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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BioAssay Express Resource Report Resource Website 1+ mentions |
BioAssay Express (RRID:SCR_017594) | data access protocol, service resource, software resource, web service | Web based tool for annotating bioassay protocols using semantic web terms. Enables searching, sorting, clustering and analyzing of assays without needing to read through original text. Exploits Common Assay Template based on underlying vocabularies and semantic standards from BioAssay Ontology, Drug Target Ontology, Cell Line Ontology and others. Users can identify similar assays and examine similarity of assays between and within organizations. | Annotating, bioassay, protocol, semantic, web, term, ontology | is listed by: OMICtools | NCATS R44 TR000185 | DOI:10.7717/peerj-cs.61 | Free, Freely available | https://github.com/cdd/bioassay-template | SCR_017594 | 2026-09-12 12:58:54 | 1 | |||||||
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GeneATLAS Resource Report Resource Website 100+ mentions |
GeneATLAS (RRID:SCR_017577) | analysis service resource, atlas, data analysis service, data or information resource, database, production service resource, service resource | Database of associations between traits and variants using UK Biobank cohort. Searchable atlas of genetic associations. Assists researchers to query UK Biobank. Provides unbiased view of phenotype and genotype associations across of traits. | Association, trait, variant, UK Biobank, cohort, atlas, genetic, phenotype, genotype, FASEB list |
is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Free, Available for download, Freely available | SCR_017577 | Gene ATLAS, Gene Atlas | 2026-09-12 12:58:54 | 158 | |||||||||
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immuneXpresso Resource Report Resource Website |
immuneXpresso (RRID:SCR_017578) | data or information resource, service resource, software application, software resource, text-mining software | Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. | Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract |
is listed by: NIDDK Information Network (dkNET) is listed by: OMICtools |
NIAID ; NIH ; Rappaport Family Institute for Research in the Medical Sciences |
PMID:29912209 | Free, Freely available | SCR_017578 | 2026-09-12 12:58:54 | 0 | ||||||||
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GADMA Resource Report Resource Website 1+ mentions |
GADMA (RRID:SCR_017680) | GADMA | data analysis software, data processing software, software application, software resource | Software tool to implement methods for automatic inferring joint demographic history of multiple populations from genetic data. Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data. | Inferring, demographic, history, population, genetic, data, allele, frequency, spectrum, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/407734 | Free, Available for download, Freely available | biotools:GADMA | https://bio.tools/GADMA | SCR_017680 | Genetic Algorithm for Demographic Model Analysis | 2026-09-12 12:58:55 | 3 | |||||
|
Bustools Resource Report Resource Website 10+ mentions |
Bustools (RRID:SCR_018210) | data analysis software, data processing software, software application, software resource | Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. | Single cell RNAseq workflow, single cell RNAseq dataset, error correct barcode, collapse UMI, produce gene count, produce transcript compatibility count matrice |
is listed by: Debian is listed by: OMICtools works with: kb_python |
DOI:10.1101/673285 | Free, Available for download, Freely available | OMICS_33004 | https://sources.debian.org/src/bustools/ | SCR_018210 | 2026-09-12 12:58:58 | 19 | |||||||
|
ChromHMM Resource Report Resource Website 50+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, data processing software, software application, software resource | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
Alfred P. Sloan Fellowship ; CAREER Award ; NHGRI RC1HG005334; NHGRI U01 HG007912; NHGRI U54 HG004570; NIEHS R01 ES024995; NIMH U01 MH105578; NSF 0905968 |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-09-12 12:58:58 | 50 | ||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2, https://sources.debian.org/src/libminimap2-dev/ | SCR_018550 | 2026-09-12 12:59:02 | 1593 | ||||||
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Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-09-12 12:59:02 | 46 | ||||||
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UniPROBE Resource Report Resource Website 100+ mentions |
UniPROBE (RRID:SCR_005803) | UniPROBE | data or information resource, database | Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences. | protein, in vitro, dna binding, protein binding, genetics, dna, nucleotide sequence, sequence variant, k-mer, position weight matrix, graphical sequence logo, motif, motif similarity, binding site, microarray, protein-dna interaction, protein binding microarray probe sequence, probe, FASEB list |
is listed by: re3data.org is listed by: OMICtools |
PMID:21037262 PMID:18842628 |
Acknowledgement requested, Academic research use license | nif-0000-03611, OMICS_00546, r3d100010557 | http://thebrain.bwh.harvard.edu/pbms/webworks_pub/, https://doi.org/10.17616/R35C9J | SCR_005803 | UniPROBE Database, Universal Protein Binding Microarray Resource for Oligonucleotide Binding Evaluation, Universal PBM Resource for Oligonucleotide Binding Evaluation | 2026-09-12 01:01:39 | 151 | |||||
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MutationAssessor Resource Report Resource Website 500+ mentions |
MutationAssessor (RRID:SCR_005762) | mutationassessor.org | analysis service resource, data analysis service, production service resource, service resource | A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cancer, protein, mutation, function, amino-acid, substitution |
is listed by: OMICtools is listed by: SoftCite |
PMID:21727090 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00134, nlx_149228 | SCR_005762 | MutationAssessor - functional impact of protein mutations, MutationAssessor - functional impact of mutations, mutationassessor.org - functional impact of protein mutations | 2026-09-12 01:01:39 | 693 | ||||||
|
GoPubMed Resource Report Resource Website 10+ mentions |
GoPubMed (RRID:SCR_005823) | GoPubMed | data or information resource, database, service resource | A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool | other analysis, literature curation and exploration, gene ontology, pubmed, literature, bio.tools |
is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: PubMed has parent organization: Biotechnology Center of the TU Dresden |
European Union IST-2004-506779 | PMID:15980585 | Free for academic use | biotools:gopubmed, nlx_149328, OMICS_01183 | https://bio.tools/gopubmed | SCR_005823 | 2026-09-12 01:01:39 | 29 | |||||
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GOSlimViewer Resource Report Resource Website 10+ mentions |
GOSlimViewer (RRID:SCR_005665) | GOSlimViewer | analysis service resource, data analysis service, production service resource, service resource | Service to summarize the GO function associated with a data set using prepared GO Slim sets. The input is a tab separated list of gene product IDs and GO IDs. | agriculture, browser, slimmer-type tool, gene ontology, gene, ontology, ontology or annotation browser |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
USDA ; Mississippi State University; Mississippi; USA ; MSU Office of Research ; MSU Bagley College of Engineering ; MSU College of College of Veterinary Medicine ; MSU Life Science and Biotechnology Institute |
PMID:17135208 PMID:16961921 |
Free for academic use | nlx_149103, OMICS_02270 | SCR_005665 | GO Slim Viewer, GOSlim Viewer | 2026-09-12 01:01:38 | 40 | |||||
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PIPE-CLIP Resource Report Resource Website 10+ mentions |
PIPE-CLIP (RRID:SCR_005820) | PIPE-CLIP | analysis service resource, data analysis service, production service resource, service resource | A Galaxy framework-based online pipeline for reliable analysis of data generated by three types of CLIP-seq protocols: HITS-CLIP, PAR-CLIP and iCLIP. It provides both data processing and statistical analysis to determine candidate cross-linking regions, which are comparable to those regions identified from the original studies or using existing computational tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | clip-seq, python, bioinformatics, r, high-thoughput sequencing, rna-binding protein, rna |
is listed by: OMICtools is related to: Galaxy has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: Google Code |
PMID:24451213 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02254 | https://github.com/QBRC/PIPE-CLIP | SCR_005820 | PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis | 2026-09-12 01:01:39 | 10 | |||||
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VirusMINT Resource Report Resource Website 10+ mentions |
VirusMINT (RRID:SCR_005987) | VirusMINT | data or information resource, database | A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome. | protein interaction, virus, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PSI-MI is related to: VirHostNet: Virus-Host Network is related to: MINT has parent organization: University of Rome Tor Vergata; Rome; Italy |
Papilloma virus, Human immunodeficiency virus, Epstein-Barr virus, Hepatitis B virus, Hepatitis C virus, Herpes virus, Simian virus 40 | PMID:18974184 | nif-0000-03636, OMICS_01909, biotools:virusmint, r3d100010685 | https://bio.tools/virusmint, https://doi.org/10.17616/R3F890 | SCR_005987 | 2026-09-12 01:01:40 | 18 | ||||||
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Mouse Genome Informatics (MGI) Resource Report Resource Website 1000+ mentions |
Mouse Genome Informatics (MGI) (RRID:SCR_006460) | MGI | data or information resource, database | International database for laboratory mouse. Data offered by The Jackson Laboratory includes information on integrated genetic, genomic, and biological data. MGI creates and maintains integrated representation of mouse genetic, genomic, expression, and phenotype data and develops reference data set and consensus data views, synthesizes comparative genomic data between mouse and other mammals, maintains set of links and collaborations with other bioinformatics resources, develops and supports analysis and data submission tools, and provides technical support for database users. Projects contributing to this resource are: Mouse Genome Database (MGD) Project, Gene Expression Database (GXD) Project, Mouse Tumor Biology (MTB) Database Project, Gene Ontology (GO) Project at MGI, and MouseCyc Project at MGI. | RIN, Resource Information Network, molecular neuroanatomy resource, human health, human disease, animal model, gene expression, phenotype, genotype, gene, pathway, orthology, tumor, strain, single nucleotide polymorphism, recombinase, function, blast, image, pathology, model, data analysis service, genome, genetics, gold standard, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Cytokine Registry is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is listed by: NIH Data Sharing Repositories is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: MONARCH Initiative is related to: MouseCyc is related to: AmiGO is related to: Gene Expression Database is related to: Bgee: dataBase for Gene Expression Evolution is related to: HomoloGene is related to: Rat Gene Symbol Tracker is related to: Enhancer Trap Line Browser is related to: Integrated Brain Gene Expression is related to: MalaCards is related to: Gene Ontology is related to: BioMart Project is related to: NIH Data Sharing Repositories is related to: RIKEN integrated database of mammals is related to: JAX Neuroscience Mutagenesis Facility is related to: PhenoGO is related to: International Mouse Strain Resource is related to: Mouse Genome Database is related to: Mouse Tumor Biology Database has parent organization: Jackson Laboratory is parent organization of: Anatomy of the Laboratory Mouse is parent organization of: Mouse Genome Informatics Transgenes is parent organization of: Federation of International Mouse Resources is parent organization of: MGI GO Browser is parent organization of: Recombinase (cre) Activity is parent organization of: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project is parent organization of: Deltagen and Lexicon Knockout Mice and Phenotypic Data Resource is parent organization of: MGI strains is parent organization of: MPO is parent organization of: Phenotypes and Mutant Alleles is parent organization of: Human Mouse Disease Connection is parent organization of: Functional Annotation is parent organization of: Strains, SNPs and Polymorphisms is parent organization of: Vertebrate Homology is parent organization of: Batch Data and Analysis Tool is parent organization of: Nomenclature |
NCI CA089713; NHGRI HG000330; NHGRI HG002273; NICHD HD033745 |
PMID:19274630 PMID:18428715 |
Free, Freely available | nif-0000-00096, OMICS_01656, r3d100010266 | http://www.informatics.jax.org/batch, http://www.informatics.jax.org/submit.shtml, http://www.informatics.jax.org/expression.shtml, https://doi.org/10.17616/R35P54 | SCR_006460 | , MGI, Mouse Genome Informatics | 2026-09-12 01:01:42 | 1220 | ||||
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PANOGA Resource Report Resource Website 1+ mentions |
PANOGA (RRID:SCR_006242) | PANOGA | analysis service resource, data analysis service, production service resource, service resource | A web server to devise functionally important pathways through the identification of single nucleotide polymorphism (SNP)-targeted genes within these pathways. The strength of the methodology stems from its multidimensional perspective, where evidence from the following five resources is combined: (i) genetic association information obtained through GWAS, (ii) SNP functional information, (iii) protein-protein interaction network, (iv) linkage disequilibrium and (v) biochemical pathways. | single nucleotide polymorphism, genome-wide association study, pathway, function, gene, genetic association, protein-protein interaction network, linkage disequilibrium, protein-protein interaction |
is listed by: OMICtools has parent organization: Sabanci University; Istanbul; Turkey |
PMID:24413675 | Free, Public, Free for academic use, (source code upon request) | OMICS_02238 | SCR_006242 | Pathway and Network-Oriented GWAS Analysis, Pathway and Network Oriented GWAS (Genome-Wide Association Study) Analysis, Pathway and Network Oriented GWAS Analysis | 2026-09-12 01:01:42 | 7 | ||||||
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HOMSTRAD - Homologous Structure Alignment Database Resource Report Resource Website 10+ mentions |
HOMSTRAD - Homologous Structure Alignment Database (RRID:SCR_006544) | HOMSTRAD | data or information resource, database | A curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER. These structure-based alignments are annotated with JOY and examined individually. | homologous structure, protein, protein family, protein structure, align, 3d structure, structure-based alignment |
is listed by: OMICtools has parent organization: National Institute of Biomedical Innovation; Osaka; Japan |
PMID:14681395 | nif-0000-02977, OMICS_00976 | http://www-cryst.bioc.cam.ac.uk/homstrad | SCR_006544 | HOMologous STRucture Alignment Database | 2026-09-12 01:01:43 | 24 | ||||||
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GeneTerm Linker Resource Report Resource Website 1+ mentions |
GeneTerm Linker (RRID:SCR_006385) | GTLinker | analysis service resource, data analysis service, production service resource, service resource | Web application that filters and links enriched output data identifying sets of associated genes and terms, producing metagroups of coherent biological significance. The method uses fuzzy reciprocal linkage between genes and terms to unravel their functional convergence and associations. It can also be accessed through its web service. | gene, functional annotation, function, functional metagroup, p-value, annotation, web service |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: InterPro has parent organization: Spanish National Research Council; Madrid; Spain |
PMID:21949701 | Acknowledgement requested | OMICS_02227 | SCR_006385 | GeneTerm Linker - post enrichment functional association by non-redundant reciprocal linkage | 2026-09-12 01:01:42 | 2 | ||||||
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MEDIE Resource Report Resource Website 1+ mentions |
MEDIE (RRID:SCR_006254) | MEDIE | analysis service resource, data analysis service, production service resource, service resource | An intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining techniques. You can find abstracts/sentences in MEDLINE by specifying semantics of correlations; for example, What activates p53 and What causes colon cancer. Semantic search uses a semantic query for finding biomedical correlations. Input a subject, a verb, and an object of a concept (or either of them) into a form. Results of the query will be shown in a second. (E.g., What does p53 activate? (subject=p53, verb=activate)) Reference: Miyao, Yusuke, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya and Jun''''ichi Tsujii (2006) Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. Proceedings COLING-ACL 2006. Sydney, Australia, pp. 1017--1024. | natural language processing, text mining, semantic search, computational linguistics, search engine |
is used by: BioLexicon is listed by: OMICtools is listed by: FORCE11 is related to: MEDLINE has parent organization: University of Tokyo; Tokyo; Japan has parent organization: National Centre for Text Mining |
nif-0000-06682, OMICS_01188 | http://www-tsujii.is.s.u-tokyo.ac.jp/medie/, https://www.force11.org/node/4643 | SCR_006254 | 2026-09-12 01:01:42 | 3 | ||||||||
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GeneTrail Resource Report Resource Website 100+ mentions |
GeneTrail (RRID:SCR_006250) | GeneTrail | analysis service resource, data analysis service, production service resource, service resource | A web-based application that analyzes gene sets for statistically significant accumulations of genes that belong to some functional category. Considered category types are: KEGG Pathways, TRANSPATH Pathways, TRANSFAC Transcription Factor, GeneOntology Categories, Genomic Localization, Protein-Protein Interactions, Coiled-coil domains, Granzyme-B clevage sites, and ELR/RGD motifs. The web server provides two statistical approaches, "Over-Representation Analysis" (ORA) comparing a reference set of genes to a test set, and "Gene Set Enrichment Analysis" (GSEA) scoring sorted lists of genes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathway, microarray, enrichment, genomic, proteomic, function, transcription factor, genomic localization, protein-protein interaction, coiled-coil domain, granzyme-b clevage site, motif, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: TRANSPATH is related to: TRANSFAC is related to: Gene Ontology has parent organization: Saarland University; Saarbrucken; Germany |
PMID:17526521 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:genetrail, OMICS_02236 | https://bio.tools/genetrail | SCR_006250 | 2026-09-12 01:01:42 | 114 |
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