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https://rrid.site/rin/sources/SCR_005400

Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.

Proper citation: SciCrunch Registry (RRID:SCR_005400) Copy   

•   Source: SciCrunch Registry
  

http://neurolex.org/wiki/Main_Page

A freely editable semantic wiki for community-based curation of the terms used in Neuroscience. Entries are curated and eventually incorporated into the formal NIFSTD ontology. NeuroLex also includes a Resource branch for community members to freely add neuroscience relevant resources that do not become part of NIFSTD ontology but rather make up the NIF Registry. As part of the NIF, we provide a simple search interface to many different sources of neuroscience information and data. To make this search more effective, we are constructing ontologies to help organize neuroscience concepts into category hierarchies, e.g., neuron is a cell. These categories provide the means to perform more effective searches and also to organize and understand the information that is returned. But an important adjunct to this activity is to clearly define all of the terms that we use to describe our data, e.g., anatomical terms, techniques, organism names. Because wikis provide an easy interface for communities to contribute their knowledge, we started the NeuroLex.

Proper citation: NeuroLex (RRID:SCR_005402) Copy   

•   Source: SciCrunch Registry
  

http://biodbcore.org

A community-defined, uniform, generic description of the core attributes of biological databases. The BioDBCore checklist is overseen by the International Society for Biocuration (ISB), in collaboration with the BioSharing forum. A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them have been partly compiled with the support of Oxford University Press and Re3Data.org. Database providers are encouraged to either create or claim their BioDBCore entry and update it as appropriate., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: bioDBcore (RRID:SCR_002781) Copy   

•   Source: SciCrunch Registry
  

https://scicrunch.org/scicrunch/data/source/nlx_154697-18/search?q=*&l=

A virtual database cataloging numerous data set resources, including: BrainMaps.org, Cell Centered Database, Clinical Trials Network (CTN) Data Share, ClinicalTrials.gov, CRCNS, Gene Expression Omnibus, ArrayExpress, MPD - Mouse Phenome Database, BioSharing, Gene Weaver, XNAT Central, 1000 Functional Connectomes Project, Health.Data.gov, SciCrunch Registry, NIF Registry Automated Crawl Data, NeuroVault, OpenfMRI, Physiobank, RanchoBiosciences, YPED, Data.gov Science, and Research Data Catalog.

Proper citation: Integrated Datasets (RRID:SCR_010503) Copy   

•   Source: SciCrunch Registry
  

http://scicrunch.org/Aging

Portal devoted to aging relevant scientific data and resources.

Proper citation: Aging Portal (RRID:SCR_000496) Copy   

•   Source: SciCrunch Registry
  

https://neuinfo.org/mynif/search.php?list=cover&q=*

Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below.

Proper citation: NIF Data Federation (RRID:SCR_004834) Copy   

•   Source: SciCrunch Registry
  

https://www.fdilab.org/toolsservices

Integrated data set and analytics platform combining Research Resource Identifiers (RRIDs), text mining and data aggregation.

Proper citation: Resource Information Network (RRID:SCR_023186) Copy   

•   Source: SciCrunch Registry
  

http://neuinfo.org

Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts.

Proper citation: Neuroscience Information Framework (RRID:SCR_002894) Copy   

•   Source: SciCrunch Registry
  

http://force11.org/

A collaboration which works to transform scholarly communications through advanced use of computers and the Web. FORCE11 advocates the digital publishing of papers in order to enable more effective scholarly communication. The virtual community also advocates the publication of software tools and research communication by means of social media channels. As such, FORCE11 provides access to information and tools for the wider scientific community.

Proper citation: FORCE11 (RRID:SCR_005334) Copy   

•   Source: SciCrunch Registry
  

http://www.neuinfo.org/developers/nif_web_services.shtm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Representational State Transfer (REST) model based service for accessing a set of Neuroscience Information Framework (NIF) data through a fixed set of operations. They are defined by a WADL file which allows clients to automatically generate code for these services. The services (AnnotateService, FederationService, LdaService, LexicalService, LiteratureService, QueryService, SummaryService, VocabularyService) include the ability to: * Retrieve a federation summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/summary?q=* * Retrieve data records from a NIF federation source for a search, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nif-0000-00007-1?q=purkinje * Retrieve registry data records from NIF, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nlx_144509-1?q=miame * Retrieve a complete search summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/search?q=cortex * Retrieve NIF auto-complete suggestions, e.g., http://nif-services.neuinfo.org/servicesv1/v1/vocabulary?prefix=hippo * Use the NIF annotator for arbitrary text, e.g., http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing These services are documented for developers in the WADL file (and client stubs should have the comments embedded in them). Visit, http://nif-services.neuinfo.org/servicesv1/ for more information

Proper citation: NIF Web Services (RRID:SCR_001631) Copy   

•   Source: SciCrunch Registry
  

https://www.fdilab.org

UCSD based bioinformatics lab composed of several projects in different biomedical disciplines. Established in 2008 as Neuroscience Information Framework and has since expanded to include broader field of biomedical research. Leader in developing and providing novel informatics infrastructure and tools for making data FAIR: Findable, Accessible, Interoperable and Reusable. FAIR Data informatics laboratory develops SciCrunch.org platform.

Proper citation: FAIR Data Informatics Laboratory (RRID:SCR_019235) Copy   

•   Source: SciCrunch Registry
  

https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-2

A virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, http://www.ncbi.nlm.nih.gov/books/NBK3807/#files.Databases_Available_for_Linking ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, http://neuinfo.org/nif_components/disco/interoperation.shtm Participating resources ( http://disco.neuinfo.org/webportal/discoLinkoutServiceSummary.do?id=4 ): * Addgene http://www.addgene.org/pgvec1 * Animal Imaging Database http://aidb.crbs.ucsd.edu * Antibody Registry http://www.neuinfo.org/products/antibodyregistry/ * Avian Brain Circuitry Database http://www.behav.org/abcd/abcd.php * BAMS Connectivity http://brancusi.usc.edu/ * Beta Cell Biology Consortium http://www.betacell.org/ * bioDBcore http://biodbcore.org/ * BioGRID http://thebiogrid.org/ * BioNumbers http://bionumbers.hms.harvard.edu/ * Brain Architecture Management System http://brancusi.usc.edu/bkms/ * Brede Database http://hendrix.imm.dtu.dk/services/jerne/brede/ * Cell Centered Database http://ccdb.ucsd.edu * CellML Model Repository http://www.cellml.org/models * CHEBI http://www.ebi.ac.uk/chebi/ * Clinical Trials Network (CTN) Data Share http://www.ctndatashare.org/ * Comparative Toxicogenomics Database http://ctdbase.org/ * Coriell Cell Repositories http://ccr.coriell.org/ * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing http://crcns.org * Drug Related Gene Database https://confluence.crbs.ucsd.edu/display/NIF/DRG * DrugBank http://www.drugbank.ca/ * FLYBASE http://flybase.org/ * Gene Expression Omnibus http://www.ncbi.nlm.nih.gov/geo/ * Gene Ontology Tools http://www.geneontology.org/GO.tools.shtml * Gene Weaver http://www.GeneWeaver.org * GeneDB http://www.genedb.org/Homepage * Glomerular Activity Response Archive http://gara.bio.uci.edu * GO http://www.geneontology.org/ * Internet Brain Volume Database http://www.cma.mgh.harvard.edu/ibvd/ * ModelDB http://senselab.med.yale.edu/modeldb/ * Mouse Genome Informatics Transgenes ftp://ftp.informatics.jax.org/pub/reports/MGI_PhenotypicAllele.rpt * NCBI Taxonomy Browser http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html * NeuroMorpho.Org http://neuromorpho.org/neuroMorpho * NeuronDB http://senselab.med.yale.edu/neurondb * SciCrunch Registry http://neuinfo.org/nif/nifgwt.html?tab=registry * NIF Registry Automated Crawl Data http://lucene1.neuinfo.org/nif_resource/current/ * NITRC http://www.nitrc.org/ * Nuclear Receptor Signaling Atlas http://www.nursa.org * Olfactory Receptor DataBase http://senselab.med.yale.edu/ordb/ * OMIM http://omim.org * OpenfMRI http://openfmri.org * PeptideAtlas http://www.peptideatlas.org * RGD http://rgd.mcw.edu * SFARI Gene: AutDB https://gene.sfari.org/autdb/Welcome.do * SumsDB http://sumsdb.wustl.edu/sums/ * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat http://www.temporal-lobe.com/ * The Cell: An Image Library http://www.cellimagelibrary.org/ * Visiome Platform http://platform.visiome.neuroinf.jp/ * WormBase http://www.wormbase.org * YPED http://medicine.yale.edu/keck/nida/yped.aspx * ZFIN http://zfin.org

Proper citation: Integrated Manually Extracted Annotation (RRID:SCR_008876) Copy   

•   Source: SciCrunch Registry
  

http://scicrunch.org/resources

Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource.

Proper citation: Resource Identification Portal (RRID:SCR_004098) Copy   

•   Source: SciCrunch Registry
  

http://www.w3.org/2001/Annotea/

Annotea is a W3C LEAD (Live Early Adoption and Demonstration) project under Semantic Web Advanced Development (SWAD). Annotea enhances collaboration via shared metadata based Web annotations, bookmarks, and their combinations. By annotations we mean comments, notes, explanations, or other types of external remarks that can be attached to any Web document or a selected part of the document without actually needing to touch the document. When the user gets the document he or she can also load the annotations attached to it from a selected annotation server or several servers and see what his peer group thinks. Similarly shared bookmarks can be attached to Web documents to help organize them under different topics, to easily find them later, to help find related material and to collaboratively filter bookmarked material. Annotea is part of the Semantic Web efforts. It provides a RDF metadata based extendible framework for rich communication about Web pages while offering a simple annotation and bookmark user interface. The annotation metadata can be stored locally or in one or more annotation servers and presented to the user by a client capable of understanding this metadata and capable of interacting with an annotation server with the HTTP service protocol.

Proper citation: Annotea (RRID:SCR_007136) Copy   

•   Source: SciCrunch Registry
  

http://www.parkinsonalliance.org

A U.S. nonprofit organization, in partnership with The Tuchman Foundation. It was formed to foster philanthropic activities to raise funds for the most promising Parkinson's disease research that will help find the cure. The Parkinson Alliance is dedicated to raising donations through special fundraising events. The Parkinson Alliance is also devoted to improving the quality of life in the DBS community through informational means and by funding promising research within the DBS field.

Proper citation: Parkinson Alliance (RRID:SCR_006961) Copy   

•   Source: SciCrunch Registry
  

http://www.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research.

Proper citation: Whole Brain Catalog (RRID:SCR_007011) Copy   

•   Source: SciCrunch Registry
  

http://www.mirecc.va.gov/

The Mental Illness Research, Education and Clinical Centers (MIRECC) were established by Congress with the goal of researching the causes and treatments of mental disorders and using education to put new knowledge into routine clinical practice in the VA. Congress established MIRECCs in October 1996 through Public Law 104-262. There are currently 10 MIRECCs. Each MIRECC focuses on mental illnesses or conditions that are common in Veterans. MIRECCs investigate the causes of mental illness, develop new treatments for mental illness, and evaluate both established and new treatments with the goal of identifying best practices. The MIRECCs also develop educational and training initiatives to implement best practices into the clinical settings of the VA. Each MIRECC works with all the facilities in its network (region) on research, education and clinical initiatives, evaluating services offered to the Veteran and helping the networks implement improved treatments, services, or practices. Several educational products are posted on this site on the Products page. These materials are in the public domain and available for your use. Many MIRECCs have additional materials that can be downloaded from their web sites or are available by request.

Proper citation: Mental Illness Research Education and Clinical Center (RRID:SCR_006956) Copy   

•   Source: SciCrunch Registry
  

http://intramural.nimh.nih.gov/sscc/index.html

Scientific and Statistical Computing Core of the NIMH Intramural Research Program supporting functional neuroimaging research at the NIH. This includes development of new data analysis techniques, their implementation in the AFNI software, advising researchers on the analysis methods, and instructing them in the use of software tools. Support methods: A. Provision of software for analysis for FMRI data (AFNI package: http://afni.nimh.nih.gov) * AFNI has been developed for the last 10 years by Dr Cox, et al. (6 years in Milwaukee, 4 years at NIMH) * Formal and informal instruction in the use of AFNI, including outlines of the statistical methods used in the programs * Installation of AFNI on NIH computers (Mac OS X, Unix, Linux) approximately 120 NIH systems have used AFNI in the last month (80 NIMH, 20 NINDS, 20 other) * Realtime monitoring of FMRI data at scanners * Continuing development of new modules for AFNI to meet needs of NIH researchers B. Consulting with NIH researchers about FMRI data analysis issues, concerns, and methods

Proper citation: NIMH DIRP Scientific and Statistical Computing Core (RRID:SCR_006958) Copy   

•   Source: SciCrunch Registry
  

http://users.utu.fi/mijopi/Pripper/

A tool that can be used to predict caspase cleavage sites from human protein sequences.

Proper citation: Pripper (RRID:SCR_007129) Copy   

•   Source: SciCrunch Registry
  

http://www.softpedia.com/get/Science-CAD/DynGO.shtml

DynGO is a client-server application that provides several advanced functionalities in addition to the standard browsing capability. DynGO allows users to conduct batch retrieval of GO annotations for a list of genes and gene products, and semantic retrieval of genes and gene products sharing similar GO annotations (which requires more disk and memory to handle the semantic retrieval). The result are shown in an association tree organized according to GO hierarchies and supported with many dynamic display options such as sorting tree nodes or changing orientation of the tree. For GO curators and frequent GO users, DynGO provides fast and convenient access to GO annotation data. DynGO is generally applicable to any data set where the records are annotated with GO terms, as illustrated by two examples. Requirements: Java Platform: Windows compatible, Linux compatible, Unix compatible

Proper citation: DynGO (RRID:SCR_007009) Copy   

•   Source: SciCrunch Registry