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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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bioPIXIE Resource Report Resource Website 1+ mentions |
bioPIXIE (RRID:SCR_004182) | bioPIXIE | analysis service resource, data analysis service, production service resource, service resource | bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it). | prediction, bayesian network, probabilistic, interaction, network | has parent organization: Princeton University; New Jersey; USA | NHGRI T32 HG003284; NIGMS R01 GM071966; NHGRI R01 HG003471; NIGMS P50 GM071508; NSF DGE-9972930; NSF IIS-0513552 |
PMID:16420673 | nlx_20893 | SCR_004182 | biological Process Inference from eXperimental Interaction Evidence | 2026-09-05 06:31:22 | 1 | ||||||
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LIPID MAPS Structure Database Resource Report Resource Website 10+ mentions |
LIPID MAPS Structure Database (RRID:SCR_003817) | LMSD | data or information resource, database | Collection of structures and annotations of biologically relevant lipids that contains unique lipid structures. Structures of lipids from : LIPID MAPS Consortium's core laboratories and partners; lipids identified by LIPID MAPS experiments; biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, Lipid Library, Cyberlipids, ChEBI and other public sources; novel lipids submitted to peer-reviewed journals; and computationally generated structures for appropriate classes. All the lipid structures adhere to the structure drawing rules proposed by the LIPID MAPS consortium. A number of structure viewing options are offered: gif image (default), Chemdraw (requires Chemdraw ActiveX/Plugin), MarvinView (Java applet) and JMol (Java applet). All lipids have been classified using the LIPID MAPS Lipid Classification System. Each lipid structure has been assigned a LIPID MAPS ID (LM_ID) which reflects its position in the classification hierarchy. In addition to a classification-based retrieval of lipids, users can search using either text-based or structure-based search options. | fatty acyl, glycerolipid, glycerophospholipid, sphingolipid, sterol lipid, prenol lipid, sacccharolipid, polyketide, lipid, structure, image, annotation, metabolomics | has parent organization: LIPID Metabolites And Pathways Strategy | NIGMS | PMID:17098933 | Public, Free, Acknowledgement required, Non-commercial, Copyrighted | nlx_158117 | SCR_003817 | LIPID MAPS Structure Database (LMSD) | 2026-09-05 06:31:21 | 24 | |||||
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IntegromeDB Resource Report Resource Website 1+ mentions |
IntegromeDB (RRID:SCR_004620) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. Search engine that integrates over 100 curated and publicly contributed data sources and provides integrated views on the genomic, proteomic, transcriptomic, genetic and functional information currently available. Information featured in the database includes gene function, orthologies, gene expression, pathways and protein-protein interactions, mutations and SNPs, disease relationships, related drugs and compounds. | catalog, search engine, gene, protein, gene regulation, gene expression, protein-protein interaction, pathway, metagenomics, mutation, disease, transcriptional regulation, genomics, transcriptomics, genetics, function, interaction, ortholog |
is related to: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters has parent organization: University of California at San Diego; California; USA |
NIH ; NIGMS R01 GM084881 |
PMID:22260095 PMID:20427517 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_63198 | SCR_004620 | Integrome DB | 2026-09-05 06:31:25 | 3 | ||||||
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ProFunc Resource Report Resource Website 50+ mentions |
ProFunc (RRID:SCR_004450) | ProFunc | analysis service resource, data analysis service, production service resource, service resource | The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time. | gold standard |
is related to: PDBsum has parent organization: European Bioinformatics Institute |
DOE contract W-31-109-Eng-38; NIGMS GM62414; European Union FP6 contract LHSG-CT-2003-503265 |
PMID:15980588 PMID:16019027 |
nlx_44430 | SCR_004450 | ProFunc - prediction of protein function from 3D structure, ProFunc: Analysis of a protein''''s 3D structure to help identify its likely biochemical function | 2026-09-05 06:31:24 | 72 | ||||||
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miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | data or information resource, database, service resource | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | Alfred W. Bressler Scholars Endowment Fund ; Atlantic Philanthropies ; NIGMS |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | MicroRNA.org. microrna.org | 2026-09-05 06:32:15 | 281 | ||||||
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Viral Integrated Structural Evolution Dynamic Database Resource Report Resource Website 1+ mentions |
Viral Integrated Structural Evolution Dynamic Database (RRID:SCR_018793) | VIStEDD | data or information resource, database | Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein. | Virus, SARS-CoV-2, COVID-19, proteins coded by virus, viral evolution, protein, data, amino acid, protein modeling, molecular dynamic simulation, evolutionary analysis, protein-protein interaction, protein- protein interaction mapping, protein data folder system, rotating protein video, protein function, molecular dynamic simulation | has parent organization: Michigan State University; Michigan; USA | COVID-19 | NIEHS K01 ES025435; NIGMS R01 GM108618 |
PMID:32511397 | Free, Freely available | SCR_018793 | Viral Integrated Structural Evolution Dynamic Database, SARS-CoV-2 dynamicome database | 2026-09-05 06:32:16 | 3 | |||||
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CIS-BP Resource Report Resource Website 100+ mentions |
CIS-BP (RRID:SCR_017236) | data access protocol, data or information resource, database, software resource, web service | Software tool as catalog of inferred sequence binding preferences. Online library of transcription factors and their DNA binding motifs. | catalog, inferred, sequence, binding, preference, transcription, factor, DNA, motif, FASEB list | Canadian Institute for Advanced Research Junior Fellows Genetic Networks Program ; Canadian Institutes of Health Research ; EU Marie Curie International Outgoing Fellowship ; Fondo Nacional de Desarrollo Científico y Tecnológico ; Gordon and Betty Moore Foundation ; Howard Hughes Medical Institute ; Millennium Nucleus for Fungal Integrative and Synthetic Biology ; NICHD P01 HD39691; NIGMS GM082971; NSF MCB-1024999 |
PMID:25215497 | Free, Freely available | r3d100013971 | https://doi.org/10.17616/R31NJN9V | SCR_017236 | Catalog of Inferred Sequence Binding Preferences | 2026-09-05 06:32:14 | 115 | ||||||
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SRMAtlas Resource Report Resource Website 1+ mentions |
SRMAtlas (RRID:SCR_016996) | SRM Atlas, SRMatlas | atlas, data or information resource, database | Resource of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. Used to quantify the complete human proteome. | collection, proteomic, assay, detect, quantify, protein, mass, spectrometry, peptide | American Recovery and Reinvestment Act ; European Research Council ; Luxembourg Centre for Systems Biomedicine University Luxembourg ; NCRR S10 RR027584; NHGRI RC2 HG005805; NIGMS P50 GM076547; NIGMS R01 GM087221; Swiss National Science Foundation |
PMID:27453469 | Publicly available, Registration required | SCR_016996 | 2026-09-05 06:32:14 | 3 | ||||||||
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WikiPathways Resource Report Resource Website 1000+ mentions |
WikiPathways (RRID:SCR_002134) | data or information resource, database, service resource | Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community. | database, knowledge environment resource, image, web service, biological pathway, diagram description, reference, pathway, FASEB list |
is used by: NIF Data Federation is used by: Open PHACTS is related to: PharmGKB is related to: Reactome is related to: NetPath is related to: ConsensusPathDB is related to: NCBI BioSystems Database is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of California at San Francisco; California; USA has parent organization: Maastricht University; Maastricht; Netherlands |
Google Summer of Code program ; Netherlands Bioinformatics Centre ; NIGMS GM080223; NIGMS R01 GM100039; NIH ; NWO - Netherlands Organization for Scientific Research |
PMID:22096230 PMID:18651794 |
Free, Freely available | nif-0000-20925, r3d100013316 | SCR_002134 | Wiki Pathways | 2026-09-05 06:31:16 | 2013 | ||||||
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Aptamer Database - The Ellington Lab Resource Report Resource Website 1+ mentions |
Aptamer Database - The Ellington Lab (RRID:SCR_001781) | data or information resource, database | The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms. | aptamer, dna molecule, in vitro selection, ribozyme, rna molecule | has parent organization: University of Texas at Austin; Texas; USA | MURI DAAD19-99-1-0207; NIGMS 1R01 GM61789-01 |
PMID:14681367 | Free, Freely available | nif-0000-02558 | http://aptamer.icmb.utexas.edu | SCR_001781 | Aptamer Database, Ellington Lab Aptamer Database | 2026-09-05 06:31:15 | 3 | |||||
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MORGAN Resource Report Resource Website 100+ mentions |
MORGAN (RRID:SCR_006906) | MORGAN | software application, software resource | Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits. | gene, genetic, genomic, c, unix, compaq-alpha, solaris, linux, linkage disequilibrium, gl_lods, ibd_haplo, identity by descent, segregation, linkage analysis, markov chain monte carlo |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Washington; Seattle; USA |
NIGMS GM-46255 | PMID:22298700 | nlx_154201, OMICS_00205 | SCR_006906 | MOnte caRlo Genetic ANalysis PANGAEA | 2026-09-05 06:32:38 | 319 | ||||||
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GLIMMPSE Resource Report Resource Website 1+ mentions |
GLIMMPSE (RRID:SCR_016297) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-05 06:30:07 | 9 | ||||||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | data analysis software, data analytics software, data processing software, software application, software resource, software toolkit | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI076327; NIAID R01 AI134246; NIAID R01 AI134713; NIAID R21 AI142667; NIAID T32 AI10667; NIAID U19 AI135976; NICHD T32 HD007233; NIGMS T32 GM007270; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-09-05 06:30:10 | 23 | |||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | data processing software, data visualization software, software application, software resource | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | 2026-09-05 06:30:11 | 4 | |||||||||
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SpiecEasi Resource Report Resource Website 10+ mentions |
SpiecEasi (RRID:SCR_022712) | SpiecEasi | data analysis software, data processing software, software application, software resource | Software R package for microbiome network analysis. Used for inference of microbial ecological networks from amplicon sequencing datasets. Combines data transformations developed for compositional data analysis with graphical model inference framework that assumes underlying ecological association network is sparse. | microbiome network analysis, amplicon sequencing datasets, microbial ecological networks inference | NIAID AI007180; NIDDK DK103358; NIGMS GM63270; Simons Foundation |
PMID:25950956 | Free, Available for download, Freely available | SCR_022712 | SParse InversE Covariance Estimation for Ecological Association Inference | 2026-09-05 06:30:16 | 20 | |||||||
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Megadepth Resource Report Resource Website 1+ mentions |
Megadepth (RRID:SCR_022779) | data analysis software, data processing software, software application, software resource | Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts. | quantifying alignments, BigWig and BAM/CRAM input files, RNA-seq reads assigned to gene in BAM file quantification, | NIGMS R01GM118568; NIGMS R01GM121459; UK Medical Research Council |
PMID:33693500 | Free, Available for download, Freely available | https://bioconductor.org/packages/megadepth | SCR_022779 | 2026-09-05 06:30:16 | 2 | ||||||||
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ZDOCK Server Resource Report Resource Website 100+ mentions |
ZDOCK Server (RRID:SCR_022518) | data access protocol, software resource, web service | Web tool as protein docking server, based on rigid body docking programs ZDOCK and M-ZDOCK, to predict structures of protein-protein complexes and symmetric multimers. | Protein docking server, ZDOCK, M-ZDOCK, predict structures, protein-protein complexes, symmetric multimers | NIGMS GM084884 | PMID:24532726 | Free, Freely available | SCR_022518 | 2026-09-05 06:30:14 | 137 | |||||||||
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sei Resource Report Resource Website 10+ mentions |
sei (RRID:SCR_022571) | data access protocol, software resource, web service | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | 2026-09-05 06:30:15 | 10 | ||||||||
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VirtualPlant Resource Report Resource Website 1+ mentions |
VirtualPlant (RRID:SCR_022576) | data access protocol, software resource, web service | Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses. | genomic data integration, support systems biology, genomic data visualization and analysis | FONDECYT ; Grape Genomics ; Millennium Nucleus for Plant Functional Genomics ; NIGMS 5F32GM75600; NIGMS R01 GM 032877; NSF DBI 0445666; NSF IOB 0519985; NSF MCB–0209754 |
PMID:20007449 | Free, Available for download, Freely available | SCR_022576 | VirtualPlant 1.3 | 2026-09-05 06:30:15 | 3 | ||||||||
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ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | controlled vocabulary, data or information resource, ontology | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/, http://bioportal.bioontology.org/ontologies/ECO | SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-09-05 06:30:19 | 19 |
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