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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
National Resource for Translational and Developmental Proteomics
 
Resource Report
Resource Website
National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) NRTDP data or information resource, organization portal, portal, service resource, training resource Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists. protein, mass, spectrometry, proteomics, measurement, targeted, untargeted, analysis has parent organization: Northwestern University; Illinois; USA
provides: ProSight Lite
NIGMS P41 GM108569 SCR_016907 The National Resource for Translational and Developmental Proteomics, NRTDP 2026-09-12 12:58:45 0
MARRVEL
 
Resource Report
Resource Website
10+ mentions
MARRVEL (RRID:SCR_016871) MARRVEL analysis service resource, data analysis service, data or information resource, database, production service resource, service resource Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools uses: OMIM
uses: ClinVar
uses: DECIPHER
uses: Geno2MP
uses: Database of Genomic Variants
is used by: Hypothesis Center
is listed by: bio.tools
is listed by: Debian
Baylor College of Medicine Medical Scientist Training Program ;
Belfer Foundation ;
CPRIT RP170387;
Houston Endowment ;
Huffington Foundation ;
NCI P30 CA06516;
NCRR R24 RR032668;
NHGRI U01 HG007709;
NIGMS R01 GM067761;
NIGMS R01 GM067858;
NIGMS R01 GM084947;
NIGMS R01 GM120033;
NIH Office of the Director R24 OD021997;
NIH Office of the Director R24 OD022005;
NINDS 1U54NS093793;
NINDS U54 NS093793;
NSF DMS 1263932;
Simons Foundation ;
T T Chao Family Foundation ;
The Robert and Janice McNair Foundation
PMID:28502612 Free, Public, Freely available biotools:marrvel https://bio.tools/marrvel SCR_016871 Model organism Aggregated Resources for Rare Variant ExpLoration 2026-09-12 12:58:45 25
PathwayMatcher
 
Resource Report
Resource Website
1+ mentions
PathwayMatcher (RRID:SCR_016759) data analysis software, data processing software, network analysis software, software application, software resource Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools is listed by: Galaxy
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
works with: Reactome
Bergen Research Foundation ;
European Research Council ;
NHGRI U41 HG003751;
NIGMS U54 GM114833;
Research Council of Norway
DOI:10.1101/375097 Free, Available for download, Freely available BioTools:PathwayMatcher, biotools:PathwayMatcher https://anaconda.org/bioconda/pathwaymatcher, https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher, https://bio.tools/PathwayMatcher SCR_016759 2026-09-12 12:58:44 1
Sashimiplot
 
Resource Report
Resource Website
Sashimiplot (RRID:SCR_016861) sashimiplot data processing software, data visualization software, software application, software resource Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. quantitative, visualization, aligned, RNA-Seq, read, data, compare, exon, usage, sample, experiment, condition, MISO is related to: MISO Alfred P. Sloan research fellowship ;
NCI R01 CA157304;
NCI U01 CA184897;
NHGRI R01 HG002439;
NIGMS R01 GM085319;
NIGMS R01 GM096193;
NSF IIS 1149662;
Starr Cancer Consortium
PMID:25617416
DOI:10.1093/bioinformatics/btv034
Free, Available for download, Freely available http://miso.readthedocs.org/en/fastmiso/sashimi.html SCR_016861 sashimi_plot 2026-09-12 12:58:45 0
Ontodog: A Web-based Ontology View Generator
 
Resource Report
Resource Website
10+ mentions
Ontodog: A Web-based Ontology View Generator (RRID:SCR_005061) Ontodog production service resource, service resource, software resource, source code Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0. ontology, interoperability has parent organization: University of Michigan Medical School; Michigan; USA Rackham Pilot Research ;
NIAID R01AI081062;
NIGMS 5R01GM93132-1
nlx_144053 SCR_005061 2026-09-12 01:00:55 17
Mouse Mutagenesis Center for Developmental Defects
 
Resource Report
Resource Website
Mouse Mutagenesis Center for Developmental Defects (RRID:SCR_007321) Mouse Mutagenesis for Developmental Defects material resource, reagent supplier THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval. mutant, embryo, post embryonic, mutagenesis, craniofacial, eye, fertility, growth, lethal, metabolism, neurological, skeletal, skin, coat, urogenital, cryopreserved, enu, defect, birth defect, , patterning defect, growth defect, endocrine defects, neurological anomaly, blood defect, mouse model, human disease, n-ethyl-n-nitrosourea, chromosome 11, phenotype is listed by: One Mind Biospecimen Bank Listing
is related to: One Mind Biospecimen Bank Listing
is related to: NIDDK Information Network (dkNET)
is related to: Mutant Mouse Resource and Research Center
is related to: Jackson Laboratory
has parent organization: Baylor University; Texas; USA
Aging NICHD ;
NIGMS ;
NIA ;
NIAMS ;
NHLBI ;
NIDDK ;
NIDCR ;
NIH Blueprint for Neuroscience Research
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00190 SCR_007321 NIH Mouse Mutagenesis Center for Developmental Defects 2026-09-12 01:00:57 0
CellProfiler Image Analysis Software
 
Resource Report
Resource Website
1000+ mentions
CellProfiler Image Analysis Software (RRID:SCR_007358) data processing software, image analysis software, software application, software resource Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types. high-throughput, high content imaging, software, image, cell, phenotype, measurement, subcellular, intensity, size, shape, analysis, algorithm is listed by: Debian
is related to: CellProfiler Analyst
has parent organization: Broad Institute
NHGRI RL1 HG004671;
NIGMS R01 GM089652;
NIGMS RC2 GM092519
PMID:21349861
PMID:17076895
PMID:19014601
PMID:19188593
Free, Available for download, Freely available SCR_010649, nlx_66812, nif-0000-00280 https://sources.debian.org/src/cellprofiler/ SCR_007358 Cell Profiler, CellProfiler - cell image analysis software 2026-09-12 01:00:57 3411
lapdftext
 
Resource Report
Resource Website
lapdftext (RRID:SCR_006167) lapdftext, LA-PDFText, software application, software resource, text extraction software Software that facilitates accurate extraction of text from PDF files of research articles for use in text mining applications. It is intended for both scientists and natural language processing (NLP) engineers interested in getting access to text within specific sections of research articles. The system extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles. The current version of LA-PDFText is a baseline system that extracts text using a three-stage process: * identification of blocks of contiguous text * classification of these blocks into rhetorical categories * extraction of the text from blocks grouped section-wise. text mining, pdf, text extraction, natural language processing is listed by: FORCE11
has parent organization: University of Southern California; Los Angeles; USA
NSF 0849977;
NIGMS RO1-GM083871;
NIMH 1R01MH079068-01A2;
NCRR U24 RR025736-01
PMID:22640904 Acknowledgement requested, GNU General Public License, v3 nlx_151668 SCR_006167 Layout-Aware PDF Text Extraction, Layout-Aware Text Extraction from Full-text PDF of Scientific Articles, lapdftext: Layout-Aware Text Extraction from Full-text PDF of Scientific Articles 2026-09-12 01:01:41 0
BioGPS: The Gene Portal Hub
 
Resource Report
Resource Website
500+ mentions
BioGPS: The Gene Portal Hub (RRID:SCR_006433) BioGPS data or information resource, database An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list is listed by: Biositemaps
is related to: bioDBcore
is related to: aGEM
has parent organization: Scripps Research Institute
Novartis Research Foundation ;
NIGMS R01GM083924
PMID:19919682 Free, The community can contribute to this resource r3d100012402, nif-0000-10168 http://biogps.gnf.org/, https://doi.org/10.17616/R33J20 SCR_006433 2026-09-12 01:01:42 814
ESEfinder 3.0
 
Resource Report
Resource Website
100+ mentions
ESEfinder 3.0 (RRID:SCR_007088) ESEfinder analysis service resource, data analysis service, production service resource, service resource A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements. exonic splicing enhancer, sr protein, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Cold Spring Harbor Laboratory
NIGMS GM42699;
NCI CA88351;
NHGRI HG01696
PMID:12824367 Free for non-profit use, Non-commercial, Acknowledgement requested, Commercial use with license biotools:esefinder, nif-0000-30496 http://rulai.cshl.edu/tools/ESE2/, https://bio.tools/esefinder http://exon.cshl.edu/ESE/ SCR_007088 2026-09-12 01:01:45 213
Add Health (National Longitudinal Study of Adolescent Health)
 
Resource Report
Resource Website
10+ mentions
Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Add Health data or information resource, database Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database. adolescent, longitudinal, adult human, interview, social, behavior, health, early adult human, FASEB list has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA Aging NICHD ;
NCI ;
CDC ;
NIAID ;
NIMHD ;
NIDCD ;
NIGMS ;
NIMH ;
NINR ;
NIA ;
NIAAA ;
NIDA ;
NSF ;
NIH ;
Department of Health and Human Services ;
MacArthur Foundation ;
Robert Wood Johnson Foundation
Restricted use nif-0000-00621 SCR_007434 National Longitudinal Study of Adolescent Health 2026-09-12 01:01:47 37
FATCAT Flexible Structural Neighborhood
 
Resource Report
Resource Website
FATCAT Flexible Structural Neighborhood (RRID:SCR_007665) FSN data or information resource, database Flexible Structural Neighborhood is a database of structural neighbors of proteins as seen by FATCAT - a flexible protein structure alignment program. The server accepts either a protein (PDB ID) or a domain (SCOP ID) as a query. For the former case, the server first displays the information of chains and domains of a given protein. Afterwards, users can retrieve similar structures for a domain (if domain information is available, i.e., the protein is collected by SCOP), or for a chain otherwise. The protein structure database we collected for similar structure search includes a representative set at 90% sequence identity of SCOP domains, and of up-to-date PDB entries that are not included in the latest release of SCOP. server, database, molecule structure, protein structure, flexibility, structure, structural neighbor, protein, domain is related to: FATCAT NIGMS GM101457;
NIGMS GM63208;
NIGMS GM076221;
NSF DBI-0349600
nif-0000-02854 http://fatcat.ljcrf.edu/fatcat-cgi/cgi/FSN/fsn.pl SCR_007665 FATCAT Flexible Structural Neighborhood Database, FSN Database 2026-09-12 01:01:49 0
Coarse grained co-translational folding analysis
 
Resource Report
Resource Website
1+ mentions
Coarse grained co-translational folding analysis (RRID:SCR_022271) software application, software resource Software for statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved, and also co-translational protein folding model. statistical approach, identify loci within genes, significantly enriched in slowly translated codons, co-translational protein folding model evolutionarily conserved, NIGMS F32GM116231;
NIGMS R01GM124044
PMID:29073068 Free, Freely available SCR_022271 Coarse-grained co-translational folding analysis 2026-09-12 01:03:00 1
Sparse Inverse Covariance Estimation for Ecological Association Inference
 
Resource Report
Resource Website
10+ mentions
Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) SPIEC-EASI software resource, software toolkit Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets. inverse covariance matrix estimation, sequencing data, microbial ecological networks inference, amplicon sequencing datasets microbial ecological networks, NIAID T32AI007180;
NIDDK R01 DK103358;
NIGMS RO1 GM63270;
Simons Foundation
PMID:25950956 Free, Available for download, Freely available SCR_022646 SParse InversE Covariance Estimation for Ecological Association Inference 2026-09-12 01:03:01 12
Bayesian Generalized Linear Regression
 
Resource Report
Resource Website
1+ mentions
Bayesian Generalized Linear Regression (RRID:SCR_022522) BGLR software resource, software toolkit Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures. Bayesian regression models, parametric variable selection and shrinkage methods, semiparametric procedures is related to: CRAN
is related to: R Project for Statistical Computing
NIGMS R01GM099992;
NIGMS R01GM101219
PMID:25009151 Free, Available for download, Freely available https://github.com/gdlc/BGLR-R SCR_022522 2026-09-12 01:03:00 6
MR-PRESSO
 
Resource Report
Resource Website
100+ mentions
MR-PRESSO (RRID:SCR_023697) software resource, software toolkit Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, American Heart Association Cardiovascular Genome Phenome Discovery ;
AstraZeneca ;
Goldfinch Bio ;
NHGRI 5U01 HG009088;
NHLBI R01 HL139865;
NIGMS R35 GM124836;
NIMH 1R01 MH094469;
NIMH 1R01 MH107649
PMID:29686387 Free, Available for download, Freely available SCR_023697 Mendelian Randomization Pleiotropy RESidual Sum and Outlier 2026-09-12 01:03:05 100
Proteomics Research Center for Integrative Biology
 
Resource Report
Resource Website
Proteomics Research Center for Integrative Biology (RRID:SCR_001098) Proteomics Resource for Integrative Biology biomedical technology research center, training resource Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use. systems biology technology center, proteomics, mass spectrometry, data management, analysis has parent organization: Pacific Northwest National Laboratory NIGMS 4P41GM103493-14 nlx_152684 SCR_001098 Proteomics Research Resource for Integrative Biology 2026-09-12 01:03:11 0
Resource for Biocomputing Visualization and Informatics
 
Resource Report
Resource Website
100+ mentions
Resource for Biocomputing Visualization and Informatics (RRID:SCR_001374) RBVI biomedical technology resource center, training resource Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas. training resource, molecular modeling, software, molecular graphics, visualization, modeling, molecular structure, analysis, computation, computing and informatics technology center, FASEB list is listed by: 3DVC
has parent organization: University of California at San Francisco; California; USA
is parent organization of: Structure-function linkage database
is parent organization of: UCSF Chimera
NIGMS nlx_152531 SCR_001374 2026-09-12 01:03:11 158
GeneWays
 
Resource Report
Resource Website
GeneWays (RRID:SCR_000572) Geneways service resource System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information. pathway, molecule, literature, natural language processing, gene, protein, interaction, database is listed by: OMICtools
has parent organization: Argonne National Laboratory
has parent organization: Columbia University; New York; USA
DOE ;
NIGMS GM61372;
NSF
PMID:15016385 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-30019, SCR_008368, OMICS_01182 http://anya.igsb.anl.gov/genewaysApp SCR_000572 GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data, GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data 2026-09-12 01:03:10 0
National Center for Macromolecular Imaging
 
Resource Report
Resource Website
1+ mentions
National Center for Macromolecular Imaging (RRID:SCR_001445) NCMI access service resource, biomedical technology research center, service resource, training resource Biomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods. cryo-electron microscopy, structure determination, structure, macromolecule, assembly, model, reconstruction, subcellular complex, electron cryo-microscopy, 3d spatial image, structural biology technology center is related to: EMDataResource.org
has parent organization: Baylor University; Texas; USA
NIGMS 3R01GM079429-05S1 THIS RESOURCE IS NO LONGER IN SERVICE nlx_152670 SCR_001445 2026-09-12 01:03:11 1

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