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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Radiotracer Chemistry Instrumentation and Biological Imaging Resource Report Resource Website 1+ mentions |
Radiotracer Chemistry Instrumentation and Biological Imaging (RRID:SCR_003258) | RCIBI | material resource, instrument supplier | Develop new scientific tools to image the movement of molecules in energy-relevant and environmentally-sensitive contexts in response to BER's call to explore the potential of radiotracer imaging in energy and environmentally-responsive contexts. Their goal is to visualize metabolic networks and regulatory systems underlying cellular communication in the living organism including plants and microbial communities. This has broad implications to DOE missions in energy and the environment and is very relevant to improvements in plant biomass for biofuel. | neuroimaging, imaging instrumentation, radiotracer chemistry, plant science | DOE ; Office of Science |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31420 | http://www.bnl.gov/ctn/mouse | SCR_003258 | Radiotracer Chemistry and Instrumentation for Biological Imaging | 2026-02-14 02:07:48 | 2 | ||||||
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miRNEST Resource Report Resource Website 1+ mentions |
miRNEST (RRID:SCR_008907) | miRNEST | data or information resource, database | A database of animal, plant and virus microRNA data maintained at the University of Poznan. The database provides: * 9980 miRNA candiates from 420 animal and plant species predicted in Expressed Sequence Tags * predicted targets for plant candidates * RNA-seq reads mapped to candidates from 29 species * external data from 12 databases that includes sequences, polymorphism, expression and regulation. miRNEST 1.0, it contains miRNA from 563 animals, plants and viruses plant species. | microrna, expressed sequence tag, rna-seq read, sequence, polymorphism, mirna sequence, small rna sequence, single nucleotide polymorphism, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Adam Mickiewicz University in Poznan; Poznan; Poland |
European Social Fund ; Adam Mickiewicz University PBWB-08/2011; Polish Ministry of Science and Higher Education N N301 160935; Polish Ministry of Science and Higher Education N N516 441938 |
PMID:22135287 | nlx_151465, biotools:mirnest | http://mirnest.amu.edu.pl https://bio.tools/mirnest |
SCR_008907 | miRNEST - a database of animal and plant microRNAs | 2026-02-14 02:06:10 | 3 | |||||
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PLACE- A Database of Plant Cis-acting Regulatory DNA Elements Resource Report Resource Website 100+ mentions |
PLACE- A Database of Plant Cis-acting Regulatory DNA Elements (RRID:SCR_013428) | PLACE | data or information resource, database | A database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included. Note: As of January 2007, PLACE is no longer updated or maintained. | motif, cis-acting regulatory dna element, FASEB list |
is listed by: OMICtools has parent organization: National Institute of Agrobiological Sciences; Ibaraki; Japan |
PMID:9847208 | Free, Acknowledgement requested | nif-0000-03296, OMICS_00557 | SCR_013428 | 2026-02-14 02:06:25 | 329 | |||||||
|
RESNET Resource Report Resource Website 1000+ mentions |
RESNET (RRID:SCR_002121) | ResNet | data or information resource, database | Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | biological relationship, biomedical, literature, interaction, FASEB list |
is listed by: Biositemaps has parent organization: Indiana University School of Medicine; Indiana; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20909 | http://www.ariadnegenomics.com/products/databases/ariadne-resnet/ | SCR_002121 | Ariadne ResNet Databases, ResNet Databases | 2026-02-14 02:05:38 | 1384 | ||||||
|
Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-02-14 02:05:44 | 4 | ||||
|
MapViewer Resource Report Resource Website 100+ mentions |
MapViewer (RRID:SCR_003092) | Map Viewer | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. | genome, mapping, sequencing, chromosome |
is listed by: OMICtools is related to: NCBI Genome is related to: Consensus CDS has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00921, nif-0000-03103 | SCR_003092 | Entrez Map Viewer, NCBI Map Viewer | 2026-02-14 02:05:49 | 242 | |||||||
|
PlantProm DB Resource Report Resource Website 1+ mentions |
PlantProm DB (RRID:SCR_003359) | PlantProm | data or information resource, database | Annotated, non-redundant database of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s) (TSS) from various plant species. It contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively (April 2014). This DB presents the published promoter sequences with TSS(s) determined by direct experimental approaches and therefore serves as the most accurate source for development of computational promoter prediction tools. | proximal promoter sequence, rna polymerase ii, transcription start site, promoter, monocot, dicot, dna sequence, taxonomy, promoter type, nucleotide frequency matrix, nucleotide composition, motif, transcription, regulatory element |
is listed by: OMICtools has parent organization: University of London; London; United Kingdom |
Pakistan European Union | PMID:12519961 | Free, Available for download, Freely available | nif-0000-03308, OMICS_01875 | http://www.softberry.com/berry.phtml?topic=plantprom&group=data&subgroup=plantprom | http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom | SCR_003359 | Plant Promoter Database, PlantProm DB | 2026-02-14 02:05:49 | 8 | |||
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GOblet Resource Report Resource Website 1+ mentions |
GOblet (RRID:SCR_006998) | GOblet | software application, data analysis service, software resource, service resource, production service resource, analysis service resource | Tool that performs annotation based on GO and pathway terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. GOblet expects query sequences to be in FASTA-Format (with header-lines). Protein and nucleotide sequences are accepted. Total size of all sequences submitted per request should not be larger than 50kb currently. For security reasons: Larger post's will be rejected. Due to limited capacities the queries may be processed in batches depending on the server load. The output of the BLAST job is filtered automatically and the relevant hits are displayed. In addition, the respective GO-terms are shown together with the complete GO-hierarchy of parent terms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, sequence, cdna, ontology or annotation browser, pathway, term enrichment, clustering, virus, genomic, protein, nucleotide |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
BMBF | PMID:20134064 PMID:15215401 PMID:12824400 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30624, OMICS_02271 | http://goblet.molgen.mpg.de | SCR_006998 | 2026-02-15 09:19:21 | 6 | |||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | database, d spatial image, service resource, storage service resource, data repository, data or information resource, image collection | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-02-15 09:19:40 | 7 | |||||
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Plantagora Resource Report Resource Website 1+ mentions |
Plantagora (RRID:SCR_001227) | Plantagora | data or information resource, data set, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies. | next-generation sequencing, genome assembly, sequencing, genome, 454, illumina, simulate |
is listed by: OMICtools has parent organization: University of Arizona; Arizona; USA |
PMID:22174807 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02116 | SCR_001227 | Plantagora - a resource for plant genome assembly | 2026-02-15 09:18:04 | 1 | ||||||
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EOL - Encyclopedia of Life Resource Report Resource Website 100+ mentions |
EOL - Encyclopedia of Life (RRID:SCR_005905) | EOL | data or information resource, database, portal | Database that gathers, generates, and shares taxa, images, videos, and sounds to freely provide knowledge about life on earth to increase awareness and understanding of living nature. Free EOL memberships are ranked so members have greater authority and editorial abilities based on their level of expertise. | life, encyclopedia, environmental sciences, ecology, ecological survey, life sciences, specie, species diversity, diversity, taxon, image, video, audio, FASEB list |
is listed by: re3data.org is related to: Pensoft is related to: Biodiversity Heritage Library |
John D. and Catherine T. MacArthur Foundation ; Alfred P. Sloan Foundation |
PMID:24891832 | Creative Commons License, Acknowledgement requested, Note that a single page may be made up of many different data elements, Each covered by a different license, Http://eol.org/info/copyright_and_linking#using_content | r3d100010229, nlx_149476 | https://doi.org/10.17616/R35S3D | SCR_005905 | Encyclopedia of Life | 2026-02-15 09:19:06 | 138 | ||||
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BOLD Resource Report Resource Website 100+ mentions |
BOLD (RRID:SCR_004278) | BOLD | data analysis service, database, service resource, storage service resource, production service resource, data repository, data or information resource, analysis service resource | DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library. | protists, taxonomy, dna, barcode, dna barcode, gene sequence, primer, publication, barcode index number, unique identifier, annotation, platform, data management, data sharing, dna sequence, bioinformatics, molecular biology, biology, geography, species, sequence cluster, map, web service, image collection, FASEB list |
is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing has parent organization: University of Guelph; Ontario; Canada |
Canada Foundation for Innovation ; Genome Canada ; Ontario Innovation Trust ; NSERC ; Gordon and Betty Moore Foundation |
PMID:18784790 | Free, Public | DOI:10.17616/R3PP7J, nlx_29236, DOI:10.25504/FAIRsharing.en9npn, DOI:10.5883, r3d100010129 | http://www.boldsystems.org/ https://doi.org/10.17616/R3PP7J https://doi.org/10.17616/r3pp7j https://doi.org/10.5883/ https://dx.doi.org/10.5883/ https://fairsharing.org/10.25504/FAIRsharing.en9npn https://doi.org/10.17616/R3KG65 |
SCR_004278 | BOLD Systems, Barcode of Life Database Systems, Barcode of Life Database, Barcode of Life Data Systems, BOLD : The Barcode of Life Data System | 2026-02-15 09:18:40 | 298 | ||||
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GoMapMan Resource Report Resource Website 10+ mentions |
GoMapMan (RRID:SCR_005060) | GoMapMan | data or information resource, database, service resource | An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes. | functional annotation, function, annotation, gene, visualization, ortholog, ontology, microarray, gene annotation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Set Enrichment Analysis is related to: MapMan is related to: Biomine is related to: SEGS has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia |
Slovenian Research Agency J4-2228; Slovenian Research Agency P2-0103 |
PMID:24194592 | Creative Commons Attribution-NonCommercial-ShareAlike License | biotools:gomapman, OMICS_02280 | https://bio.tools/gomapman | SCR_005060 | 2026-02-15 09:18:54 | 28 | |||||
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MapMan Resource Report Resource Website 1000+ mentions |
MapMan (RRID:SCR_003543) | MapMan | software application, software resource | Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes. | metabolic pathway, biological process, genomics, pathway, array, visualization, gene, transcript, protein, enzyme, metabolite |
is related to: GoMapMan has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany |
PMID:19389052 PMID:14996223 PMID:16009995 PMID:16649112 |
nlx_157682 | SCR_003543 | MapMan Application Software | 2026-02-15 09:18:32 | 1225 | |||||||
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I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France Resource Report Resource Website |
I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France (RRID:SCR_006991) | I3-CRB | material resource, biomaterial supply resource | Project to improve data and sample exchanges and to facilitate large scale analysis of data by improving interoperability of French Biological Resources Centres (BRC or biobanks) IT systems and biological databases. The work done in this project will be linked to other national (IBiSA, ANR, R��seau des Biobanques, Club 3C-R), European (BBMRI, ELIXIR) or international project (P3G). In the preliminary phase (2009-2010) I3-CRB has developed a directory of French Biological Resource Centres / Biobanks where one may register their French BRC or perform a search across all of them. Detail by overall data or kingdom is provided as well as many filtering options. Access to biological samples is provided by the participating BRC''''s. Biological Resources Centres (BRC or biobanks) collect annotated biological samples from various sources (human, animal, plant, bacteria...). The type of samples depends on the collection and the associated thematic (DNA, proteins, cells, tissues, blood, serum, organisms...). The aims of these centers are to collect, to store, to transform and to distribute the biological samples. They constitute a vital infrastructure for life science and health research. Goals of the French Biobanks/Biological Resource Centres: * List French biobanks and their biological collections * Improve sample exchanges * Improve the international visibility of the French biological collections MeSH terms have been integrated: Domains, diseases, and location of the disease (Anatomy). Collections/species are based on NCBI Taxonomy. | plant, animal, human, micro-organism, microorganism, bacteria, dna, protein, cell, tissue, blood, serum, organism, research |
is listed by: One Mind Biospecimen Bank Listing is related to: MeSH has parent organization: University of Lyon; France |
GIS IBiSA | Varying: Access to biological samples is provided by the participating BRC''''s., The community can contribute to this resource | nlx_36068 | SCR_006991 | Infrastructure Informatique Interop��rable pour les CRB | 2026-02-15 09:19:21 | 0 | ||||||
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iLoc-Plant Resource Report Resource Website 1+ mentions |
iLoc-Plant (RRID:SCR_011973) | iLoc-Plant | service resource, analysis service resource, data analysis service, production service resource | Data analysis service for predicting subcellular localization of plant proteins with single and multiple sites. | subcellular localization, protein, classifier | is listed by: OMICtools | PMID:21984117 | Acknowledgement requested | OMICS_01624 | SCR_011973 | iLoc-Plant: Predicting subcellular localization of plant proteins with single and multiple sites | 2026-02-15 09:20:28 | 1 | ||||||
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Global Crop Diversity Trust Resource Report Resource Website |
Global Crop Diversity Trust (RRID:SCR_010658) | material resource, tissue bank, biomaterial supply resource | Not yet vetted by NIF curator | nlx_68877 | SCR_010658 | 2026-02-15 09:20:01 | 0 | ||||||||||||
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BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | service resource, analysis service resource, data analysis service, production service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-02-15 09:20:28 | 45 | ||||||||
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Cell-PLoc Resource Report Resource Website 100+ mentions |
Cell-PLoc (RRID:SCR_011966) | Cell-PLoc | service resource, analysis service resource, data analysis service, production service resource | A package of web-servers for predicting subcellular localization of proteins in different organisms. | subcellular localization, protein, gram-negative protein, gram-positive protein, virus |
is listed by: OMICtools has parent organization: Shanghai Jiao Tong University; Shanghai; China is parent organization of: Euk-mPLoc |
PMID:18274516 | OMICS_01617 | SCR_011966 | Cell-PLoc: A package of web-servers for predicting subcellular localization of proteins in different organisms | 2026-02-15 09:20:25 | 203 | |||||||
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Genevestigator Resource Report Resource Website 100+ mentions |
Genevestigator (RRID:SCR_002358) | Genevestigator | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource, commercial organization | A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools. | gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similarity, FASEB list | is parent organization of: RefGenes | 4 products:, Free, Free for academic use, Account required, Paid subscription, Local installation | nif-0000-21172, OMICS_00763 | SCR_002358 | 2026-02-15 09:18:17 | 396 |
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