Searching the RRID Resource Information Network

Our searching services are busy right now. Please try again later

  • Register
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X

Leaving Community

Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.

No
Yes
X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

Preparing word cloud

×

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.

Search

Type in a keyword to search

Filter by records added date
See new records

Options


Current Facets and Filters

  • Keywords:gene (facet)

Facets


Recent searches

Snippet view Table view
Click the to add this resource to a Collection

1,737 Results - per page

Show More Columns | Download Top 1000 Results

Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
MedBlast
 
Resource Report
Resource Website
1+ mentions
MedBlast (RRID:SCR_008202) software resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. An algorithm that finds articles most relevant to a genetic sequence. In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here, a new literature-mining tool MedBlast is developed, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. The genome sequencing projects generate such a large amount of data every day that many molecular biologists often encounter some sequences that they know nothing about. Literature is usually the principal resource of such information. It is relatively easy to mine the articles cited by the sequence annotation; however, it is a difficult task to retrieve those relevant articles without direct citation relationship. The related articles are those described in the given sequence (gene/protein), or its redundant sequences, or the close homologs in various species. They can be divided into two classes: direct references, which include those either cited by the sequence annotation or citing the sequence in its text; indirect references, those which contain gene symbols of the given sequence. A few additional issues make the task even more complicated: (1) symbols may have aliases; and (2) one sequence may have a couple of relatives that we want to take into account too, which include redundant (e.g. protein and gene sequences) and close homologs. Here the issues are addressed by the development of the software MedBlast, which can retrieve the related articles of the given sequence automatically. MedBlast uses BLAST to extend homology relationships, precompiled species-specific thesauruses, a useful semantics technique in natural language processing (NLP), to extend alias relationship, and EUtilities toolset to search and retrieve corresponding articles of each sequence from PubMed. MedBlast take a sequence in FASTA format as input. The program first uses BLAST to search the GenBank nucleic acid and protein non-redundant (nr) databases, to extend to those homologous and corresponding nucleic acid and protein sequences. Users can input the BLAST results directly, but it is recommended to input the result of both protein and nucleic acid nr databases. The hits with low e-values are chosen as the relatives because the low similarity hits often do not contain specific information. Very long sequences, e.g. 100k, which are usually genomic sequences, are discarded too, for they do not contain specific direct references. User can adjust these parameters to meet their own needs. gene, article, biological, data, genome, genomic, homolog, literature, medline interfaces, mining, molecular, protein, sequence, specie National Natural Science Foundation of China 39990600-03;
Knowledge Innovation Program of the Chinese Academy of Sciences KSCX2-2-07;
Knowledge Innovation Program of the Chinese Academy of Sciences KJCX1-08
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-21253 SCR_008202 MedBlast 2026-02-14 02:01:37 1
DynGO
 
Resource Report
Resource Website
1+ mentions
DynGO (RRID:SCR_007009) DynGO software resource 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 gene, annotation, browser, ontology or annotation browser is listed by: Gene Ontology Tools
is related to: Gene Ontology
NSF IIS-0430743 PMID:16091147 Free for academic use nlx_149118 http://gauss.dbb.georgetown.edu/liblab SCR_007009 DynGO: a tool for visualizing and mining of Gene Ontology and its associations 2026-02-14 02:01:26 6
Manatee
 
Resource Report
Resource Website
50+ mentions
Manatee (RRID:SCR_005685) Manatee software resource Manatee is a web-based gene evaluation and genome annotation tool; Manatee can store and view annotation for prokaryotic and eukaryotic genomes. The Manatee interface allows biologists to quickly identify genes and make high quality functional assignments, such as GO classifications, using search data, paralogous families, and annotation suggestions generated from automated analysis. Manatee can be downloaded and installed to run under the CGI area of a web server, such as Apache. Platform: Online tool, Linux compatible, Solaris gene, genome, annotation, ontology or annotation browser, ontology or annotation editor is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: J. Craig Venter Institute
has parent organization: University of Maryland School of Medicine; Maryland; USA
has parent organization: SourceForge
Open unspecified license - Free for academic use nlx_149128 SCR_005685 2026-02-14 02:01:10 64
tranSMART
 
Resource Report
Resource Website
10+ mentions
tranSMART (RRID:SCR_005586) tranSMART software resource tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work. tranSMART is licensed through GPL 3. The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART''s specific applications include: * Revalidating previous hypotheses * Testing and refining novel hypotheses * Conducting cross-study meta-analysis * Searching across multiple data sources to find associations of concepts, such as a gene''s involvement in biological processes or experimental results * Comparing biological processes and pathways among multiple data sets from related diseases or even across multiple therapeutic areas Data Repository The tranSMART Data Repository combines a data warehouse with access to federated sources of open and commercial databases. tranSMART accommodates: * Phenotypic data, such as demographics, clinical observations, clinical trial outcomes, and adverse events * High content biomarker data, such as gene expression, genotyping, pharmacokinetic and pharmaco-dynamics markers, metabolomics data, and proteomics data * Unstructured text-data, such as published journal articles, conference abstracts and proceedings, and internal studies and white papers * Reference data from sources such as MeSH, UMLS, Entrez, GeneGo, Ingenuity, etc. * Metadata providing context about datasets, allowing users to assess the relevance of results delivered by tranSMART Data in tranSMART is aligned to allow identification and analysis of associations between phenotypic and biomarker data, and it is normalized to conform with CDISC and other standards to facilitate search and analysis across different data sources. tranSMART also enables investigators to search published literature and other text sources to evaluate their analysis in the context of the broader universe of reported research. External data can also be integrated into the tranSMART data repository, either from open data projects like GEO, EBI Array Express, GCOD, or GO, or from commercially available data sources. Making data accessible in tranSMART enables organizations to leverage investments in manual curation, development costs of automated ETL tools, or commercial subscription fees across multiple research groups. Dataset Explorer tranSMART''s Dataset Explorer provides flexible, powerful search and analysis capabilities. The core of the Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, and GenePattern analytical tools. Connections to other open source and commercial analytical tools such as Galaxy, Integrative Genomics Viewer, Plink, Pathway Studio, GeneGo, Spotfire, R, and SAS can be established to expand tranSMART''s capabilities. tranSMART''s design allows organizations flexibility in selecting analytical tools accessible through the Dataset Explorer, and provides file export capabilities to enable researchers to use tools not accessible in the tranSMART portal. source code, genetic, phenotype, gene, data storage repository, data analysis service is used by: eTRIKS
is used by: RanchoBiosciences
nlx_146211 http://www.transmartproject.org/ SCR_005586 2026-02-14 02:00:57 13
JEPETTO
 
Resource Report
Resource Website
10+ mentions
JEPETTO (RRID:SCR_005909) JEPETTO software resource A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. gene set enrichment analysis, topological analysis, interaction network, java, enrichment analysis, functional analysis, gene prioritization, integrated analysis, network analysis, interaction, pathway, process, topology, gene is listed by: OMICtools
has parent organization: Cytoscape
has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom
PMID:24363376 GNU General Public License OMICS_02247 SCR_005909 Java Enrichment of Pathways Extended To Topology 2026-02-14 02:01:12 15
Cascade
 
Resource Report
Resource Website
50+ mentions
Cascade (RRID:SCR_005861) Cascade software resource R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. r, windows, gene expression, perturbation, network, diffusion, signal, temporal gene network, gene regulatory network, gene, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: University of Strasbourg; Strasbourg; France
PMID:24307703 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02249, biotools:cascade http://www-math.u-strasbg.fr/genpred/spip.php?rubrique4
https://bio.tools/cascade
SCR_005861 2026-02-14 02:01:12 92
BiNGO: A Biological Networks Gene Ontology tool
 
Resource Report
Resource Website
500+ mentions
BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) BiNGO software resource The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene ontology, gene, ontology, statistical analysis, term enrichment, biological network, plugin, bio.tools is listed by: Gene Ontology Tools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Cytoscape
has parent organization: Ghent University; Ghent; Belgium
PMID:15972284 Open unspecified license - Free for academic use nlx_149196, biotools:bingo https://bio.tools/bingo SCR_005736 Biological Networks Gene Ontology 2026-02-14 02:01:00 790
Illumina
 
Resource Report
Resource Website
1000+ mentions
Illumina (RRID:SCR_010233) Illumina, Inc. commercial organization American company incorporated that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Provides a line of products and services that serve the sequencing, genotyping and gene expression and proteomics markets. Its headquarters are located in San Diego, California. Commercial, organization, develope, manufacture, system, analysis, genetic, sequencing, genotyping, gene, expression, proteomic is related to: fermi-lite
is related to: Illumina NextSeq 2000 system
is parent organization of: Strelka
is parent organization of: Tk-GO
is parent organization of: BaseSpace
is parent organization of: Illumina iSeq 100 Sequencing System
nlx_156846, grid.185669.5, Wikidata: Q2068984, ISNI: 0000 0004 0507 3954 https://ror.org/05k34t975 SCR_010233 Inc., Illumina 2026-02-14 02:01:54 2340
rSeqDiff
 
Resource Report
Resource Website
rSeqDiff (RRID:SCR_001683) rSeqDiff software resource An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions. The approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing. rna-seq, gene expression, differential expression, differential splicing, gene is listed by: OMICtools
has parent organization: University of Michigan; Ann Arbor; USA
PMID:24260225 Free, Available for download, Freely available OMICS_01968 SCR_001683 rSeqDiff: Detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test 2026-02-14 02:00:05 0
QuasiSeq
 
Resource Report
Resource Website
10+ mentions
QuasiSeq (RRID:SCR_001715) QuasiSeq software resource Software package to apply the QL, QLShrink and QLSpline methods to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data. differential expression, gene, rna-seq, next generation sequencing, gene expression, mrna is listed by: OMICtools PMID:23104842 Free, Available for download, Freely available OMICS_01963 http://cran.r-project.org/web/packages/QuasiSeq/index.html SCR_001715 2026-02-14 02:00:16 20
International Neuroinformatics Coordinating Facility: Blue Gene/L Access
 
Resource Report
Resource Website
International Neuroinformatics Coordinating Facility: Blue Gene/L Access (RRID:SCR_001755) data computation service Through this site, INCF provides he neuroinformatics community with access to an IBM Blue Gene/L supercomputer. INCF owns a share of a BlueGene/L (BG/L) supercomputer located at the Parallel Computer Center (PDC) at The Royal Institute of Technology (KTH) in Stockholm. Allocations are now available through the INCF Secretariat. During an initial evaluation phase, a limited numbers of large-scale computing projects will be selected, based on the suitability of the project for supercomputing. Research groups with limited access to supercomputers at their home institutions are given priority. Approved projects are regularly re-evaluated. New projects are approved based on availability and usage load of the BG/L. The Blue Gene/L supercomputer project is aimed at expanding the horizon of high-performance computing to unprecedented levels of scale and performance. Blue Gene/L is the first supercomputer in the Blue Gene family. The full Blue Gene/L consists of 64 racks containing 65,536 high-performance compute nodes. Each node (nodes and chips are the same in the Blue Gene system) contains two embedded 32-bit PowerPC processors. Furthermore, the same chip that is used for compute nodes is also used for the 1,024 I/O nodes. A three-dimensional torus network and a collective network are used to interconnect all nodes. The full system contains 33 terabytes of main memory; it is designed to achieve 183.5 teraflops peak performance using one of the processors of each node for computation and the other processor for communication, and 367 teraflops using both processors for computation. Another key architectural feature of this supercomputer is the link chip component and five Blue Gene/L networks, the PowerPC 440 core and floating-point enhancements, the on-chip and off-chip distributed memory system, the node- and system-level design for high reliability, and the comprehensive approach to fault isolation. One of the key objectives in Blue Gene/L design is to achieve cost/performance comparable to the COTS (Commodity Off The Shelf) approach, while at the same time incorporating a processor and network combination so powerful that it revolutionizes the performance of supercomputer systems. Sponsors: This resource is supported by the INCF. gene, chip, computation, computing project, memory, neuroinformatics, node, parallel computer, processor, supercomputer THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10263 SCR_001755 INCF Blue Gene/L Access 2026-02-14 02:00:10 0
Functional Annotation
 
Resource Report
Resource Website
1+ mentions
Functional Annotation (RRID:SCR_017519) service resource MGI GO project provides functional annotations for mouse gene products using Gene Ontology. Functional annotation using Gene Ontology (GO). MGI, GO, functional, annotation, mouse, gene, product, Gene Ontology uses: Gene Ontology
has parent organization: Mouse Genome Informatics (MGI)
Free, Freely available SCR_017519 2026-02-14 02:03:13 4
Knockout Mouse Project Repository at JAX
 
Resource Report
Resource Website
Knockout Mouse Project Repository at JAX (RRID:SCR_017512) data or information resource Information from JAX about their contributions to KOMP project coordinated by International Mouse Phenotyping Consortium. National Institutes of Health has funded three KOMP2 centers in United States, including one at Jackson Laboratory, to work together on task of producing and phenotyping mice to establish resource of knockout mice and related database of gene function. KOMP, JAX, knockout, mice, data, gene, function, phenotype is related to: International Mouse Phenotyping Consortium (IMPC)
is related to: JAX Mice and Services
has parent organization: Knockout Mouse Project
Free, Freely available https://www.jax.org/mouse-search?searchTerm=repository SCR_017512 2026-02-14 02:03:28 0
Dietary Restriction Gene Database
 
Resource Report
Resource Website
1+ mentions
Dietary Restriction Gene Database (RRID:SCR_013720) GenDR Database of genes associated with dietary restriction. It includes genes inferred from experiments in model organisms in which genetic manipulations cancel out or disrupt the life-extending effects of dietary restriction and genes robustly altered due to dietary restriction, derived from a meta-analysis of microarray studies in mammals. gene, dietary restriction, microarray has parent organization: University of Liverpool; Liverpool; United Kingdom Wellcome Trust MEB050495MES;
Biotechnology and Biological Sciences Research Council H0084971
Free, Public SCR_013720 The GenDR Database of Dietary Restriction-Related Genes 2026-02-14 02:02:54 3
MultiNet
 
Resource Report
Resource Website
10+ mentions
MultiNet (RRID:SCR_016149) software resource Software for an integrated network combining multiple biological network database sources into a single human protein interactome. The software package contains gene interaction pairs corresponding to the unified global network. network, integration, human, protein, interactome, gene, interaction PMID:23505346 Free, Available for download SCR_016149 2026-02-14 02:03:00 12
TAIR
 
Resource Report
Resource Website
5000+ mentions
TAIR (RRID:SCR_004618) TAIR, AGI LocusCode data or information resource, database Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided. genetic, molecular biology, gene, genome, structure, product, metabolism, gene expression, dna, seed stock, genome map, genetic marker, physical marker, genome sequence, gene product, blast, experimental protocol, gold standard is used by: NIF Data Federation
is listed by: OMICtools
is listed by: re3data.org
is listed by: DataCite
is related to: AmiGO
is related to: Saskatoon Arabidopsis T-DNA mutant population SK Collection
is related to: CLENCH
has parent organization: Carnegie Institution for Science
is parent organization of: TAIR Keyword Browser
is parent organization of: PubSearch
NSF DBI-0850219;
corporate and nonprofit organizations
PMID:22140109
PMID:17986450
PMID:12444417
PMID:12519987
PMID:18287693
r3d100010185, nlx_61477, OMICS_01662 https://doi.org/10.17616/R3QW21 SCR_004618 AGI LocusCode, The Arabidopsis Information Resource 2026-02-14 02:00:59 7421
SnpEff
 
Resource Report
Resource Website
5000+ mentions
SnpEff (RRID:SCR_005191) SnpEff software resource Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs. genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, java, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: Galaxy
is related to: GATK
has parent organization: SourceForge
has parent organization: Wayne State University; Michigan; USA
works with: SnpSift
Cancer PMID:22728672 Free, Freely available biotools:snpeff, OMICS_00186 https://bio.tools/snpeff
https://sources.debian.org/src/snpeff/
SCR_005191 SnpEff - Genetic variant annotation and effect prediction toolbox 2026-02-14 02:01:05 5186
EBIMed
 
Resource Report
Resource Website
1+ mentions
EBIMed (RRID:SCR_005314) EBIMed service resource A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading. protein, gene, annotation, drug, specie, association, database is listed by: OMICtools
is related to: MEDLINE
is related to: PubMed
is related to: Gene Ontology
is related to: UniProt
is related to: NCBI Taxonomy
is related to: MedlinePlus
has parent organization: European Bioinformatics Institute
OMICS_01180 SCR_005314 2026-02-14 02:01:04 1
CoIN
 
Resource Report
Resource Website
100+ mentions
CoIN (RRID:SCR_005332) CoIN service resource A web-based system that assess articles according to their term correlations among sentences. It employs the co-occurrence relations and their network centralities to evaluate the influence of biomedical terms from Comparative Toxicogenomics Database (CTD)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. gene, disease, chemical, biomedical, association, document triage, database, FASEB list is listed by: OMICtools
has parent organization: National Cheng Kung University; Tainan; Taiwan
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01177 SCR_005332 Co-occurrence Interaction Nexus, CoIN: A network exploration for document triage, CoIN: Co-occurrence Interaction Nexus 2026-02-14 02:01:05 138
Gramene
 
Resource Report
Resource Website
500+ mentions
Gramene (RRID:SCR_002829) GR data or information resource, database Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site. crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web service, bio.tools, FASEB list is used by: NIF Data Federation
is listed by: re3data.org
is listed by: bio.tools
is listed by: Debian
is related to: AmiGO
is related to: Gene Ontology
is related to: Plant Ontology
is related to: Trait Ontology
is related to: EnvO
is related to: BioCyc
has parent organization: Cold Spring Harbor Laboratory
has parent organization: Cornell University; New York; USA
is parent organization of: Trait Ontology
is parent organization of: Plant Environmental Conditions
is parent organization of: Plant Trait Ontology
is parent organization of: Cereal Plant Development Ontology
is parent organization of: Cereal Plant Gross Anatomy Ontology
USDA IFAFS 00-52100-9622;
USDA 58-1907-0-041;
USDA 1907-21000-030;
NSF 0321685;
NSF 0703908;
NSF 0851652
PMID:21076153
PMID:17984077
PMID:16381966
Free, Freely available r3d100010856, nif-0000-02926, nlx_65829, biotools:gramene https://bio.tools/gramene
https://doi.org/10.17616/R3GG7M
SCR_002829 GR PROTEIN, RiceGenes, GR REF, GR GENE, Gramene: A Resource for Comparative Grass Genomics, GR QTL 2026-02-14 02:00:19 778

Can't find your Tool?

We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.

Can't find the RRID you're searching for? X
X
  1. Neuroscience Information Framework Resources

    Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.

  2. Navigation

    You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.

  3. Logging in and Registering

    If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.

  4. Searching

    Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:

    1. Use quotes around phrases you want to match exactly
    2. You can manually AND and OR terms to change how we search between words
    3. You can add "-" to terms to make sure no results return with that term in them (ex. Cerebellum -CA1)
    4. You can add "+" to terms to require they be in the data
    5. Using autocomplete specifies which branch of our semantics you with to search and can help refine your search
  5. Collections

    If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.

  6. Facets

    Here are the facets that you can filter the data by.

  7. Further Questions

    If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.