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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cell Type Ontology Resource Report Resource Website 1+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | controlled vocabulary, data or information resource, ontology | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | cellontology.org, Obo-cell-type, Cell Ontology | 2026-08-03 09:32:23 | 6 | |||
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CRCNS Resource Report Resource Website 100+ mentions |
CRCNS (RRID:SCR_005608) | CRCNS | data repository, data or information resource, funding resource, storage service resource, collaborative tool, service resource | Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources. | collaborative research, data sharing, computational model, brain, computational neuroscience, data set, FASEB list |
is used by: NIF Data Federation is used by: DataLad is used by: Integrated Datasets is recommended by: National Library of Medicine is listed by: DataCite is related to: Integrated Manually Extracted Annotation has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: University of California; California; USA |
NIH ; NSF IIS-0749049; NSF 0636838 |
PMID:18259695 | Free, Freely available | nif-0000-00255, r3d100011269 | https://api.datacite.org/dois?prefix=10.6080, https://doi.org/10.17616/R31S7P | SCR_005608 | CRCNS Data sharing, Collaborative Research in Computational Neuroscience - Data sharing, Collaborative Research in Computational Neuroscience, CRCNS - Data sharing | 2026-08-03 09:32:53 | 119 | ||||
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FaceBase Resource Report Resource Website 50+ mentions |
FaceBase (RRID:SCR_005998) | FaceBase | portal, disease-related portal, community building portal, topical portal, research forum portal, data or information resource | A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse. | microct, dna microarray, craniofacial, genome, imaging, FASEB list, DRKB |
has parent organization: University of Pittsburgh; Pennsylvania; USA is parent organization of: 3D Facial Norms Database is parent organization of: OCDM - Ontology of Craniofacial Development and Malformation is parent organization of: FaceBase Biorepository is parent organization of: FishFace - An atlas of zebrafish craniofacial development |
NIH DE034163 | Open and restricted access. Open-access data is available on the FaceBase website to any interested user and does not require any formal registration. Open-access data will be limited to summary-level human data (ex: averaged facial measures), And all non-human data. In contrast, All individual-level human data (ex: demographic descriptors, Phenotypic measures, 3D images) will fall under the restricted category and will require the requestor to fill out the Data Access Request form. | nlx_151372 | SCR_005998 | FaceBase - A Resource For Craniofacial Researchers | 2026-08-03 09:32:59 | 72 | ||||||
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Pubmed Commons Resource Report Resource Website 1+ mentions |
Pubmed Commons (RRID:SCR_014021) | narrative resource, data or information resource, discussion, forum | A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments. | forum, PubMed, commuication |
is listed by: Connected Researchers is related to: PubMed is related to: Connected Researchers |
NIH ; NLM |
Free, Membership required, The community can contribute to this resource | SCR_014021 | 2026-08-03 09:35:34 | 3 | |||||||||
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METAGENOTE Resource Report Resource Website 1+ mentions |
METAGENOTE (RRID:SCR_018494) | web service, data access protocol, software resource | Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository. | Annotate data, genomics study, microbiome, metadata, genomics, data |
is related to: NCBI Sequence Read Archive (SRA) is related to: NCBI |
NIH | Free, Freely available | SCR_018494 | METAdata of GEnomics studies on a web based NOTEbook | 2026-08-03 09:37:16 | 1 | ||||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | software resource, software application, data processing software | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-08-03 09:32:11 | 5 | |||||
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NIH Human Pluripotent Stem Cell Registry Resource Report Resource Website 1+ mentions |
NIH Human Pluripotent Stem Cell Registry (RRID:SCR_003149) | NIH Human Embryonic Stem Cell Registry | material resource, biomaterial supply resource, cell repository | A listing of human embryonic cell lines that are eligible for use in NIH funded research. Those lines that carry disease-specific mutations are noted as such under the line name. Total Eligible Lines = 200. The purpose of the Registry is to provide investigators with: # a unique NIH Code for each cell line that must be used when applying for NIH funding and # contact information to facilitate investigators' acquisition of stem cells. Before submitting a new grant application and supporting materials for consideration of a human embryonic stem cell line, scientists may wish to see what lines are already under consideration: * Human embryonic stem cell lines submitted to NIH that are being reviewed to determine if they may be used in NIH-supported research, http://grants.nih.gov/stem_cells/registry/pending.htm President George W. Bush required that the name of the registry be changed in his Executive Order #13435, issued on June 20, 2007. As a result of this Executive Order, the former National Institutes of Health Human Embryonic Stem Cell Registry will now be called the National Institutes of Health Human Pluripotent Stem Cell Registry. The registry will now include both human embryonic stem cells that were derived consistent with the President's policy of August 9, 2001 and human pluripotent stem cells derived from non-embryonic sources. | embryonic, cell, human, registry, stem cell, embryonic stem cell, cell line, human embryonic stem cell line, human pluripotent stem cell, adult, fetal, mutation |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: Wisconsin International Stem Cell Bank is related to: National Stem Cell Bank is related to: NIF Data Federation is related to: Integrated Cell Lines has parent organization: National Institutes of Health |
NIH ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00565 | SCR_003149 | NIH Human Embryonic Stem Cell Registry, National Institutes of Health Human Pluripotent Stem Cell Registry | 2026-08-03 09:32:12 | 7 | ||||||
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Knockout Mouse Project Resource Report Resource Website 10+ mentions |
Knockout Mouse Project (RRID:SCR_005571) | KOMP, NIH KOMP | data or information resource, portal, project portal | Project is providing critical tools for understanding gene function and genetic causes of human diseases. Project KOMP is focused on generating targeted knockout mutations in mouse ES cells. Second phase, KOMP2, relies upon successful generation of strains of knockout mice from these ES cells. Information from JAX about their contributions to KOMP project. | Generating, knockout, mutation, mouse, ES cell, embryonic, stem, c57bl/6 |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources is related to: KOMP2 is related to: KOMP2 is related to: StatPackets has parent organization: International Knockout Mouse Consortium has parent organization: National Institutes of Health is parent organization of: Knockout Mouse Project Repository is parent organization of: Knockout Mouse Project Repository at JAX |
NIH ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nlx_145296, SCR_017527 | https://grants.nih.gov/grants/guide/rfa-files/rfa-rr-06-005.html | http://www.nih.gov/science/models/mouse/knockout/index.html | SCR_005571 | NIH Knockout Mouse Project, Knock-Out Mouse Project | 2026-08-03 09:32:52 | 10 | ||||
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NIH Clinical Collection Resource Report Resource Website 10+ mentions |
NIH Clinical Collection (RRID:SCR_007349) | NCC | reagent supplier, material resource | A plated array of approximately 450 small molecules that have a history of use in human clinical trials. The collection was assembled by the National Institutes of Health (NIH) through the Molecular Libraries Roadmap Initiative as part of its mission to enable the use of compound screens in biomedical research. Similar collections of FDA approved drugs have proven to be rich sources of undiscovered bioactivity and therapeutic potential. The clinically tested compounds in the NCC are highly drug-like with known safety profiles. These compounds can provide excellent starting points for medicinal chemistry optimization and, for high-affinity targets, may even be appropriate for direct human use in new disease areas. | clinical, collection, drug, compound, chemistry, medicinal chemistry, target, affinity, human, disease, disorder, small molecule | is related to: Molecular Libraries Program | NIH | nif-0000-00254 | SCR_007349 | 2026-08-03 09:33:26 | 14 | ||||||||
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Human Microbiome Project Resource Report Resource Website 100+ mentions |
Human Microbiome Project (RRID:SCR_012956) | HMP, NIH HMP, HMP1 | data or information resource, portal, project portal | NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.HMP was supported by the Common Fund from 2007 to 2016. | generate, resource, human, body, microbiota, analyze, health, disease, metagenomic, DNA, sequesncing, data |
lists: Pathogen Portal lists: DNACLUST lists: QIIME lists: mothur lists: Greengenes lists: Ribosomal Database Project lists: DeconSeq lists: FragGeneScan lists: MetAMOS lists: MetaPhlAn lists: MetaPhyler lists: METAREP lists: PRINSEQ lists: TagCleaner lists: BioCyc lists: MG-RAST lists: Core Gene Evaluation Script lists: IMG System lists: RAST Server lists: GINGKO lists: inVUE lists: LEfSe lists: Metastats lists: MicrobiomeUtilities lists: Hypothesis Testing and Power Calculations for Comparing Metagenomic Samples from HMP lists: HMPTrees lists: Simrank lists: speciateIT lists: Unifrac lists: Fast-Unifrac lists: SitePainter lists: BMTagger lists: HUMAnN lists: Metapath lists: IMG System is related to: biobakery is related to: Integrative Human Microbiome Project is related to: MicrobiomeDB is related to: Broad Institute Genomics Platform has parent organization: National Institutes of Health is parent organization of: HMP Data Analysis and Coordination Center |
NIH | nif-0000-25316 | https://www.hmpdacc.org/ihmp/, https://www.hmpdacc.org/hmp | http://nihroadmap.nih.gov/hmp/ | SCR_012956 | Human Microbiome Project, NIH HMP, HMP1, HMP, NIH Human Microbiome Project | 2026-08-03 09:35:07 | 385 | |||||
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SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | image analysis software, software resource, software application, data processing software | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | NIH ; NLM ; LHNCBC HHSN276201500692P |
Free, Available for download | SCR_016215 | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-08-03 09:36:39 | 4 | |||||||||
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Nonhuman Primate Reference Transcriptome Resource Resource Report Resource Website 10+ mentions |
Nonhuman Primate Reference Transcriptome Resource (RRID:SCR_017534) | NHPRTR | data or information resource, portal, project portal | Nonhuman Primate reference transcriptome resource consisting of deep sequencing complete transcriptomes (RNA-seq) from multiple NHP species. | Nonhuman, primate, reference, transcriptome, deep, sequencing, RNAseq, data, species | NIH | Free, Freely available | SCR_017534 | Nonhuman Primate Reference Transcriptome Resource | 2026-08-03 09:36:39 | 10 | ||||||||
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Mouse Connectome Project Resource Report Resource Website |
Mouse Connectome Project (RRID:SCR_017313) | MCP | data or information resource, portal, project portal | Project to create complete mesoscale connectivity atlas of the C57Black/6 mouse brain and to subsequently generate its global neural networks. | mesoscale, connectivity, atlas, C57Black/6, mouse, brain, neural, network |
is used by: BICCN has parent organization: University of Southern California; Los Angeles; USA |
NIH | Free, Freely available | SCR_017313 | The Mouse Connectome Project, Mouse Connectome Project | 2026-08-03 09:37:02 | 0 | |||||||
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Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | data or information resource, database, portal, project portal | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-08-03 09:38:28 | 55 | |||||||
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Mouse Models For Alzheimer's Disease Research Resource Report Resource Website 1+ mentions |
Mouse Models For Alzheimer's Disease Research (RRID:SCR_000708) | narrative resource, model, data or information resource | An information resource about several models for mice to develop Alzheimer's-related characteristics as they age. | alzheimer's, aging, mouse, mice, model, transgenic, research | has parent organization: Jackson Laboratory | Aging | NIH | Non-Commercial, Personal Use | nif-0000-00183 | http://jaxmice.jax.org/research/neurobiology/alzheimers-agedmodels.html, http://research.jax.org/grs/alzheimers.html | SCR_000708 | MMFADR | 2026-08-03 09:31:07 | 1 | |||||
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Human Nutrition Research Information Management Resource Report Resource Website |
Human Nutrition Research Information Management (RRID:SCR_001471) | HNRIM | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of human nutrition research and research training activities supported by the federal government. Information regarding trends in nutrition research, specific institutions and investigators involved in this research, or areas of agency emphases can be obtained from database searches or from published summary reports. Data for the system is prepared and submitted by participating agencies, and is updated annually. The database contains several thousand projects for each of fiscal years 1985present. Participating agencies include the Department of Health and Human Services, the U.S. Department of Agriculture, the Department of Veteran Affairs, the Agency for International Development, the Department of Defense, Department of Commerce, National Science Foundation, and the National Aeronautics and Space Administration. | nutrition |
is listed by: NIDDK Information Network (dkNET) is related to: CARDS Database has parent organization: NIH Division of Nutrition Research Coordination |
NIH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152702 | SCR_001471 | HNRIM System Database, Federal Human Nutrition Research and Information Management (HNRIM) System Database, Federal Human Nutrition Research and Information Management System Database | 2026-08-03 09:31:21 | 0 | ||||||
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MPIDB Resource Report Resource Website 1+ mentions |
MPIDB (RRID:SCR_001898) | MPIDB | data or information resource, database | Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included. | 3d domain, conservation, co-purification, interaction, microbial, protein, microbial interaction, protein interaction, interaction conservation, interaction co-purification, 3d domain contact, protein-protein interaction, microbial protein, microbiology |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: IntAct is related to: Database of Interacting Proteins (DIP) is related to: BIND is related to: MINT is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry has parent organization: J. Craig Venter Institute |
J. Craig Venter Institute ; Indgen Life Technologies ; NIH ; NIMH R01GM79710 |
PMID:18556668 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100010673, nif-0000-10467 | http://jcvi.org/mpidb/ | SCR_001898 | The Microbial Protein Interaction Database, Microbial Protein Interaction Database | 2026-08-03 09:31:28 | 5 | ||||
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LocusZoom.org Resource Report Resource Website 10+ mentions |
LocusZoom.org (RRID:SCR_021374) | web service, data access protocol, software resource | Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. | Generate interactive plots, shareable plots, GWAS summary statistics, visualizing statistical genetic data, genetic association study | NHGRI HG009976; NIH BOEH15AMP |
DOI:10.1093/bioinformatics/btab186 | Free, Freely available | SCR_021374 | LocusZoom.js | 2026-08-03 09:37:36 | 32 | ||||||||
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App for searching human and mimivirus homologous proteins Resource Report Resource Website 1+ mentions |
App for searching human and mimivirus homologous proteins (RRID:SCR_022140) | web service, data access protocol, software resource | Web interactive and searchable genome wide comparison tool for browsing human and mimivirus homologous proteins. User friendly Shinny app helps users browse protein sequence homology between humans and mimivirus at genome wide level for querying new homologs and generating new hypotheses. | genome wide comparison tool, browsing human and mimivirus homologous proteins, Shinny app, protein sequence homology | NIH R00 CA225633 | Free, Freely available | SCR_022140 | 2026-08-03 09:37:47 | 1 | ||||||||||
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Harmony Resource Report Resource Website 100+ mentions |
Harmony (RRID:SCR_022206) | software resource, data processing software, software application, data analysis software | Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data. | cells grouping, cell type, experimental factors, biological factors, single cell data integration | is used by: harmonypy | NIAID U19 AI111224; NIH R01 AR063759; NIH UH2 AR067677; NIH T32 AR007530 |
PMID:31740819 | Free, Available for download, Freely available | SCR_022206 | Harmony for immunogenomics | 2026-08-03 09:37:35 | 171 |
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