they are connected. It is essentially a searcheable database of three-dimensional structures has been developed from the chemistry database of the NCI Drug Information System (DIS), a file of about 450,000 primarily organic compounds which have been tested by NCI for anticancer activity. The DIS database is very similar in size and content to the proprietary databases used in the pharmaceutical industry; its development began in the 1950s; and this history led to a number of problems in the generation of 3D structures. This information can be searched to find drugs that share similar patterns of connections, which can correlate with similar biological activity. But the cellular targets for drug action, as well as the drugs themselves, are 3 dimensional objects and advances in computer hardware and software have reached the point where they can be represented as such. In many cases the important points of interaction between a drug and its target can be represented by a 3D arrangement of a small number of atoms. Such a group of atoms is called a pharmacophore. The pharmacophore can be used to search 3D databases and drugs that match the pharmacophore could have similar biological activity, but have very different patterns of atomic connections. Having a diverse set of lead compounds increases the chances of finding an active compound with acceptable properties for clinical development. Sponsor: The ICBG are supported by the Cooperative Agreement mechanism, with funds from nine components of the NIH, the National Science Foundation, and the Foreign Agricultural Service of the USDA.

Proper citation: National Cancer Institute 3D Structure Database (RRID:SCR_008211) Copy   

•   Source: SciCrunch Registry

http://www.ohsu.edu/xd/research/centers-institutes/neurology/alzheimers/research/data-tissue/clinical-data.cfm

A database housing longitudinal relational research data from over 4,000 research subjects. The database includes the following types of data: physical and neurological exam findings, neurocognitive test scores, personal and family history of dementia, personal demographic genotypes (APOE, HLA), age at service evaluations, age at onset, age at death, clinical diagnosis, neuropathology diagnosis, tissue inventory information (when available), health status, medications, laboratory tests, and MRI data.

Proper citation: Layton Center Clinical Data Resources (RRID:SCR_008822) Copy   

•   Source: SciCrunch Registry

http://www.cnio.es/ES/grupos/plantillas/presentacion.asp?grupo=50004308

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The need to use human neoplastic tissue under ideal conditions is currently of particular importance due to the development molecular pathology techniques that allow large-scale studies of genetic expression that are also of clinical significance. The Tumour Bank Network (TBN), instigated and coordinated by the Molecular Pathology Programme (MMP) aims to respond to this need by the promoting of Tumour Banks in Spanish hospitals. This will be achieved through the application of homogeneous procedures for the collection, processing and storage of neoplastic and normal tissue samples in such a way as to make molecular studies possible, avoiding that avoid the intrinsic bias of multi-centre studies possible. These Hospital Tumour Banks are based within the Pathology Departments of the collaborating Hospitals, that are interconnected through a computer-based network. In this way, each Centre''s tissue remains in the Hospital itself, thereby playing a key role in the development of the welfare, teaching and research activities within the Hospital. At the same time, it represents a tool to encourage of multi-hospital cancer research and of cooperation between basic and clinical researchers, constituting important collaboration between biomedical disciplines. The design does not correspond to a Central Tumour Bank, but that of a cooperative and coordinated Network of Hospital Banks, based on simple, homogeneous and optimal tissue treatment protocols. This Network is promoted by the Centro Nacional de Investigaciones Oncologicas (CNIO), which thereby undertakes the work of coordinating the network, using and maintaining the database, adhering to quality control. The aim of the CNIO's TBN is to acquire neoplastic and control non-neoplastic material of all types of malignant neoplasias, in the form of tissue fixed in formalin and paraffin embedded, of samples that are unfixed or frozen according to conventional methods as set out in Annexe 1 and even, exceptionally as fresh tissue. When other types of samples are required to carry out a specific project, the central office of the TBN will draw up a protocol with the group leading the project for the collection and maintenance of the tissue and clinicopathological data required for the proposed research. These protocols will be disseminated among the Associated Hospitals in order to gather the previously agreed number cases. Basic data surrounding the processing and preservation conditions for each case will be sent to the central office of the Bank, which under no circumstances will reveal the identity of the patient. Any Spanish cancer research team will be able to request tissue from the Tissue Bank Network. Absolute priority will be afforded to projects whose principal researcher belongs to one of the Associated Centres of the TNB, to other institutions with special agreements concerning the exchange of samples, and to the CNIO's researchers.

Proper citation: Spanish National Tumour Bank Network (RRID:SCR_008707) Copy   

•   Source: SciCrunch Registry

http://sciblogs.co.nz/

Sciblogs brings together the best science bloggers in the country (New Zealand) on one website, creating a hub for scientific analysis and discussion and facilitating reader interaction. The website is for scientists who want to reach out to a general audience to explain their science and how it relates to society. Some Sciblog contributors spend most of their time in the lab or buried in research. Others are authors or entrepreneurs. All of them know what they are talking about and have an interest in engaging in discussion on the big science-related issues facing society. Over time more bloggers will be added to the Sciblogs roster. If you would like to inquire about hosting a blog on Sciblogs contact us. You can easily keep an eye on new Sciblogs posts by subscribing via RSS or email or by following our Twitter feed. Alternatively, there is a Facebook page as well as a Facebook group feel free to join in! Categories: * Science * Agriculture * Technology * Health and Medicine * Environment and Ecology * Science and Society

Proper citation: Sciblogs (RRID:SCR_005219) Copy   

•   Source: SciCrunch Registry

http://yh.genomics.org.cn

This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.

Proper citation: YanHuang Project (RRID:SCR_006077) Copy   

•   Source: SciCrunch Registry