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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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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
Blip: Biomedical Logic Programming
 
Resource Report
Resource Website
1+ mentions
Blip: Biomedical Logic Programming (RRID:SCR_005733) Blip, blipkit software resource Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog''''s excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible biology, biomedical, ontology, annotation, software library, bioinformatics, module is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Berkeley Bioinformatics Open-Source Projects
GNU Lesser General Public License nlx_149193 SCR_005733 Blip - Biomedical Logic Programming, Biomedical Logical Programming (Blip), Biomedical Logic Programming 2026-09-12 12:56:30 2
Brains Matter
 
Resource Report
Resource Website
Brains Matter (RRID:SCR_005847) Brains Matter data or information resource, narrative resource, podcast Welcome to the Brains Matter podcast where brains really do matter. A discussion of science, trivia, history, and general knowledge. The show started in September 2006, and includes discussion on various topics, as well as interviews with experts in their field. You can subscribe to the show via iTunes, a standard RSS reader, or listen to the individual MP3 shows from the ''flash player'' on the website, or direct download. brain, science Copyright under the Creative Commons licence where appropriate, Except where otherwise specified. nlx_149376 SCR_005847 Brains Matter - The Podcast on Science Curiosities and General Knowledge. Brains Really Do Matter! 2026-09-12 12:56:32 0
Brain Networks
 
Resource Report
Resource Website
1+ mentions
Brain Networks (RRID:SCR_005841) Brain Networks data analysis software, data processing software, software application, software resource, source code Brain Networks: Code to perform network analysis on brain imaging data. brain, imaging, network analysis, brain imaging, neuroimaging has parent organization: SourceForge PMID:21031030 Open unspecified license - GNU General Public License (GPL) nlx_149364 SCR_005841 brainnetworks 2026-09-12 12:56:32 1
Cell Line Ontology
 
Resource Report
Resource Website
1+ mentions
Cell Line Ontology (RRID:SCR_005840) CLO controlled vocabulary, data or information resource, ontology A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan. cell line, owl, ontology, standardization, information integration is listed by: BioPortal
is listed by: OBO
is related to: Cell Line Knowledge Base
has parent organization: University of Michigan Medical School; Michigan; USA
The community can contribute to this resource nlx_149363 http://bioportal.bioontology.org/ontologies/1245, http://purl.obolibrary.org/obo/clo.owl SCR_005840 2026-09-12 12:56:32 2
University of Neuchatel; Neuchatel; Switzerland
 
Resource Report
Resource Website
University of Neuchatel; Neuchatel; Switzerland (RRID:SCR_005875) UniNE university French-speaking university based in Neuchâtel, Switzerland. The university has four faculties and more than a dozen institutes, including arts and human sciences, natural sciences, law and economics. is related to: Pharma-Planta Consortium grid.10711.36, nlx_158304, ISNI:0000 0001 2297 7718, Crossref funder ID:501100005353, Wikidata:Q541548 https://ror.org/00vasag41 SCR_005875 University of Neuchatel, Universite de Neuchatel, University of Neuch�tel, Universit� de Neuch�tel 2026-09-12 12:56:32 0
American Cancer Society
 
Resource Report
Resource Website
500+ mentions
American Cancer Society (RRID:SCR_005756) ACS non profit organization The American Cancer Society is the nationwide, community-based, voluntary health organization dedicated to eliminating cancer as a major health problem by preventing cancer, saving lives, and diminishing suffering from cancer, through research, education, advocacy, and service. Together with our millions of supporters, the American Cancer Society (ACS) saves lives and creates a world with less cancer and more birthdays by helping people stay well, helping people get well, by finding cures, and by fighting back. Headquartered in Atlanta, Georgia, the ACS has 12 chartered Divisions, more than 900 local offices nationwide, and a presence in more than 5,100 communities. cancer, breast cancer, colon, lung, prostate, skin, breast Cancer grid.422418.9, Wikidata: Q463665, nlx_149219, ISNI: 0000 0004 0371 6485, Crossref funder ID: 100000048 https://ror.org/02e463172 SCR_005756 American Cancer Society - The Official Sponsor of Birthdays 2026-09-12 12:56:31 527
ccPDB - Compilation and Creation of datasets from PDB
 
Resource Report
Resource Website
1+ mentions
ccPDB - Compilation and Creation of datasets from PDB (RRID:SCR_005870) ccPDB data access protocol, data or information resource, database, software resource, web service ccPDB (Compilation and Creation of datasets from PDB) is designed to provide service to scientific community working in the field of function or structure annoation of proteins. This database of datasets is based on Protein Data Bank (PDB), where all datasets were derived from PDB. ccPDB have four modules; i) compilation of datasets, ii) creation of datasets, iii) web services and iv) Important links. * Compilation of Datasets: Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. We are in process of collecting PDB datasetsfrom literature and maintaining at ccPDB. We are also requesting community to suggest datasets. In addition, we generate datasets from PDB, these datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution. * Creation of datasets: This module developed for creating customized datasets where user can create a dataset using his/her conditions from PDB. This module will be useful for those users who wish to create a new dataset as per ones requirement. This module have six steps, which are described in help page. * Web Services: We integrated following web services in ccPDB; i) Analyze of PDB ID service allows user to submit their PDB on around 40 servers from single point, ii) BLAST search allows user to perform BLAST search of their protein against PDB, iii) Structural information service is designed for annotating a protein structure from PDB ID, iv) Search in PDB facilitate user in searching structures in PDB, v)Generate patterns service facility to generate different types of patterns required for machine learning techniques and vi) Download useful information allows user to download various types of information for a given set of proteins (PDB IDs). * Important Links: One of major objectives of this web site is to provide links to web servers related to functional annotation of proteins. In first phase we have collected and compiled these links in different categories. In future attempt will be made to collect as many links as possible. secondary structure, nucleic acid interaction, ligand interaction, structure, nucleic acid, interaction, ligand, data set, function, protein, annotate, tight-turn, nucleotide interacting residue, metals interacting residue, dna/rna binding residue, bio.tools is listed by: Debian
is listed by: bio.tools
is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
has parent organization: Institute of Microbial Technology; Chandigarh; India
OSDD ;
DBT ;
Council of Scientific and Industrial Research; New Delhi; India
PMID:22139939 biotools:ccpdb, nlx_149416 https://bio.tools/ccpdb SCR_005870 Compilation and Creation of datasets from PDB, ccPDB - Compilation Creation of datasets from PDB 2026-09-12 12:56:32 2
Antigenix America
 
Resource Report
Resource Website
1+ mentions
Antigenix America (RRID:SCR_005871) commercial organization An Antibody supplier nlx_152276 SCR_005871 Antigenix America Inc. 2026-09-12 12:56:32 1
UTRdb/UTRsite
 
Resource Report
Resource Website
10+ mentions
UTRdb/UTRsite (RRID:SCR_005868) data or information resource, portal, topical portal UTRdb/UTRsite is a portal to other databases, including Nucleotide Sequence Databases, Protein Sequence Databases, other Sequence databanks, Untranslated Nucleotide Sequence Databases, Mitochondrial Databases, Mutation Databases, and others. The site also allows users to start long-term permanent projects or just to do quick searches, depending on the user''s needs. bio.tools, FASEB list is listed by: bio.tools
is listed by: Debian
biotools:utrdb, nif-0000-03619 https://bio.tools/utrdb http://bighost.area.ba.cnr.it/srs6/ SCR_005868 UTRdb/UTRsite 2026-09-12 12:56:32 41
ClueGO
 
Resource Report
Resource Website
1000+ mentions
ClueGO (RRID:SCR_005748) ClueGO software resource A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. statistical analysis, function, gene ontology, pathway, annotation, network, plugin, gene is listed by: Gene Ontology Tools
is listed by: SoftCite
is related to: Gene Ontology
is related to: Cytoscape
is related to: KEGG
is related to: BioCarta Pathways
has parent organization: National Institute of Health and Medical Research; Rennes; France
National Institute of Health and Medical Research; Rennes; France ;
Ville de Paris ;
INCa ;
Austrian Ministry for Science and Research ;
BINII ;
European Union 7FP 202230
PMID:19237447 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149209 SCR_005748 2026-09-12 12:56:31 2951
ORNL DAAC Data Product Citation Policy
 
Resource Report
Resource Website
ORNL DAAC Data Product Citation Policy (RRID:SCR_005902) ORNL DAAC Data Product Citation Policy data or information resource, narrative resource, standard specification Data Product Citation Policy of including a bibliographic citation for the products that were used in publications to acknowledge the scientists who have provided archived ORNL DAAC (Oak Ridge National Laboratory Distributed Active Archive Center) data products. Such citations will help others find the products and see how they have been used. Citation information is provided in the documentation that accompanies all data products. ORNL DAAC is operated by the ORNL Environmental Sciences Division and is responsible for data archival, product development and distribution, and user support for biogeochemical and ecological data and models. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemcial dynamics is one of the NASA Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project, which is responsible for providing scientific and other users access to data from NASA''s Earth Science Missions. data citation, bibliographic citation is listed by: FORCE11
has parent organization: Oak Ridge National Laboratory
nlx_149492 SCR_005902 Oak Ridge National Laboratory Distributed Active Archive Center Data Product Citation Policy 2026-09-12 12:56:33 0
University of Louisville; Kentucky; USA
 
Resource Report
Resource Website
1+ mentions
University of Louisville; Kentucky; USA (RRID:SCR_005749) UL university Public research university in Louisville, Kentucky. It is part of the Kentucky state university system. is parent organization of: University of Louisville Labs and Facilities
is parent organization of: University of Louisville Micro/Nano Technology Center
is parent organization of: University of Louisville Micro/Nano Technology Center Core Facility
is parent organization of: University of Louisville School of Medicine Molecular Modeling Core Facility
is parent organization of: University of Louisville Biophysical Core Facility
is parent organization of: University of Louisville Medicinal Chemistry Core Facility
is parent organization of: University of Louisville Protein Expression and Purification Core Facility
is parent organization of: University of Louisville Nuclear Magnetic Resonance Spectroscopy Core Facility
is parent organization of: University of Louisville Sequencing Technology Center Genomics Services Core Facility
is parent organization of: University of Louisville Proteomics Technology Center PTC Core Facility
is parent organization of: University of Louisville KY INBRE Data Science Core Facility
is parent organization of: University of Louisville Computing and Research Advanced Computing Core Facility
is parent organization of: University of Louisville Micro/Nano Technology Center Bioimaging Core Facility
is parent organization of: University of Louisville Micro/Nano Technology Center Imaging and Characterization Core Facility
Wikidata:Q1317143, grid.266623.5, Crossref funder ID:100007924, nlx_26318, ISNI:0000 0001 2113 1622 https://ror.org/01ckdn478 SCR_005749 UofL, U of L, University of Louisville 2026-09-12 12:56:31 3
ESTScan
 
Resource Report
Resource Website
100+ mentions
ESTScan (RRID:SCR_005742) ESTScan data analysis software, data processing software, software application, software resource ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics. dna, dna sequence, coding region, perl module, c, btlib perl module is listed by: Debian
is listed by: OMICtools
has parent organization: SourceForge
PMID:10786296 OMICS_08423, nlx_149202 https://sources.debian.org/src/estscan/ SCR_005742 ESTScan project 2026-09-12 12:56:30 291
AD Clinical Trials Database
 
Resource Report
Resource Website
AD Clinical Trials Database (RRID:SCR_005863) clinical database, data or information resource, database A database of Alzheimer's disease and dementia clinical trials currently in progress at centers throughout the U.S. alzheimer's disease, cause, clinical trial, cure, dementia, treatment, database, clinical database has parent organization: Alzheimer's Disease Education and Referral Center Aging Public nif-0000-10344 SCR_005863 2026-09-12 12:56:32 0
University of Louisiana; Louisiana; USA
 
Resource Report
Resource Website
University of Louisiana; Louisiana; USA (RRID:SCR_005743) university Public research university in Lafayette, Louisiana. It has the largest enrollment within the nine-campus University of Louisiana System and the second largest enrollment in Louisiana. is parent organization of: New Iberia Research Center Wikidata:Q116485, grid.266621.7, Crossref funder ID:100008520, ISNI:0000 0000 9831 5270, nlx_12312 https://ror.org/01x8rc503 SCR_005743 2026-09-12 12:56:30 0
Andrew W. Mellon Foundation
 
Resource Report
Resource Website
10+ mentions
Andrew W. Mellon Foundation (RRID:SCR_005864) Andrew W. Mellon Foundation funding resource The Andrew W. Mellon Foundation currently makes grants in five core program areas: * Higher Education and Scholarship * Scholarly Communications and Information Technology * Art History, Conservation, and Museums * Performing Arts * Conservation and the Environment Within each of its core programs, the Foundation concentrates most of its grantmaking in a few areas. Institutions and programs receiving support are often leaders in fields of Foundation activity, but they may also be promising newcomers, or in a position to demonstrate new ways of overcoming obstacles to achieve program goals. Our grantmaking philosophy is to build, strengthen and sustain institutions and their core capacities, rather than be a source for narrowly defined projects. As such, we develop thoughtful, long-term collaborations with grant recipients and invest sufficient funds for an extended period to accomplish the purpose at hand and achieve meaningful results. grant, higher education, scholarship, scholarly communication, information technology, art history, conservation, museum, performing arts, environment nlx_149404 SCR_005864 2026-09-12 12:56:32 13
SIMILE
 
Resource Report
Resource Website
1+ mentions
SIMILE (RRID:SCR_005862) SIMILE data or information resource, portal, topical portal SIMILE, a joint project conducted by the MIT Libraries and MIT CSAIL, was focused on developing robust, open source tools that empower users to access, manage, visualize and reuse digital assets. SIMILE seeks to enhance interoperability among digital assets, schemata/vocabularies/ontologies, metadata, and services. A key challenge is that the collections which must inter-operate are often distributed across individual, community, and institutional stores. We seek to be able to provide end-user services by drawing upon the assets, schemata/vocabularies/ontologies, and metadata held in such stores. SIMILE will leverage and extend DSpace, enhancing its support for arbitrary schemata and metadata, primarily though the application of RDF and semantic web techniques. The project also aims to implement a digital asset dissemination architecture based upon web standards. The dissemination architecture will provide a mechanism to add useful views to a particular digital artifact (i.e. asset, schema, or metadata instance), and bind those views to consuming services. To guide the SIMILE effort we will focus on well-defined, real-world use cases in the libraries domain. Since parallel work is underway to deploy DSpace at a number of leading research libraries, we hope that such an approach will lead to a powerful deployment channel through which the utility and readiness of semantic web tools and techniques can be compellingly demonstrated in a visible and global community. The SIMILE Project and its members are fully committed to the open source principles of software distribution and open development and for this reason, it releases the created intellectual property (both software and reports) under a BSD-style license. The SIMILE Project Team Members gladly welcome community efforts. semantic, interoperability, metadata, information is related to: DSpace
has parent organization: Massachusetts Institute of Technology; Massachusetts; USA;
Andrew W. Mellon Foundation Open unspecified license - BSD-style license nlx_149403 SCR_005862 Semantic Interoperability of Metadata and Information in unLike Environments, SIMILE Project 2026-09-12 12:56:32 3
CLENCH
 
Resource Report
Resource Website
1+ mentions
CLENCH (RRID:SCR_005735) CLENCH data processing software, software application, software resource, source code Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible, gene, microarray, function, functional categorization, statistical analysis, slimmer-type tool, gene ontology, annotation is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: TAIR
has parent organization: Stanford Center for Biomedical Informatics Research
PMID:14764555 Free for academic use nlx_149216 http://www.personal.psu.edu/nhs109/Clench SCR_005735 CLENCH - Cluster Enrichment, CLENCH: A program for calculating cluster enrichment using the Gene Ontology, Cluster Enrichment, Cluster Enrichment (CLENCH) 2026-09-12 12:56:30 4
SBUR - Society for Basic Urologic Research
 
Resource Report
Resource Website
SBUR - Society for Basic Urologic Research (RRID:SCR_005856) SBUR community building portal, data or information resource, funding resource, meeting resource, portal, topical portal, training resource The Society for Basic Urologic Research (SBUR) is a society of scientists whose expertise includes the study of urologic cancers (prostate, bladder, kidney, testis, penis), the biology of prostate growth, kidney and bladder function, autoimmune urologic diseases, infectious diseases, neuro-urologic diseases, male reproductive biology, infertility and erectile dysfunction. Members include molecular biologists, immunologists, epidemiologists, oncologists, biochemists and clinical urologic scientists. SBUR members serve on a wide variety of advisory panels, study sections, editorial boards and in the pharmaceutical industry. The SBUR organizes two annual meetings to share new findings at a multidisciplinary level, to promote interaction among members and other interested scientists and to highlight new areas of research and funding opportunities. The Society was organized to address the following: * To provide a forum for the presentation and discussion of basic scientific topics related to urology * To develop educational forums concerning scientific advancements related to the field of urology * To promote collaborative investigations among member scientists with an emphasis on the interchange of expertise among clinical and basic scientists * To promote the communication and interests of urologic disease investigators with national funding agencies, industry representatives and academic institutions with regards to urology related research * To serve as a resource for research information and expertise to clinical urologists through the American Urological Association urology, prostate, bladder, kidney, testis, penis, award is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology Urologic disease, Urologic cancer, Neuro-urologic disease, Infertility, Erectile dysfunction nlx_149393 SCR_005856 Society for Basic Urologic Research (SBUR), Society for Basic Urologic Research 2026-09-12 12:56:32 0
American Urological Association
 
Resource Report
Resource Website
100+ mentions
American Urological Association (RRID:SCR_005859) AUA institution The American Urological Association (AUA), founded in 1902, is the premier professional association for the advancement of urologic patient care, and works to ensure that its more than 18,000 members are current on the latest research and practices in urology. The AUA also pursues its mission of fostering the highest standards of urologic care by providing a wide range of servicesincluding publications, research, the Annual Meeting, continuing medical education (CME) and the formulation of health policy. urology, research is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology
is parent organization of: AmerUrological's channel - YouTube
Urologic disease grid.422576.0, ISNI: 0000 0001 2222 2235, Wikidata: Q4745327, Crossref funder ID: 100006280, nlx_149398 https://ror.org/00sbaqa70 SCR_005859 American Urological Association (AUA) 2026-09-12 12:56:32 270

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