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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Human Disease Ontology
 
Resource Report
Resource Website
1+ mentions
Human Disease Ontology (RRID:SCR_000476) DO data or information resource, controlled vocabulary, database, ontology Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, is used by: DOAF
is listed by: BioPortal
is listed by: OBO
is listed by: bio.tools
is listed by: Debian
is related to: PharmGKB Ontology
is related to: GWASdb
is related to: NUgene Project
is related to: FunDO
is related to: Neurocarta
has parent organization: University of Maryland School of Medicine; Maryland; USA
NHGRI U24 HG012557 PMID:22080554 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology http://disease-ontology.org/, https://bio.tools/disease_ontology, http://purl.obolibrary.org/obo/doid.obo, http://do-wiki.nubic.northwestern.edu/index.php/Main_Page SCR_000476 Human Disease Ontology Knowledgebase, Disease Ontology 2026-08-12 10:48:13 5
Gazetteer
 
Resource Report
Resource Website
1+ mentions
Gazetteer (RRID:SCR_000473) GAZ data or information resource, topical portal, portal THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available. obo, owl is listed by: BioPortal
is listed by: OBO
has parent organization: Genomic Standards Consortium
THIS RESOURCE IS NO LONGER IN SERVICE nlx_157412 http://purl.obolibrary.org/obo/gaz.owl, http://build.berkeleybop.org/job/build-gaz/lastSuccessfulBuild/artifact/gaz.obo http://gensc.org/gc_wiki/index.php/GAZ_Project SCR_000473 2026-08-12 10:48:13 1
AETIONOMY
 
Resource Report
Resource Website
1+ mentions
AETIONOMY (RRID:SCR_000232) AETIONOMY data or information resource, portal, consortium, organization portal 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. drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany
IMI ;
EFPIA
nlx_157972, biotools:AETIONOMY https://bio.tools/AETIONOMY SCR_000232 2026-08-12 10:48:11 3
Denver University Department of Psychology
 
Resource Report
Resource Website
Denver University Department of Psychology (RRID:SCR_000474) data or information resource, department portal, portal, organization portal The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental. psychology, graduate, doctoral, affect, social, child, clinical, cognitive, developmental, neuroscience has parent organization: University of Denver; Colorado; USA nif-0000-01928 SCR_000474 DU Dept. of Psychology, University of Denver Department of Psychology 2026-08-12 10:48:13 0
ECNP
 
Resource Report
Resource Website
1+ mentions
ECNP (RRID:SCR_000501) ECNP data or information resource, community building portal, portal A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity. brain, neuroscience, disease mechanism, medicine, clinical, disease is parent organization of: Preclinical Data Forum Network Brain disorder nlx_158605 SCR_000501 European College of Neuropsychopharmacology, ECNP - neuroscience applied 2026-08-12 10:48:14 1
National MS Society
 
Resource Report
Resource Website
10+ mentions
National MS Society (RRID:SCR_000104) National MS Society portal, data or information resource, funding resource, disease-related portal, topical portal THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward. multiple sclerosis, award, grant, postdoctoral fellowship Multiple Sclerosis THIS RESOURCE IS NO LONGER IN SERVICE nlx_143693 SCR_000104 National Multiple Sclerosis Society 2026-08-12 10:48:10 34
RSEM
 
Resource Report
Resource Website
100+ mentions
RSEM (RRID:SCR_000262) data processing software, data analysis software, software resource, software application Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools is listed by: OMICtools
is listed by: GitHub
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Wisconsin-Madison; Wisconsin; USA
PMID:21816040 Free, Available for download, Freely available OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ SCR_000262 RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 2026-08-12 10:48:11 115
TEDDY
 
Resource Report
Resource Website
1+ mentions
TEDDY (RRID:SCR_000383) TEDDY portal, data or information resource, database, clinical trial, organization portal, consortium International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes. consortium, gene, infectious agent, dietary factor, environmental factor, young human, insulin, child, pediatric, autoantibody, blood, stool, biomaterial supply resource, longitudinal, neonate, parent, genetic risk, genetic factor, observation, prospective, serum, plasma, peripheral blood mononuclear cell, saliva, nasal swab, nail clipping, water, dna, virus, nutrition, toxic agent, socioeconomic, psychosocial, male, female, environment, exposure, diet, toxin, infectious agent, bacterial, viral, immunization is listed by: One Mind Biospecimen Bank Listing
is listed by: ClinicalTrials.gov
is listed by: NIDDK Information Network (dkNET)
is listed by: NIDDK Central Repository
is related to: Teddy study IA prediction
has parent organization: University of South Florida; Florida; USA
Type 1 diabetes, Diabetes NIDDK 2UC4DK063829 PMID:21564455 nlx_152857 SCR_000383 The Environmental Determinants of Diabetes in the Young, TEDDY study 2026-08-12 10:48:12 3
Trans-Institute Angiogenesis Research Program
 
Resource Report
Resource Website
Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) TARP data or information resource, topical portal, resource, portal Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests. blood vessel, growth, development, target, therapeutic, vascularization, angiogenesis, lymphangiogenesis is listed by: NIDDK Information Network (dkNET)
has parent organization: National Institutes of Health
Angiogenesis, Lymphangiogenesis JDRF ;
NEI ;
NHLBI ;
NCI ;
NICHD ;
NIDDK ;
NINDS
THIS RESOURCE IS NO LONGER IN SERVICE nlx_152866 SCR_000384 Trans-Institute Angiogenesis Research Program (TARP) 2026-08-12 10:48:12 0
M(at)CBETH
 
Resource Report
Resource Website
M(at)CBETH (RRID:SCR_000265) M(at)CBETH software resource, data access protocol, web service THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset. microarray, classification, performing microarray classification, is listed by: OMICtools
has parent organization: Catholic University of Leuven; Flemish Brabant; Belgium
PMID:15890742 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02292 SCR_000265 MicroArray Classification BEnchmarking Tool on Host server 2026-08-12 10:48:11 0
Local Binary Pattern Analysis Tools for MR Brain Images
 
Resource Report
Resource Website
1+ mentions
Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) LBP Analysis Tools for MR Brain Images image analysis software, image processing software, software application, data processing software, software resource The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology. free for non-commercial use only, mr is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) Free, Available for download, Freely available nlx_155652 SCR_000412 2026-08-12 10:48:13 1
PSCBS
 
Resource Report
Resource Website
PSCBS (RRID:SCR_000417) sequence analysis software, software application, data processing software, software resource, data analysis software Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. abnormal copy number regions detection, allele specific DNA copy number data segmentation, is listed by: OMICtools
is listed by: Debian
is related to: CRAN
has parent organization: University of California at San Francisco; California; USA
PMID:21666266
DOI:10.1093/bioinformatics/btr329
Free, Available for download, Freely available OMICS_05545 https://sources.debian.org/src/r-cran-pscbs/ SCR_000417 PSCBS: Analysis of Parent-Specific DNA Copy Numbers 2026-08-12 10:48:13 0
Open Colleges
 
Resource Report
Resource Website
Open Colleges (RRID:SCR_000418) Open Colleges online course, training resource A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia. open source, accredited, accounting, beauty, animal care, writing, journalism, education, business, building, real estate is parent organization of: Open Colleges Interactive Brain
is parent organization of: Open Colleges Group
nlx_155866 SCR_000418 2026-08-12 10:48:13 0
uManager
 
Resource Report
Resource Website
100+ mentions
uManager (RRID:SCR_000415) software toolkit, data acquisition software, software application, data processing software, software resource Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories. microscopy, plugin, data acquisition, automated microscope control, is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: ImageJ
has parent organization: University of California at San Francisco; California; USA
Free, Available for download, Freely available SCR_016865, nlx_155812 https://micro-manager.org/wiki/Download_Micro-Manager_Latest_Release, https://sources.debian.org/src/micromanager/, http://www.nitrc.org/projects/micromanager SCR_000415 Micro-Manager, Micro Manager 2026-08-12 10:48:13 285
BSmooth-align
 
Resource Report
Resource Website
1+ mentions
BSmooth-align (RRID:SCR_000013) image analysis software, software application, data processing software, alignment software, software resource, data analysis software Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements. bisulfite sequence, read-level methylation, bisulfite sequence reads alignment, is listed by: OMICtools Free, Available for download, Freely available OMICS_01846 SCR_000013 2026-08-12 10:48:08 1
Sequence Read Format
 
Resource Report
Resource Website
1+ mentions
Sequence Read Format (RRID:SCR_000132) SRF data or information resource, narrative resource, standard specification, interchange format A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology. dna sequence, dna sequencing, interchange format is listed by: OMICtools
has parent organization: SourceForge
Public, A C++ implementation of Sequence Read Format is available OMICS_05130 SCR_000132 Sequence Read Format (SRF) 2026-08-12 10:48:10 1
Aging Portal
 
Resource Report
Resource Website
Aging Portal (RRID:SCR_000496) Aging portal, data or information resource, database, topical portal, catalog Portal devoted to aging relevant scientific data and resources. late adult human, senescence uses: Aging Genes and Interventions Database
uses: anage
uses: Human Life-Table Database
uses: Gene Ontology
uses: Grants.gov
uses: Integrated Blogs
uses: Integrated Clinical Trials
uses: Integrated Videos
uses: Integrated Grants
uses: Lifespan Observations Database
uses: One Mind Biospecimen Bank Listing
uses: Gait in Parkinson's Disease
uses: SciCrunch Registry
has parent organization: SciCrunch
Aging NIA 1R03AG043018-01 Restricted nlx_158366 SCR_000496 2026-08-12 10:48:14 0
EPIGEN
 
Resource Report
Resource Website
10+ mentions
EPIGEN (RRID:SCR_000093) EPIGEN data or information resource, portal, consortium, organization portal 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. epilepsy, genetics, gene, mri, genetic variation, clinical has parent organization: Duke University; North Carolina; USA
has parent organization: University College London; London; United Kingdom
has parent organization: Beaumont Hospital; Dublin; Ireland
has parent organization: Royal College of Surgeons in Ireland; Dublin; Ireland
has parent organization: Free University of Brussels; Brussels; Belgium
Epilepsy THIS RESOURCE IS NO LONGER IN SERVICE nlx_143740 SCR_000093 EPIGEN: An international consortium dedicated to tackling epilepsy through genetics, EPIGEN Consortium 2026-08-12 10:48:10 24
Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates
 
Resource Report
Resource Website
Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates (RRID:SCR_000490) BFSUKMCPI data or information resource, portal, consortium, organization portal Project aiming to establish a range of new technologies to enable the synthesis of a range of chemicals from sugar beet pulp (SBP) in a cost-effective and sustainable manner. The chemical and pharmaceutical industries are currently reliant on petrochemical derived intermediates for the synthesis of a wide range of valuable products. Decreasing petrochemical reserves and concerns over costs and greenhouse gas emissions are driving the search for renewable sources of organic synthons. The UK is self-sufficient in the production of SBP which is a by-product of sugar beet production (8 million tonnes grown per year) and processing. The ability to convert SBP into chemicals and pharmaceutical intermediates will therefore have significant economic and environmental benefits. SBP is rich in carbohydrate (nearly 80% by weight) which is made up of roughly equal proportions of 2 biological polymers; cellulose and pectin. To be cost-effective it will be necessary to find uses for each of these substances. The consortium will develop a biorefinery approach for the selective breakdown of both polymers, purification of the breakdown compounds and their use to synthesize a range of added value products such as speciality chemicals, pharmaceuticals and biodegradable polymers. It is already known that cellulose can be broken down into hexose sugars and fermented to ethanol for use in biofuels. The focus is on the release of galacturonic acid and arabinose (from pectin) and their conversion, by chemical or enzymatic means, into added value products. Synthetic Biology methods will also be explored to test the feasibility of metabolically engineering microbial cells to simultaneously breakdown the polymeric feed material and synthesize a desired product, such as aromatic compounds, in a single integrated process. In conducting this research the consortium will adopt a holistic, systems-led, approach to biorefinery design and operation. Computer-based modelling tools will be used to assess the efficiency of raw material, water and energy utilization. Economic and Life Cycle Analysis (LCA) approaches will then be employed to identify the most cost-effective and environmentally benign product and process combinations. The project is supported by a range of industrial partners from raw material producer to intermediate technology providers and end-user chemical and pharmaceutical companies. This is crucial in providing business and socio-economic insights regarding the adoption of renewable resources into their current product portfolios. The company partners will also provide the material and equipment resources for the large-scale verification of project outcomes and their ultimate transition into commercial manufacture. The Intellectual Property (IP) expected to be generated by the consortium will most likely be related to new biocatalysts, synthetic routes, USD devices and modelling software. The data is accessible programmatically using one of three application programming interfaces GtR, GtR-2 and CERIF. chemical, drug, drug development, pharmaceutical, manufacture, product development, sugar beet pulp, sugar beet, polymer, galacturonic acid, arabinose, biorefinery, cellulose, pectin, ethanol, biofuel is listed by: Consortia-pedia
has parent organization: University College London; London; United Kingdom
EPSRC THIS RESOURCE IS NO LONGER IN SERVICE nlx_158450 SCR_000490 2026-08-12 10:48:14 0
Neuroshare - Open data specifications and software for neurophysiology
 
Resource Report
Resource Website
Neuroshare - Open data specifications and software for neurophysiology (RRID:SCR_000005) software library, software toolkit, software resource Neuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. The neuroshare.org website is a collaborative, vendor-neutral area dedicated to public domain standards and software for neurophysiology.This website is part of an SBIR program funded by the National Institute for Neural Disorders and Stroke and it is currently being administered by Bionic Technologies, LLC. The goals of the SBIR program are to (Phase I) create open library and format standards for neurophysiological experiment data and (Phase II) create a set of free, open-source software tools for low-level handling and processing of neurophysiological data. Upon completion of Phase I and II, neuroshare.org will be maintained by a yet to be determined consortium of government, academic and industry partners. The SBIR was awarded in the fall of 2001 and Phase I officially began in Dec, 2001. The detailed goals of the program are summarized below:Phase I goals :(1) Establish a working group to develop and define the API library of functions.(2) A vendor-neutral web site to facilitate the development of the standards and software and publish the completed products. This site has been dubbed Neuroshare. The home page can be found at neuroshare.sourceforge.net.(3) An open, standardized API library definition for accessing neurophysiology data files. This will allow developers to produce analysis programs that can access a variety of proprietary data formats through libraries supplied by the data format owners. The manner of support will be completely determined by the research groups and vendors that supply the libraries. The Phase I standard was created by a working group consisting of international members from industry and academia. Draft standards were published for public review and comment on the neuroshare web site and revised by the working group.The grant has been awarded as a fast-track program so that Phase II begins immediately upon completion of the Phase I milestones in June 2002. Phase II will produce :(1) A set of neuroshare-compliant API libraries for existing data formats developed in collaboration with individual equipment vendors and research groups.(2) A utility for analyzing compliant API libraries for integrity and specification conformance, as well as for error checking imported data files.(3) A set of template programs in C that are meant to be used as an example on how to create a Neuroshare API compliant library and how to call it from an application,(4) An open, standardized file format for neurophysiological experiment data. This format will provide research groups and vendors with a file format for exchanging and/or publishing neural data. The format will also be powerful enough for use as a native format for researchers or vendors that wish to support it in data acquisition hardware/software.(5) Import filters that interface neuroshare-compliant API libraries to Visual Basic, MATLAB, and LabVIEW, NeuroExplorer, and Stranger analysis environments.(6) A utility program for quick header information viewing and searching to aid the organization and management of data files in the standard and proprietary formats.(7) A data file editing program for reviewing, editing, annotating, and splicing neural data files through the neuroshare API libraries and/or standard file formats. The suite will be developed in C, optimized for speed, and will run within 32-bit Windows operating systems. The availability of source code will enable eventual ports to Unix/Linux if desired(8) An add-on for the editing program that will allow review and real-time playback of multi-modal data accessible through the API and/or standard file format. These modes will include neurophysiological signals such as spikes, local field potentials and EEG, as well as experimental signals such as kinematics, stimulation, audio, video, and imaging data.(9) C and MATLAB framework programs for detection and classification of extracellular spikes in the standard data files based on classical and user-supplied algorithms.(10) A complete MATLAB application for reading data from the standard format and performing reverse correlation analysis. This program will serve as a tutorial and modifiable template for users performing analysis in MATLAB.(11) A set of export filters for creating neurophysiological data files with the neural simulation environments NEURON, NEOSIM, GENESIS, and NSL.(12) A comprehensive documentation, and help file set for all of the developed applications.Phase II will require two years of development work and software products will be made available as they are completed. As stated above, the Phase II software products will be made available as free, open-source tools. We have not decided on a license model yet, but are currently leaning towards the GNU General Public License. Revisions and bug-fixes will be maintained through the neuroshare.org website. The mission of neuroshare.org is very focused, but the specific goal list of Phase II may evolve somewhat as software is released and user feedback is received. We very interested in public suggestions about how to improve this development effort and web site. Please direct your feedback to commentsneuroshare.org or refer to our contacts page for other addresses.BackgroundThis endeavor grew out of a meeting held at the Society for Neuroscience 2000 Annual Conference in New Orleans (agenda posted here) to discuss the development of standard data formats for neuroscience. From this meeting, it was clear that although everyone supported the idea of better data portability, many vendors present wanted a standardized API (Application Program Interface) library rather than a universal data format. Based on this meeting, we submitted an SBIR application (with letters of support from key attendants of the SFN meeting) to fund the development of a standardized API definition, data format, and a suite of open source data handling and review tools. data management, development, interoperability software, software is related to: BrainLiner nif-0000-00023 SCR_000005 Neuroshare.org 2026-08-12 10:48:08 0

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