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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
Phymm and PhymmBL
 
Resource Report
Resource Website
10+ mentions
Phymm and PhymmBL (RRID:SCR_004751) Phymm, PhymmBL software resource Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read is listed by: OMICtools
has parent organization: University of Maryland; Maryland; USA
NLM R01-LM006845 PMID:19648916
PMID:21527926
Open-source license OMICS_01461 SCR_004751 2026-08-01 12:02:44 12
ROSTLAB
 
Resource Report
Resource Website
1+ mentions
ROSTLAB (RRID:SCR_000792) group A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research. protein, structure, function, dna, rna, gene, machine learning, statistics, analysis, protein, biomedical has parent organization: Columbia University; New York; USA
is parent organization of: PredictNLS
is parent organization of: SNPdbe
NLM LM007329;
NLM GM50291
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-31417 http://cubic.bioc.columbia.edu/services/disis SCR_000792 Rost Group 2026-08-01 12:01:19 1
LexGrid
 
Resource Report
Resource Website
1+ mentions
LexGrid (RRID:SCR_006627) LexGrid software resource LexGrid (Lexical Grid) provides support for a distributed network of lexical resources such as terminologies and ontologies via standards-based tools, storage formats, and access/update mechanisms. The Lexical Grid Vision is for a distributed network of terminological resources. It is the foundation of the National Center for Biomedical Ontology BioPortal interface and web-services, and can parse OBO format, as well as other formats such as OWL. Currently, there are many terminologies and ontologies in existence. Just about every terminology has its own format, its own set of tools, and its own update mechanisms. The only thing that most of these pieces have in common with each other is their incompatibility. This makes it very hard to use these resources to their full potential. We have designed the Lexical Grid as a way to bridge terminologies and ontologies with a common set of tools, formats and update mechanisms. The Lexical Grid is: * accessible through a set of common APIs * joined through shared indices * online accessible * downloadable * loosely coupled * locally extendable * globally revised * available in web-space on web-time * cross-linked The realization of this vision requires three interlocking components, which are: * Standards - access methods and formats need to be published and openly available * Tools - standards based tools must be readily available * Content - commonly used terminologies have to be available for access and download Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible software library, parse, ontology is listed by: BioPortal
is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: OBO
has parent organization: European Bioinformatics Institute
has parent organization: National Cancer Institute
NIH ;
Cancer Biomedical Informatics Grid ;
NLM LM07319
PMID:19261933 Free for academic use nlx_149194 http://www.lexgrid.org/ SCR_006627 Lexical Grid 2026-08-01 12:03:16 1
NCBI Resource List
 
Resource Report
Resource Website
NCBI Resource List (RRID:SCR_005628) NCBI Resources organization portal, data or information resource, portal The National Center for Biotechnology Information''s listing of resources. Sort by alphabetical character, Databases, Downloads, Submissions, Tools and How-To; or by Topic: Chemicals & Bioassays; Data & Software; DNA & RNA; Domains & Structures; Genes & Expression; Genetics & Medicine; Genomes & Maps; Homology; Literature; Proteins; Sequence Analysis; Taxonomy; Training & Tutorials; Variation. database, download, submission, tool, chemical, bioassay, data, software, dna, rna, domain, structure, gene, expression, genetics, medicine, genomes, map, homology, literature, protein, sequence analysis, taxonomy, training, tutorial, variation, gold standard has parent organization: NCBI NLM nlx_146242 SCR_005628 NCBI Resource Guide, NCBI Resource List (A-Z) 2026-08-02 09:04:29 0
LINCS Data Portal 2.0
 
Resource Report
Resource Website
1+ mentions
LINCS Data Portal 2.0 (RRID:SCR_022566) LDP v2 data or information resource, portal Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures. LINCS Data Portal, Cell, molecules, drug is related to: LINCS Data Portal NHLBI U54HL127624;
BD2K-LINCS Data Coordination and Integration Center ;
NCATS U24TR002278;
NLM U01LM012630
PMID:31701147 Free, Freely available SCR_022566 Library of Integrated Network Based Cellular Signatures 2.0 2026-08-02 09:08:32 2
SimpleITK
 
Resource Report
Resource Website
10+ mentions
SimpleITK (RRID:SCR_024693) software library, software toolkit, software resource Open source software library for multi dimensional image analysis in Python, R, Java, C#, Lua, Ruby, TCL and C++. New interface to Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. Provides easy to use and simplified interface to ITK's algorithms. multi dimensional image analysis, Insight Segmentation and Registration Toolkit, is related to: Insight Segmentation and Registration Toolkit NLM PMID:24416015 Free, Available for download, Freely available https://github.com/SimpleITK/SimpleITK SCR_024693 Simple Insight Segmentation and Registration Toolkit 2026-08-02 09:09:07 37
Robot Reviewer
 
Resource Report
Resource Website
1+ mentions
Robot Reviewer (RRID:SCR_018961) text extraction software, software resource, software application Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments. Automated review, data mining, manuscript screening, artificial intelligence, automatic evidence synthesis, evidence synthesis, trial conduct information, data trial, bias, bias assessement NLM R01 LM012086;
NCI UH2 CA203711;
UK Medical Research Council
PMID:26104742 Free, Freely available SCR_018961 2026-08-02 09:07:54 5
SCORE
 
Resource Report
Resource Website
100+ mentions
SCORE (RRID:SCR_014165) narrative resource, data or information resource, experimental protocol A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard. experiment protocol, method, different image algorithm, quantitative score is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: University of Utah; Utah; USA
NLM HHSN276201000584P;
NIBIB 1R41 EB011796
SCR_014165 2026-08-02 09:06:27 458
pRESTO
 
Resource Report
Resource Website
50+ mentions
pRESTO (RRID:SCR_001782) pRESTO software toolkit, software resource Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. lymphocyte, high throughput sequencing, processing, raw reads, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Yale School of Medicine; Connecticut; USA
EMD/Merck/Serono ;
United States-Israel Binational Science Foundation 2009046;
NCRR RR19895;
NLM T15 LM07056;
NIAAA U19AI089992;
NIAAA U19AI050864
PMID:24618469 Free, Freely available SCR_001782 REpertoire Sequencing TOolkit 2026-08-02 09:03:16 70
ReBATE
 
Resource Report
Resource Website
ReBATE (RRID:SCR_017139) software toolkit, software resource Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic has parent organization: University of Pennsylvania; Philadelphia; USA NIAID AI116794;
NIDDK DK112217;
NIEHS ES013508;
NEI EY022300;
NHLBI HL134015;
NLM LM009012;
NLM LM010098;
NLM LM011360;
NCATS TR001263;
Warren Center for Network and Data Science
PMID:30030120 Free, Available for download, Freely available https://epistasislab.github.io/ReBATE/ SCR_017139 Relief Based Algorithm Training Environment 2026-08-02 09:07:35 0
Predictive Networks
 
Resource Report
Resource Website
Predictive Networks (RRID:SCR_006110) PN production service resource, data analysis service, service resource, database, source code, analysis service resource, data or information resource, software resource A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
has parent organization: Dana-Farber Cancer Institute
has parent organization: SourceForge
NLM 1R01LM010129 PMID:22096235 Apache License, v2 nlx_151582, biotools:predictivenetworks https://bio.tools/predictivenetworks SCR_006110 2026-08-03 09:32:53 0
Ligand Expo
 
Resource Report
Resource Website
Ligand Expo (RRID:SCR_006636) resource, data or information resource, database An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, chemical, component, depot, ligand, molecular, molecule, nitrogen, nucleic acid, nucleotide, pharmaceutical, protein, small molecule, structure, macromolecule, model uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
uses: Worldwide Protein Data Bank (wwPDB)
has parent organization: Rutgers University; New Jersey; USA
has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB)
NSF ;
NIGMS ;
DOE ;
NLM ;
NCI ;
NCRR ;
NIBIB ;
NINDS ;
NIDDK
PMID:15059838 nif-0000-21237, OMICS_02751 http://ligand-depot.rutgers.edu/ SCR_006636 Ligand Depot 2026-08-03 09:33:06 0
Unified Medical Language System
 
Resource Report
Resource Website
10+ mentions
Unified Medical Language System (RRID:SCR_006363) UMLS standard specification, web service, data access protocol, database, narrative resource, international standard specification, data or information resource, software resource Database of key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services, including electronic health records. This set of files and software brings together many health and biomedical vocabularies and standards to enable interoperability between computer systems. Users can use the UMLS to enhance or develop applications, such as electronic health records, classification tools, dictionaries and language translators. The UMLS has three tools, which we call the Knowledge Sources: * Metathesaurus: Terms and codes from many vocabularies, including CPT, ICD-10-CM, LOINC, MeSH, RxNorm, and SNOMED CT * Semantic Network: Broad categories (semantic types) and their relationships (semantic relations) * SPECIALIST Lexicon and Lexical Tools: Natural language processing tools We use the Semantic Network and Lexical Tools to produce the Metathesaurus. Metathesaurus production involves: * Processing the terms and codes using the Lexical Tools * Grouping synonymous terms into concepts * Categorizing concepts by semantic types from the Semantic Network * Incorporating relationships and attributes provided by vocabularies * Releasing the data in a common format Although we integrate these tools for Metathesaurus production, you can access them separately or in any combination according to your needs. The UMLS Terminology Services (UTS) provides three ways to access the UMLS: Web Browsers, Local Installation, and Web Services APIs. interoperability, electronic health record, classification tool, dictionary, language translator, classification, terminology, semantic, metathesaurus, vocabulary, thesaurus, natural language processing is used by: DisGeNET
is related to: MeSH
is related to: ConceptWiki
has parent organization: National Library of Medicine
NLM License required and only issued to individuals, Not to groups or organizations - no charge for licensing the UMLS from NLM. nlx_152104 SCR_006363 Unified Medical Language System (UMLS) 2026-08-03 09:33:06 44
EVidenceModeler
 
Resource Report
Resource Website
1000+ mentions
EVidenceModeler (RRID:SCR_014659) EVM sequence analysis software, software application, data processing software, data analysis software, software resource Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format). sequence analysis software, framework, ab intio gene, gene prediction, protein alignment, transcript alignment, consensus gene structure NIAID N01 AI30071;
NLM R01 LM006845
PMID:18190707 Free, Available for download, Freely available SCR_017649 SCR_014659 2026-08-03 09:35:47 1135
GLIMMPSE
 
Resource Report
Resource Website
1+ mentions
GLIMMPSE (RRID:SCR_016297) software resource, data processing software, software application, data analysis software Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. power, multivariate, linear, models, Gaussian, error, Java, web, calculate NIGMS R01 GM121081;
NIGMS R25 GM111901;
NLM G13 LM011879
PMID:24403868
PMID:40901910
THIS RESOURCE IS NO LONGER IN SERVICE SCR_016297 , GLIMMPSE Version 3 2026-08-03 09:36:20 8
MUMmerGPU
 
Resource Report
Resource Website
1+ mentions
MUMmerGPU (RRID:SCR_001200) MUMmerGPU software resource, software application, data processing software Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer. parallel computation 4, high-throughput sequencing, sequence alignment, dna, graphics processing unit is listed by: OMICtools
is related to: MUMmer
has parent organization: SourceForge
has parent organization: University of Maryland; Maryland; USA
NLM R01 LM006845;
NIGMS R01 GM083873
PMID:20161021 Free, Available for download, Freely available OMICS_02151 SCR_001200 High-throughput sequence alignment using Graphics Processing Units 2026-08-03 09:31:16 5
Anne O'Tate
 
Resource Report
Resource Website
1+ mentions
Anne O'Tate (RRID:SCR_023086) software resource, web application Web search tool to gain overview of set of articles retrieved by PubMed query. Used to support user driven summarization, drill down and browsing of PubMed search results. Value-added PubMed search engine for analysis and text mining. Value added PubMed search engine, analysis and text mining has parent organization: University of Illinois at Chicago; Illinois; USA NLM LM 007292;
NLM LM 08364
PMID:18279519
PMID:33684153
Free, Freely available SCR_023086 2026-08-03 09:38:07 1
Gene functional conservation across cell types and species
 
Resource Report
Resource Website
Gene functional conservation across cell types and species (RRID:SCR_023292) data or information resource, portal, project portal We aligned single-nucleus atlases of middle temporal gyrus (MTG) of 5 primates (human, chimp, gorilla, macaque and marmoset) and identified 57 consensus cell types common to all species. We provide this resource for users to: 1) explore conservation of gene expression across primates at single cell resolution; 2) compare with conservation of gene coexpression across metazoa, and 3) identify genes with changes in expression or connectivity that drive rapid evolution of human brain. Brain Initiative Cell Census Network, single-nucleus atlases, middle temporal gyrus, human, chimp, gorilla, macaque, marmoset, 57 consensus cell types common to all species, 57 consensus cell types identification, is related to: BICCN NLM R01LM012736;
NLM R01MH113005;
NLM U19MH114821;
NLM F32MH114501;
NARSAD Young Investigator Award ;
NHGRI R01HG009318;
NLM U01MH114812
DOI:10.1101/2022.09.20.508736 Free, Freely available SCR_023292 2026-08-03 09:37:58 0
MedGen
 
Resource Report
Resource Website
1+ mentions
MedGen (RRID:SCR_000111) MedGen data or information resource, database A database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution. medical genetics, medical, genetics, disease, clinical is listed by: OMICtools
is listed by: Genetic Testing Registry
has parent organization: NCBI
NLM 1ZIHLM200888-05 PMID:32329672 nlx_156941, OMICS_01549 SCR_000111 2026-08-03 09:30:57 6
Automated Microarray Pipeline
 
Resource Report
Resource Website
Automated Microarray Pipeline (RRID:SCR_001219) AMP data analysis service, service resource, analysis service resource, production service resource THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis. microarray, normalization is listed by: OMICtools
is related to: Gene Ontology
has parent organization: TM4
NLM R01-LM008795 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_02125 http://www.tm4.org/amp.html SCR_001219 TM4 AMP, AMP: Automated Microarray Pipeline, AMP (TM4 Microarray Software Suite), TM4 Microarray Software Suite: Automated Microarray Pipeline, TM4 Microarray Software Suite: AMP 2026-08-03 09:31:17 0

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