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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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AutismKB Resource Report Resource Website 10+ mentions |
AutismKB (RRID:SCR_006937) | AutismKB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Genetic factors contribute significantly to ASD. AutismKB is an evidence-based knowledgebase of Autism spectrum disorder (ASD) genetics. The current version contains 2193 genes (99 syndromic autism related genes and 2135 non-syndromic autism related genes), 4617 Copy Number Variations (CNVs) and 158 linkage regions associated with ASD by one or more of the following six experimental methods: # Genome-Wide Association Studies (GWAS); # Genome-wide CNV studies; # Linkage analysis; # Low-scale genetic association studies; # Expression profiling; # Other low-scale gene studies. Based on a scoring and ranking system, 99 syndromic autism related genes and 383 non-syndromic autism related genes (434 genes in total) were designated as having high confidence. Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with a prevalence of 1.0-2.6%. The three core symptoms of ASD are: # impairments in reciprocal social interaction; # communication impairments; # presence of restricted, repetitive and stereotyped patterns of behavior, interests and activities. | gene, copy number variation, linkage region, genome-wide association study, family-based association study, case-control association study, expression profile, blast, syndromic, non-syndromic, snp, vntr, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
Autism spectrum disorder, Autism | Merck ; Johnson and Johnson ; Natural Science Foundation of China 31025014; Natural Science Foundation of China 2011CBA01102 |
PMID:22139918 | biotools:autismkb, nlx_151318 | https://bio.tools/autismkb | SCR_006937 | Autism Knowledgebase | 2026-09-12 12:56:47 | 34 | ||||
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LifeDB Resource Report Resource Website 1+ mentions |
LifeDB (RRID:SCR_006899) | LifeDB | data or information resource, database, image collection | Database that integrates large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. LifeDB integrates data regarding full length cDNA clones and data on expression of encoded protein and their subcellular localization on mammalian cell line. LifeDB enables the scientific community to systematically search and select genes, proteins as well as cDNA of interest by specific database identifiers as well as gene name. It enables to visualize cDNA clone and subcellular location of proteins. It also links the results to external biological databases in order to provide a broader functional information. LifeDB also provides an annotation pipeline which facilitates an improved mapping of clones to known human reference transcripts from the RefSeq database and the Ensembl database. An advanced web interface enables the researchers to view the data in a more user friendly manner. Users can search using any one of the following search options available both in Search gene and cDNA clones and Search Sub-cellular locations of human proteins: By Keyword, By gene/transcript identifier, By plate name, By clone name, By cellular location. * The Search genes and cDNA clones results include: Gene Name, Ensemble ID, Genomic Region, Clone name, Plate name, Plate position, Classification class, Synonymous SNP''s, Non- synonymous SNP''s, Number of ambiguous positions, and Alignment with reference genes. * The Search sub-cellular locations of human proteins results include: Subcellular location, Gene Name, Ensemble ID, Clone name, True localization, Images, Start tag and End tag. Every result page has an option to download result data (excluding the microscopy images). On click of ''Download results as CSV-file'' link in the result page the user will be given a choice to open or save result data in form of a CSV (Comma Separated Values) file. Later the CSV file can be easily opened using Excel or OpenOffice. | human, protein, gene, cdna clone, subcellular, open reading frame, functional genomics | has parent organization: German Cancer Research Center | BMBF 01GR0101; BMBF 01GR0420; European Union grant 503438 |
PMID:16381901 PMID:14681468 |
nif-0000-03081 | SCR_006899 | 2026-09-12 12:56:47 | 1 | |||||||
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OBIS Resource Report Resource Website 100+ mentions |
OBIS (RRID:SCR_006933) | OBIS | data or information resource, data repository, database, service resource, storage service resource | Accepts and provides access to biogeographic data collected throughout the global oceans. The datasets are integrated so you can search them all seamlessly by species name, higher taxonomic level, geographic area, depth, and time; and then map and find environmental data related to the locations. Created by the Census of Marine Life, OBIS is now part of the Intergovernmental Oceanographic Commission (IOC) of UNESCO, under its International Oceanographic Data and Information Exchange (IODE) programme | ocean, marine, data set, oceanography, FASEB list | is listed by: CINERGI | The community can contribute to this resource | nlx_154698, r3d100010088 | https://doi.org/10.17616/R33K5G | SCR_006933 | Ocean Biogeographic Information System Marine | 2026-09-12 12:56:47 | 179 | ||||||
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Diabetes Autoantibody Standardization Program Resource Report Resource Website 10+ mentions |
Diabetes Autoantibody Standardization Program (RRID:SCR_006929) | DASP | knowledge environment | Program that develops materials and methods to improve measurements of autoantibodies that are predictive of type 1 diabetes. These are the most sensitive and meaningful measures for predicting this disease. Historically, autoantibody measures have been variable among laboratories; therefore, this program, in collaboration with the Immunology of Diabetes Society, was established. The goals of DASP are to improve laboratory methods, evaluate laboratory performance, support the development of sensitive and specific measurement technologies, and develop reference methods. Currently, 48 key laboratories from 19 countries participate in DASP. | autoantibody, quality assurance, standardization, standard, laboratory method, laboratory performance, measurement, method |
is related to: NIDDK Information Network (dkNET) has parent organization: Centers for Disease Control and Prevention |
Type 1 diabetes, Diabetes | PMID:12716742 | nlx_152868 | http://www.idsoc.org/committees/antibody/dasphome.html | SCR_006929 | Diabetes Autoantibody Standardization Program (DASP) | 2026-09-12 12:56:47 | 14 | |||||
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C. elegans Phenotype Vocabulary Resource Report Resource Website |
C. elegans Phenotype Vocabulary (RRID:SCR_006924) | WB-PHENOTYPE | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of Caenorhabditis elegans phenotypes. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157348 | SCR_006924 | 2026-09-12 12:56:47 | 0 | |||||||||
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ABSORB: Atlas Building by Self-Organized Registration and Bundling Resource Report Resource Website 1+ mentions |
ABSORB: Atlas Building by Self-Organized Registration and Bundling (RRID:SCR_007018) | ABSORB | data processing software, image analysis software, registration software, software application, software resource, source code | This software package implements an algorithm for effective groupwise registration. The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5). The images should be pre-processed before applying ABSORB: * All brain MR images used as inputs to ABSORB should be in the same situation (e.g., skull-stripped or not, cerebellum removed or not, etc.). * The input images should be in Analyze format with paired header and image files. This software was developed in IDEA group in UNC-Chapel Hill. | image, registration, bundling, atlas, magnetic resonance, algorithm or reusable library, intermodal, intersubject, intrasubject, image-to-template, affine warp, nonlinear warp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:20226255 | Free, Public | nlx_144409 | http://www.nitrc.org/projects/absorb | SCR_007018 | ABSORB: Atlas Building by Self-Organized Registration Bundling, Atlas Building by Self-Organized Registration Bundling, Atlas Building by Self-Organized Registration and Bundling | 2026-09-12 12:56:49 | 1 | |||||
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Image Workflow Resource Report Resource Website |
Image Workflow (RRID:SCR_007017) | Image Workflow | data processing software, image analysis software, registration software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Software to support registering brain images to the stereotaxic coordinate system of a brain atlas. It was specifically designed to work with the large scale brain mosaics. When data are uploaded to the CCDB, users may launch Jibber, a custom tool for defining correspondence points between the image and an atlas overlay. Jibber automatically downsamples the data, so that users can define the warping and scaling parameters with good interactive performance on the smaller copy. Once the warping transformation is computed, the original image and the transformation matrix are sent to a cluster of computers for warping. The current version of Jetsam is running on a 30 Sun V20 nodes and the execution time is roughly about 20 minutes per GB. The warped images are then automatically registered with an image web server that supports spatial queries based on stereotaxic coordinates. These servers generate optimized downsampled images, which can be displayed by standard online clients regardless of the size of the original image. | brain, image | has parent organization: Cell Centered Database | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156721 | SCR_007017 | 2026-09-12 12:56:49 | 0 | ||||||||
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Jinx Resource Report Resource Website 1+ mentions |
Jinx (RRID:SCR_007012) | Jinx | data processing software, image analysis software, segmentation software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 2, 2019. Ontology-based segmentation and analysis tools for electron tomographic data. | electron tomography |
is related to: Subcellular Anatomy Ontology has parent organization: Cell Centered Database |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156722 | SCR_007012 | 2026-09-12 12:56:49 | 5 | ||||||||
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Matlab Neuroshare Library Resource Report Resource Website |
Matlab Neuroshare Library (RRID:SCR_006957) | NeuroshareLibrary | software library, software resource, software toolkit | This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file. | console (text based), eeg, meg, electrocorticography, format conversion, japanese, linux, macos, matlab, microsoft, posix/unix-like, windows, neuroshare, data format, data sharing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ATR; Kyoto; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | GNU General Public License | nlx_155880 | http://www.nitrc.org/projects/nslib_v1_3_1 | SCR_006957 | Neuroshare Library | 2026-09-12 12:56:48 | 0 | |||||
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The WWW Virtual Library: Model Organisms Resource Report Resource Website |
The WWW Virtual Library: Model Organisms (RRID:SCR_007007) | data or information resource, portal, topical portal | Catalog of internet resources relating to biological model organisms, and is part of the Biosciences area of the Virtual Library project. The main Model Organisms Library discussed in this website are: * E. coli (bacterium) * Yeasts (Saccharomyces cerevisiae, and other species) * Dictyostelium discoideum (slime mold) * Drosophila melanogaster (fruit fly) * Xenopus laevis (African clawed frog) Many aspects of biology are similar in most or all organisms, but it is frequently much easier to study particular aspects in particular organisms - for instance, genetics is easier in small organisms that breed quickly, and very difficult in humans! The most popular model organisms have strong advantages for experimental research, and become even more useful when other scientists have already worked on them, discovering techniques, genes and other useful information. | bacterium, cerevisiae, model organism, saccharomyces, s. cerevisiae, slime mold, xenopus, catalog, link aggregator | is listed by: 3DVC | nif-0000-20953 | SCR_007007 | VL | 2026-09-12 12:56:49 | 0 | |||||||||
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MetMap Resource Report Resource Website 1+ mentions |
MetMap (RRID:SCR_006954) | MetMap | software resource | A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00618 | SCR_006954 | 2026-09-12 12:56:48 | 9 | |||||||||
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Comparative Sequencing of Plant Small RNAs Resource Report Resource Website 1+ mentions |
Comparative Sequencing of Plant Small RNAs (RRID:SCR_007003) | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | This project has developed a sequence dataset of plant small RNAs based on the hypothesis that most if not all plants utilize important small RNA signaling networks. Different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles. Comparative genomics approaches can be applied to distinguish potential miRNAs from siRNAs and to match the miRNAs to the target sequences. This project develops an unparalleled resource of millions of plant small RNAs for comparative analyses. The project includes sequencing of small RNAs from a diverse and agronomically-relevant set of plant species, focused analyses of important members of the Solanaceae and Poaceae, and development of a small RNA database and web interface for public access and analysis of data. These data will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, and will be tremendously useful to a broad set of plant biologists interested in development, stress responses, epigenetics, evolution, RNA biology and other traits impacted by small RNAs. We offer a variety of tools to query the small RNA data set, with options to identify sequences based on homology, expression levels, conservation, or potential function: 1. Small RNA mapping tool: searches for small RNAs perfectly matching a genomic sequence provided by the user. 2. Small RNA mismatch tool: searches the database for small RNAs or other short sequences provided by the user, allowing mismatches. 3. Library-comparison tool to identify conserved small RNAs. 4. Library-comparison tool to identify differentially regulated small RNAs. 5. Reverse Target Prediction. | has parent organization: University of Delaware; Delaware; USA | NSF 0638525 | nlx_37749 | SCR_007003 | 2026-09-12 12:56:48 | 1 | ||||||||||
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Myrna Resource Report Resource Website 1+ mentions |
Myrna (RRID:SCR_006951) | Myrna | software resource | A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. | mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20701754 | Artistic License | OMICS_01310, biotools:myrna | https://github.com/BenLangmead/myrna, https://bio.tools/myrna | SCR_006951 | Myrna: Cloud-scale differential gene expression for RNA-seq | 2026-09-12 12:56:48 | 2 | |||||
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CCDB Image Converter Resource Report Resource Website |
CCDB Image Converter (RRID:SCR_007005) | Image Converter | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. A command line program in Unix to convert images to a variety of formats (PNG, TIFF, JPEG, PPM..etc). It is uniquely different from other programs such as Adobe Photoshop or ImageMagick because it is designed for dealing with the high-resolution images with file sizes of several gigabytes. Image Converter does not require any additional RAM or virtual memory to run. Also, run-time is relatively fast for high resolution data. | image | has parent organization: Cell Centered Database | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156720 | SCR_007005 | 2026-09-12 12:56:48 | 0 | ||||||||
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Minnesota Center for Twin and Family Research Resource Report Resource Website 1+ mentions |
Minnesota Center for Twin and Family Research (RRID:SCR_006948) | MCTFR | data or information resource, disease-related portal, portal, research forum portal, topical portal | Composed of many projects, including the Minnesota Twin Family Study (MTFS) and The Sibling Interaction and Behavior Study (SIBS), this research center seeks to identify genetic and environmental influences on development and psychological traits. Both projects are longitudinal research studies including twins, siblings, and parents. Over 9800 individuals have contributed to these exciting projects! By studying twins and siblings and their families, we can estimate how genes and environment interact to influence character, strengths, vulnerabilities and values. Participants in the MTFS include families with same-sex identical or fraternal twins who were born in Minnesota. The SIBS study is comprised of adoptive and biological siblings and their parents. Most participants partake in day-long visits to the MCTFR, and due to the longitudinal nature of our projects, they return every 3-4 years for follow-up visits. | longitudinal study, clinical study, twin, sibling, parent, longitudinal, gene, environment, adolescent, development, behavior, dna | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Identical twin, Fraternal twin, Sibling, Parent, Twin | NIH | nlx_151990 | SCR_006948 | SIBS, Minnesota Twin Study, MTFS, Sibbling Interaction and Behavior Study, Minnesota Twin Family Study | 2026-09-12 12:56:48 | 3 | ||||||
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SimSeq Resource Report Resource Website 10+ mentions |
SimSeq (RRID:SCR_006947) | SimSeq | simulation software, software application, software resource | An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential for chimeric reads, and non-biotinylated fragment pull down in mate-pair libraries . | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Free | biotools:simseq, OMICS_00258 | https://bio.tools/simseq | SCR_006947 | 2026-09-12 12:56:48 | 30 | |||||||
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Concierge Resource Report Resource Website 10+ mentions |
Concierge (RRID:SCR_002386) | Concierge | data management software, software application, software resource | A data management tool which stores, classifies and manages digital resources such as publications, experimental data, presentation files, etc, together with its metadata. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. It has a function of sharing data with open digital archives based on the XooNIps system, such as neuroinformatics platforms in operation and publicly available at J-Node (http://www.neuroinf.jp). The Concierge Project is a part of neuroinformatics research by Laboratory for Neuroinformatics in RIKEN Brain Science Institute. Concierge's primary goal is to encourage research resource sharing in neuroscience communities. A key feature of the software is its pluggable configuration. Based on the basic functions, various applications can be developed as plug-ins. It has already developed several application plug-ins specific to neuroscience research, e.g. literature manager, electronic laboratory notebook, etc. | literature manager, labnote, electronic laboratory notebook, plug-in, resource management, resource sharing |
is related to: XooNIps - Neuroinformatics Base Platform System has parent organization: RIKEN Brain Science Institute |
PMID:18974800 | Open unspecified license; Mac OS X and Windows XP versions | nif-0000-00379 | SCR_002386 | Concierge: Personal Database Software for Managing Digital Research Resources, Concierge Project, Concierge: Personal Database Software for Digital Research Resources, The Concierge Project: Personal Database Software for Digital Research Resources | 2026-09-12 12:55:40 | 12 | ||||||
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University of Amsterdam; Amsterdam; Netherlands Resource Report Resource Website |
University of Amsterdam; Amsterdam; Netherlands (RRID:SCR_002385) | UvA | university | Public research university in the Netherlands that offers programs in humanities, social and behavioural sciences, economics and business, science, law, medicine, and dentistry. | netherlands public university, public university, netherlands research, degree program |
is affiliated with: OpenMinTeD is parent organization of: A modular structure for scientific articles in an electronic environment is parent organization of: X-linked Adrenoleukodystrophy Database is parent organization of: T-profiler is parent organization of: 7T Structural MRI scans ATAG is parent organization of: ENVRI-KMS is parent organization of: R2 Genomics Analysis and Visualization Platform |
nlx_19684 | SCR_002385 | University of Amsterdam, Universiteit van Amsterdam | 2026-09-12 12:55:40 | 0 | ||||||||
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Cancer Genomics Consortium Resource Report Resource Website 1+ mentions |
Cancer Genomics Consortium (RRID:SCR_002384) | CGC | community building portal, data or information resource, organization portal, portal | Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization. | cytogenetics, molecular genetics, molecular pathology, microarray technology, cancer diagnosis, cancer research, microarry, cytogenomics, cancer cytogenomics, cancer genetics, genetics | is listed by: OMICtools | Cancer | Membership fee, Account required | OMICS_01776 | SCR_002384 | CCMC, Cancer Cytogenomics Microarray Consortium | 2026-09-12 12:55:40 | 6 | ||||||
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GeneNetwork Resource Report Resource Website 100+ mentions |
GeneNetwork (RRID:SCR_002388) | GeneNetwork, WebQTL | data or information resource, data repository, database, service resource, storage service resource | Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. | Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list |
is used by: NIF Data Federation is used by: Hypothesis Center is related to: NIH Data Sharing Repositories has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
NCI U01 CA105417; NCRR U24 RR021760; NIAAA U01 AA014425; NIAAA U01 AA016662; NIAAA U01 AA13499; NIAAA U24 AA13513; NIA R01 AG043930; NIDA P20 DA21131; NIGMS R01 GM123489 |
PMID:8043953 PMID:11737945 PMID:15043217 PMID:15114364 PMID:15043220 PMID:15043219 PMID:15711545 PMID:18368372 PMID:27933521 |
Restricted | nif-0000-00380 | SCR_002388 | GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL | 2026-09-12 12:55:40 | 499 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
