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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NCI Office of Biospecimens Resource Report Resource Website 1+ mentions |
NCI Office of Biospecimens (RRID:SCR_007076) | OBBR | narrative resource, topical portal, portal, data or information resource, standard specification | The NCI Office of Biorepositories and Biospecimen Research (OBBR) was established in 2005 in recognition of the critical role that biospecimens play in cancer research. The OBBR is responsible for developing a common biorepository infrastructure that promotes resource sharing and team science, in order to facilitate multi-institutional, high throughput genomic and proteomic studies. OBBR is focused on the following objectives: * Establish biobanking as a new area of research, in order to determine the impact of various collection and processing protocols on the usefulness of biospecimens in genomic and proteomic studies * Disseminate first-generation Best Practices in order to harmonize policies and procedures of NCI-supported biorepositories * Develop future generations of biorepository best practices, based on the data generated in the biobanking research programs above * Promote professional oversight of biospecimen standards development by standards organizations * Develop new technologies for biorepository operations * Develop a biorepository accreditation program * Coordinate with the international biobanking community to harmonize policies and procedures to facilitate multi-national research | has parent organization: National Cancer Institute | NCI | nlx_29021 | SCR_007076 | Office of Biorepositories and Biospecimen Research, NCI OBBR, NCI Office of Biorepositories and Biospecimen Research, National Cancer Institute Office of Biorepositories and Biospecimen Research | 2026-02-16 09:46:52 | 2 | ||||||||
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ModelDB Resource Report Resource Website 100+ mentions |
ModelDB (RRID:SCR_007271) | ModelDB | data repository, database, storage service resource, service resource, data or information resource | Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions. | repository, collection, network, neuron, computational, neuroscience, model, simulation, neural, data |
is used by: NIF Data Federation lists: ModelRun is listed by: 3DVC is listed by: Biositemaps is listed by: Integrated Models is related to: SimToolDB is related to: NeuronDB is related to: NeuronVisio is related to: Integrated Manually Extracted Annotation is related to: Allen Institute for Brain Science has parent organization: Yale University; Connecticut; USA works with: MicrocircuitDB |
NIMH ; NINDS ; NCI ; Human Brain Project ; NIDCD P01 DC004732; NIDCD R01 DC009977 |
PMID:15218350 PMID:15055399 PMID:8930855 |
Free, Freely available, Acknowledgement requested | nif-0000-00004, r3d100011330 | https://doi.org/10.17616/R3P61F | SCR_007271 | Model_DB, Model Database, Model DB, Model-DB | 2026-02-16 09:46:56 | 304 | ||||
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Drug Target Ontology Resource Report Resource Website 1+ mentions |
Drug Target Ontology (RRID:SCR_015581) | DTO | ontology, data or information resource, controlled vocabulary | Ontology of drug targets to be used as a reference for drug targets, with the longer-term goal of creating a community standard that will facilitate the integration of diverse drug discovery information from numerous heterogeneous resources. The project itself aims to develop a novel semantic framework to formalize knowledge about drug targets with a focus on the current IDG protein families. | drug ontology, drug target ontology, protein family | has parent organization: University of Miami; Florida; USA | NCI U54CA189205; NHLBI U54HL127624 |
Available for download | https://github.com/DrugTargetOntology/DTO http://bioportal.bioontology.org/ontologies/DTO | SCR_015581 | Drug Target Ontology (DTO) | 2026-02-16 09:48:50 | 2 | ||||||
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CRowd Extracted Expression of Differential Signatures Resource Report Resource Website 1+ mentions |
CRowd Extracted Expression of Differential Signatures (RRID:SCR_015680) | CREEDS | software application, data processing software, data visualization software, database, software resource, web application, data or information resource | Software resource that allows students or the general public find variants that may be significantly associated with some disease. CREEDS also visualizes and analyzes gene expression signatures. | variant, disease expression, disease marker | NIGMS R01GM098316; NHLBI U54HL127624; NCI U54CA189201 |
PMID:27667448 | Freely available, Free, Available for download | SCR_015680 | CREEDS: CRowd Extracted Expression of Differential Signatures | 2026-02-16 09:48:51 | 3 | |||||||
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Rosetta Resource Report Resource Website 100+ mentions |
Rosetta (RRID:SCR_015701) | software application, software resource, simulation software, software toolkit | Molecular modeling software package for 3D structure prediction and high resolution design of proteins, nucleic acids, and non natural polymers. Used in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes. | Molecular modeling, structure prediction, computational modeling, protein analysis, enzyme design, macromolecular complexes |
is used by: trRosetta is related to: PyRosetta works with: ROSIE |
Hertz Foundation Fellowship ; NSF Graduate Research Fellowship ; Simons Foundation ; NIGMS GM078221; NIGMS GM73141; NIGMS GM114961; NIGMS GM084453; NIGMS GM111819; NSF BMAT 1507736; NCI F32 CA189246; NIGMS GM092802; NIGMS GM110089; NIGMS GM117189 |
PMID:28430426 PMID:21829626 PMID:18442991 |
Restricted | SCR_015701 | Rosetta modeling software | 2026-02-16 09:48:51 | 212 | |||||||
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VaDiR Resource Report Resource Website 10+ mentions |
VaDiR (RRID:SCR_015797) | VaDiR | software application, data processing software, sequence analysis software, data analysis software, algorithm resource, software resource | Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets. | rna-seq, somatic variant calling, ovarian cancer, cancer genomes transcriptome, orthogonal validation, genetic mutation, sequence variation analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
NCI P30 CA168524; Department of Defense Ovarian Cancer Research Program W81XWH-10-1-0386; University of Kansas Endowment Association ; Biostatistics and Informatics Shared Resource (BISR) ; Cancer Center Cancer Biology program |
DOI:10.5524/100360 | Free, Available for download | biotools:vadir | ftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/ https://bio.tools/vadir |
SCR_015797 | VaDiR: an integrated approach to Variant Detection in RNA | 2026-02-16 09:48:53 | 13 | ||||
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Tscratch Resource Report Resource Website 10+ mentions |
Tscratch (RRID:SCR_014282) | software application, data processing software, data analysis software, image analysis software, software resource, standalone software | Software tool for automated analysis of monolayer wound healing assays. Available as a stand alone application for Macintosh and Windows and as a source code. Offers a graphical user interface for inspection of analysis results and manual modification of analysis parameters., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | analyze, wound, scratch, healing, assay, cell, migration, monolayer |
uses: MATLAB has parent organization: ETH Zurich; Zurich; Switzerland |
NCI CA69184; Swiss National Fund ; Austrian Science Foundation ; Cancer League Zurich ; Commission of the European Communities ; NCCR CO-ME |
PMID:19450233 | THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/cselab/TScratch | SCR_014282 | 2026-02-16 09:48:37 | 45 | |||||||
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SCSORS - Semi-Custom Synthesis On-line Request System Resource Report Resource Website 1+ mentions |
SCSORS - Semi-Custom Synthesis On-line Request System (RRID:SCR_005636) | SCSORS | production service resource, material service resource, reagent manufacture, service resource | ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years. | compound, pharmaceutical, chemistry, drug discovery, research | NCI | nlx_146249 | SCR_005636 | SCSORS Project, Semi-Custom Synthesis On-line Request System | 2026-02-16 09:46:30 | 1 | ||||||||
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WebArrayDB Resource Report Resource Website 1+ mentions |
WebArrayDB (RRID:SCR_005577) | WebArrayDB | data analysis service, analysis service resource, data repository, database, storage service resource, software resource, production service resource, service resource, data or information resource | An open source integrated microarray database and analysis suite that features convenient uploading of data for storage in a MIAME (Minimal Information about a Microarray Experiment) compliant fashion. It allows data to be mined with a large variety of R-based tools, including data analysis across multiple platforms. Different methods for probe alignment, normalization and statistical analysis are included to account for systematic bias. Student's t-test, moderated t-tests, non-parametric tests and analysis of variance or covariance (ANOVA/ANCOVA) are among the choices of algorithms for differential analysis of data. Users also have the flexibility to define new factors and create new analysis models to fit complex experimental designs. All data can be queried or browsed through a web browser. The computations can be performed in parallel on symmetric multiprocessing (SMP) systems or Linux clusters. | is listed by: OMICtools | Prostate Cancer Foundation ; Mary Kay Ash Foundation ; NIH ; NIAI R01AI034829; NIAI R01AI052237; NCI R01CA68822; NCI U01CA114810 |
PMID:19602526 | Open source, Account required, The software package is available for the use on a public web server or can be downloaded | OMICS_00782 | SCR_005577 | 2026-02-16 09:46:40 | 8 | |||||||
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PeptideMapper Resource Report Resource Website 1+ mentions |
PeptideMapper (RRID:SCR_005763) | PeptideMapper | data access protocol, software resource, web service | The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter. | peptide, sequence, protein, alignment, expressed sequence tag, mrna, est, htc, genbank, refseq, uniprot, ipi, vega, embl, hinvdb | has parent organization: Edwards Lab | NCI CA126189 | PMID:17437027 | nlx_149229 | SCR_005763 | PeptideMapper Web-Service, Peptide Mapper | 2026-02-16 09:46:41 | 4 | ||||||
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CGAP GO Browser Resource Report Resource Website 1+ mentions |
CGAP GO Browser (RRID:SCR_005676) | CGAP GO Browser | data set, service resource, data or information resource | With the CGAP GO browser, you can browse through the GO vocabularies, and find human and mouse genes assigned to each term. GO data updated every few months. Platform: Online tool | gene, biological process, cellular component, molecular function, browser, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Cancer Genome Anatomy Project |
NCI | Free for academic use | nlx_149116 | SCR_005676 | Cancer Genome Anatomy Project GO Browser | 2026-02-16 09:46:31 | 4 | ||||||
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Geneshot Resource Report Resource Website 1+ mentions |
Geneshot (RRID:SCR_017582) | data access protocol, software resource, web service | Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations. | Ranking, gene, arbitrary, text, query, list, predict, association, data, integration, interactive, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114885 | Free, Freely available | biotools:Geneshot | https://bio.tools/Geneshot | SCR_017582 | 2026-02-16 09:49:16 | 4 | ||||||
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Structure Harvester Resource Report Resource Website 100+ mentions |
Structure Harvester (RRID:SCR_017636) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Visualizing, STRUCTURE, Evanno, method, collating, result, detection, genetic, group, fit, data, reformat |
is related to: University of California at Santa Cruz; California; USA is related to: University of California at Irvine; California; USA is related to: University of California at Los Angeles; California; USA works with: STRUCTURE |
NCI U24 CA143858; NCI R21 CA135937 |
DOI:10.1007/s12686-011-9548-7 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017636 | StructureHarvester | 2026-02-16 09:49:17 | 297 | |||||||
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Interactive Line Graph Resource Report Resource Website |
Interactive Line Graph (RRID:SCR_018334) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service resource | Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions. | Line graph, scientific publication, summary statistics, examine lines, time point, changes between time points, data, statistic, plot | NCI P50 AG44170; Office of Research on Women Health |
PMID:27332507 | Free, Freely available | SCR_018334 | 2026-02-16 09:49:26 | 0 | |||||||||
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Combined Annotation Dependent Depletion Resource Report Resource Website 500+ mentions |
Combined Annotation Dependent Depletion (RRID:SCR_018393) | CADD | software application, data processing software, web service, sequence analysis software, data analysis software, data access protocol, software resource, service resource | Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome. | Human genome, disease, prediction, injurious variant, single nucleotide variant, insertion variant, deletion variant, deleteriousness scoring | has parent organization: University of Washington; Seattle; USA | NCI R01 CA197139; NHGRI U54 HG006493; Brotman Baty Institute for Precision Medicine ; Berlin Institute of Health ; Howard Hughes Medical Institute ; German Research Foundation ; Charite University Medicine Berlin |
PMID:30371827 PMID:24487276 |
Restricted | SCR_018393 | Combined Annotation Dependent Depletion | 2026-02-16 09:49:30 | 579 | ||||||
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GeoDa Resource Report Resource Website 100+ mentions |
GeoDa (RRID:SCR_018559) | software application, data processing software, data visualization software, data analysis software, software resource | Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression. | Spatial analysis, data analysis, spatial autocorrelation visualization, spatial regression, mapping | NSF BCS 9978058; NCI R01 CA95949 |
DOI:10.1111/j.0016-7363.2005.00671.x | Free, Freely available | SCR_018559 | 2026-02-16 09:49:31 | 192 | |||||||||
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FairSubset Resource Report Resource Website |
FairSubset (RRID:SCR_019102) | data access protocol, software resource, web service | Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices. | Representative data subsets, different sample sizes groups, different sample sizes replicates, retaining distribution information, fair publishing | NCI CA207729; Polish government grant |
PMID:31583263 | Free, Freely available | SCR_019102 | 2026-02-16 09:49:37 | 0 | |||||||||
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Cancer Imaging Archive (TCIA) Resource Report Resource Website 100+ mentions |
Cancer Imaging Archive (TCIA) (RRID:SCR_008927) | TCIA | image repository, data set, data repository, database, storage service resource, catalog, service resource, data or information resource | Archive of medical images of cancer accessible for public download. All images are stored in DICOM file format and organized as Collections, typically patients related by common disease (e.g. lung cancer), image modality (MRI, CT, etc) or research focus. Neuroimaging data sets include clinical outcomes, pathology, and genomics in addition to DICOM images. Submitting Data Proposals are welcomed. | dicom, imaging, ct, pet, pt, x-ray, mri, magnetic resonance, medical, clinical, research, clinical neuroinformatics, computed tomography, dicom, imaging genomics, magnetic resonance, pet, spect, test data, web service, image collection, image, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing is affiliated with: BraTumIA (Brain Tumor Image Analysis) is related to: NIH Data Sharing Repositories is related to: NCI Imaging Data Commons has parent organization: Frederick National Laboratory for Cancer Research has parent organization: NCI-Frederick |
Cancer | NCI | Restricted | DOI:10.25504/FAIRsharing.jrfd8y, DOI:10.17616/R3NH0V, DOI:10.7937, nlx_151749, r3d100011559 | http://www.nitrc.org/projects/tcia http://www.cancerimagingarchive.net/ http://www.cancerimagingarchive.net/primary-data/ https://wiki.cancerimagingarchive.net/display/Public/Collections https://doi.org/10.17616/R3NH0V https://doi.org/10.17616/r3NH0V https://doi.org/10.7937/ https://dx.doi.org/10.7937/ https://fairsharing.org/10.25504/FAIRsharing.jrfd8y https://doi.org/10.17616/R3NH0V https://doi.org/10.17616/R3NH0V |
SCR_008927 | TCIA, Cancer Imaging Archive, The Cancer Imaging Archive (TCIA), Cancer Imaging Archive (TCIA), The Cancer Imaging Archive | 2026-02-16 09:47:18 | 287 | ||||
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GeneTests Resource Report Resource Website 10+ mentions |
GeneTests (RRID:SCR_010725) | GeneTests | narrative resource, training material, analysis service resource, material analysis service, biomaterial analysis service, database, topical portal, portal, production service resource, service resource, data or information resource | The GeneTests Web site, a publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, is available at no cost to all interested persons. By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making. At This Site: * GeneReviews: Expert-authored peer-reviewed disease descriptions * Laboratory Directory: International directory of genetic testing laboratories * Clinic Directory: International directory of genetics and prenatal diagnosis clinics * Educational Materials: Illustrated glossary, information on genetic services, PowerPoint presentations, annotated Internet resources We comply with the HONcode standard for trustworthy health information. |
has parent organization: University of Washington; Seattle; USA has parent organization: NCBI |
NCI ; NHGRI 1 P41 LM/HG 06029; NLM 1 P41 LM/HG 06029; NLM contract N01-LM-4-3505; NLM 5 P41 LM07242; NLM 2 P41 LM 06001; DOE DE-FG03-02ER63301/A00 |
nlx_94696 | SCR_010725 | GeneTests: Clinical Genetic Information Resource | 2026-02-16 09:47:52 | 12 | ||||||||
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MUSC DNA Microarray Database Resource Report Resource Website 1+ mentions |
MUSC DNA Microarray Database (RRID:SCR_010977) | microArrayDB, ��ArrayDB | data repository, database, storage service resource, service resource, data or information resource | Database that is a repository for DNA microarray data generated by MUSC investigators as well as researchers in the global research community. | gene expression, dna microarray |
is listed by: OMICtools is related to: ArrayQuest has parent organization: Medical University of South Carolina; South Carolina; USA |
University Research Resource Foundation ; NCI R24CA095841; NCRR P20RR016434 |
PMID:14668234 | Public, The community can contribute to this resource | OMICS_00868 | SCR_010977 | MUSC DNA Microarray Database and Project Management System, Medical University of South Carolina DNA Microarray Project Management System and the MUSC DNA Microarray Database, MUSC DNA Microarray Project Management System and MUSC DNA Microarray Database, ��ArrayDB, Medical University of South Carolina DNA Microarray Database | 2026-02-16 09:47:55 | 1 |
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