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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Arabidopsis Hormone Database Resource Report Resource Website 10+ mentions |
Arabidopsis Hormone Database (RRID:SCR_001792) | AHD, AHD2.0 | database, data repository, storage service resource, controlled vocabulary, ontology, data or information resource, service resource | Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions. | arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis service |
is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 30625003; National Natural Science Foundation of China 30730011; Ministry of Science and Technology of China 2009CB119101; Ministry of Education of China ED20060047 |
PMID:21045062 PMID:19015126 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02559 | SCR_001792 | Arabidopsis Hormone Database 2.0 | 2026-08-15 11:22:02 | 28 | |||||
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SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | data processing software, software application, data analysis software, software resource | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-08-15 11:22:03 | 9 | ||||
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myExperiment Resource Report Resource Website 10+ mentions |
myExperiment (RRID:SCR_001795) | myExperiment | database, data repository, workflow software, data processing software, storage service resource, portal, data or information resource, software application, software resource, community building portal, service resource | Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation. | workflow, pipeline, platform, component, data sharing, publish, digital object, experimental method, workflow management, virtual research environment, collaborative computing, taverna workflow workbench, bioinformatics, web service, bio.tools |
is listed by: FORCE11 is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Taverna is related to: Workflow4Ever is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: University of Southampton; Southampton; United Kingdom has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: University of Oxford; Oxford; United Kingdom |
JISC ; Microsoft Technical Computing Initiative ; EPSRC |
PMID:20501605 | Free, Freely available | nif-0000-10309, r3d100010473, biotools:myexperiment | https://www.force11.org/node/4638, https://bio.tools/myexperiment | SCR_001795 | my experiment | 2026-08-15 11:22:03 | 23 | ||||
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Open Provenance Model Resource Report Resource Website 1+ mentions |
Open Provenance Model (RRID:SCR_001829) | OPM | data or information resource, narrative resource, standard specification | A model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any "thing", whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation. | provenance, model |
is listed by: 3DVC is listed by: FORCE11 is related to: Open Provenance Model Vocabulary |
Free | nif-0000-10392 | http://openprovenance.org/ | SCR_001829 | The OPM Provenance Model (OPM), OPM Provenance Model, The OPM Provenance Model | 2026-08-15 11:22:09 | 1 | ||||||
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Royal Institute of Technology: PDC Resource Report Resource Website 1+ mentions |
Royal Institute of Technology: PDC (RRID:SCR_001828) | topical portal, portal, data or information resource, job resource, software resource | PDC operates leading-edge, high-performance computers on a national level. PDC offers easily accessible computational resources that primarily cater to the needs of Swedish academic research and education. PDC also takes part in major international projects to develop high-performance computing for the future and stay a leading national resource in parallel computing. | education, computer, computational, research | Free, Freely available | nif-0000-10408 | SCR_001828 | KTH PDC | 2026-08-15 11:22:04 | 1 | |||||||||
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TEMP Resource Report Resource Website 100+ mentions |
TEMP (RRID:SCR_001788) | software resource | Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
PMID:24753423 | Free, Available for download, Freely available | OMICS_03821, biotools:temp | https://bio.tools/temp | SCR_001788 | 2026-08-15 11:22:02 | 216 | |||||||
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EXTREME Resource Report Resource Website 10+ mentions |
EXTREME (RRID:SCR_001821) | software resource | A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data. | java, perl, python | is listed by: OMICtools | PMID:24532725 | Free, Available for download, Freely available | OMICS_03428 | SCR_001821 | 2026-08-15 11:22:02 | 28 | ||||||||
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GLiMMPS Resource Report Resource Website 1+ mentions |
GLiMMPS (RRID:SCR_001787) | GLiMMPS | software resource | Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data. | alternative splicing, rna-seq, genetic variation, splicing quantitative trait loci |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
PMID:23876401 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01947 | SCR_001787 | 2026-08-15 11:22:09 | 2 | |||||||
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Online Papers on Consciousness Resource Report Resource Website 1+ mentions |
Online Papers on Consciousness (RRID:SCR_001826) | data or information resource, portal, database, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. This is a directory of 5311 free online papers on consciousness in philosophy and in science, and of related topics in the philosophy of mind. The papers in this directory are drawn from PhilPapers, a database of both online and offline works in philosophy. Sponsors: Sponsored by the Joint Information Systems Committee as part of the Information Environment Programme. | consciousness, mind, paper, philosophy, science | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10389 | SCR_001826 | Consciousness Papers | 2026-08-15 11:22:02 | 1 | |||||||||
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wikiCancer Resource Report Resource Website 1+ mentions |
wikiCancer (RRID:SCR_001824) | wikiCancer | topical portal, patient-support portal, portal, data or information resource, disease-related portal | A place where people connected to cancer can share real-life experiences -- fears, insights, stories, and advice. Adding perspectives is easy, and every contribution builds the site into a more valuable and unique community resource. Content, resources, and support on wikiCancer: * Just been diagnosed with cancer? * Living with cancer * For cancer survivors * How to support someone with cancer * Connect with other cancer patients, survivors, family and caregivers | wiki | Cancer | Free, Freely available | nlx_15428 | SCR_001824 | 2026-08-15 11:22:04 | 2 | ||||||||
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SAMstrt Resource Report Resource Website 10+ mentions |
SAMstrt (RRID:SCR_001780) | SAMstrt | software resource | Software package that provides the significance analysis of sequencing data with spike-in normalization. The statistical backgrounds and the benefits depend on SAMseq of the samr package. | differential expression, r |
is listed by: OMICtools has parent organization: Karolinska Institute; Stockholm; Sweden |
Karolinska Institutet ; Strategic Research Area Grant for Diabetes |
PMID:23995393 | Free, Available for download, Freely available | OMICS_01951 | SCR_001780 | 2026-08-15 11:22:01 | 18 | ||||||
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MLRN Resource Report Resource Website 1+ mentions |
MLRN (RRID:SCR_001899) | MLRN | topical portal, funding resource, portal, data or information resource, meeting resource, training resource | A project of the Mind and Life Institute, fosters multidisciplinary communication about scientific research on meditation and other contemplative practices. It is dedicated to fostering dialog and research at the highest possible level between modern science and the great living contemplative traditions, especially Buddhism. It builds on a deep commitment to the power and value of both of these ways of advancing knowledge and their potential to alleviate suffering. Membership is free, and this loose affiliation of scientists, meditators, and people interested in research promotes opportunities for researchers and meditators to communicate together. All perspectives, scientific fields, and styles of meditation are welcome. The MLRN includes cognitive neuroscientists who skillfully use scientific methods in the study of meditation, meditation scholars interested in scientific interfaces, and people who can help support meditation research. MLRN members are likely to be recruited to serve as advisors, referees, participants, and collaborators in upcoming studies on meditation. The MLRN encompasses a variety of meditation practices, and incorporates both contemplative and scientific approaches. The MLRN includes a low-volume, moderated electronic announcement list. This list maintains a high signal-to-noise ratio by distributing infrequent but important messages to large numbers of recipients. Members of this announcement list receive bibliographic updates on recent publications, announcements of upcoming conferences, calls for papers for special-issue journals and conference symposia, synopses of recent meetings, announcements of relevant email lists, websites, and other resources, and other announcements appropriate for widespread distribution. Sponsors: The Hershey Family Foundation has been patron since 1990. This Institute has received generous financial support from the Fetzer Institute, The Nathan Cummings Foundation, Branco Weiss, Adam Engle, Michael Sautman, Mr. and Mrs. R. Thomas Northcote, Christine Austin, Dennis Perlman, Marilyn and the late Don Gevirtz, Michele Grennon, Klaus Hebben, Joe and Mary Ellyn Sensenbrenner, and Edwin and Adrienne Joseph. | buddhism, cognitive neuroscientist, communication, life, meditation, meditator, mind, modern science, multidisciplinary, scientist | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10468 | http://www.mindandlife.org/research-initiatives/mlern1/ | http://www.mindandlife.org/ml.research.network.html | SCR_001899 | The Mind and Life Research Network | 2026-08-15 11:22:04 | 1 | ||||||
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Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | database, data repository, storage service resource, data or information resource, service resource | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-08-15 11:22:10 | 8 | ||||
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Nutrition and Obesity Research Centers Resource Report Resource Website 10+ mentions |
Nutrition and Obesity Research Centers (RRID:SCR_004131) | NORC | topical portal, portal, data or information resource, resource, disease-related portal, organization portal | Portal to research centers and core facilities specifically support obesity research and better understand the relationship between health and nutrition. | obesity core facility, obesity portal, obesity research center |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers is affiliated with: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has organization facet: Boston Nutrition and Obesity Research Centers has organization facet: Nutrition and Obesity Research Centers at Harvard has organization facet: Mid-Atlantic Nutrition Obesity Research Center has organization facet: New York Obesity Nutrition Research Center has organization facet: Pennington Biomedical Research Center Nutrition and Obesity Research Center has organization facet: University of Alabama at Birmingham Nutrition and Obesity Research Center has organization facet: University of California San Francisco Nutrition and Obesity Research Center has organization facet: University of Colorado Anschutz Medical Campus Nutrition and Obesity Research Center has organization facet: University of Michigan Nutrition and Obesity Research Center has organization facet: University of North Carolina at Chapel Hill Nutrition and Obesity Research Center has organization facet: University of Washington Nutrition and Obesity Research Center has organization facet: Washington University St. Louis Nutrition Obesity Research Center |
Obesity, Nutrition-related disease, Eating disorder, Anorexia nervosa, AIDS, Cancer | NIDDK RFA-DK16-006 | Available to the research community | nlx_158684 | SCR_004131 | 2026-08-15 11:22:51 | 46 | ||||||
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UCSF Chimera Resource Report Resource Website 1000+ mentions |
UCSF Chimera (RRID:SCR_004097) | Chimera | data processing software, d visualization software, software application, software resource | Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials. | molecular modeling, electron microscopy, interactive visualization and analysis, molecular structures |
is used by: Structure-function linkage database is listed by: 3DVC is listed by: SoftCite is related to: Integrative Modeling Platform is related to: UCSF ChimeraX is related to: UCSF ChimeraX has parent organization: Resource for Biocomputing Visualization and Informatics |
NIGMS P41 GM103311; NCRR P41 RR001081 |
PMID:15264254 | Restricted | nlx_143560 | http://plato.cgl.ucsf.edu/chimera/ | SCR_004097 | Chimera - an Extensible Molecular Modeling System, UCSF Chimera - an Extensible Molecular Modeling System | 2026-08-15 11:22:50 | 2257 | ||||
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EuroRec Resource Report Resource Website 1+ mentions |
EuroRec (RRID:SCR_004090) | EuroRec | institution | An independent not-for-profit organization promoting in Europe the use of high quality Electronic Health Record systems (EHRs). One of its main missions is to support, as the European authorized certification body, EHRs certification development, testing and assessment by defining functional and other criteria. EuroRec is organized as a permanent network of National ProRec centers and provides services to industry (developers and vendors), healthcare providers (buyers), policy makers and patients. | electronic healthcare record, interoperability, clinical data, clinical, archetype | is related to: EMIF | Wikidata: Q17053004, nlx_158552, grid.424835.c | https://ror.org/01sc1ca25 | SCR_004090 | European Institute for Health Records, EuroRec - European Institute for Health Records, EuroRec Institute | 2026-08-15 11:22:46 | 1 | |||||||
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PubMed Central Resource Report Resource Website 100+ mentions |
PubMed Central (RRID:SCR_004166) | PMC | data or information resource, storage service resource, service resource, database | Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access. | literature, biomedical, life, science, journal, repository, electronic, literature, gold standard |
uses: PubReader is used by: NIH Heal Project is listed by: OMICtools is related to: PubMed is related to: JISC Open Citations is related to: Biotea is related to: NIF Registry Automated Crawl Data is related to: NIF Literature is related to: Europe PubMed Central is related to: PubReader has parent organization: NCBI |
NIH | Free, Some open access - authors retain copyright, | nlx_18862, OMICS_01193 | SCR_004166 | 2026-08-15 11:22:48 | 253 | |||||||
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GenomeNet Resource Report Resource Website 1000+ mentions |
GenomeNet (RRID:SCR_004165) | database, portal, data or information resource, computation service resource, organization portal | GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University as part of the research projects. GenomeNet is operated using the Supercomputer System of the Institute for Chemical Research, Kyoto University. LinkDB is supported by the National Bioscience Database Center of the Japan Science and Technology Agency. | FASEB list |
lists: DINIES has parent organization: Kyoto University; Kyoto; Japan is parent organization of: Amino Acid Index Database |
nlx_18770 | SCR_004165 | 2026-08-15 11:22:43 | 1074 | ||||||||||
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EpiGRAPH Resource Report Resource Website 10+ mentions |
EpiGRAPH (RRID:SCR_004326) | EpiGRAPH | software resource | A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00633, biotools:epigraph | https://bio.tools/epigraph | SCR_004326 | 2026-08-15 11:22:45 | 18 | |||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | database, data repository, storage service resource, data or information resource, service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-08-15 11:22:53 | 15598 |
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