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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BIOBASE Corporation Resource Report Resource Website 100+ mentions |
BIOBASE Corporation (RRID:SCR_010271) | commercial organization | THIS RESOURCE IS OUT OF SERVICE, documented on February 1st,2022. BIOBASE offers academic and non-profit organizations free access to TRANSFAC?? non-professional version with much reduced functionality and content compared to our professional database. | FASEB list |
is related to: Human Gene Mutation Database is parent organization of: Genome Trax is parent organization of: TRANSPATH is parent organization of: Gene Regulation Programs is parent organization of: TRANSCompel is parent organization of: Gene Regulation Databases |
THIS RESOURCE IS OUT OF SERVICE | nlx_156933 | SCR_010271 | 2026-09-12 12:57:16 | 184 | |||||||||
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Bionutrition Ontology Resource Report Resource Website 1+ mentions |
Bionutrition Ontology (RRID:SCR_010272) | BNO | controlled vocabulary, data or information resource, ontology | Ontology that relates concepts and terminologies used for human nutrition in a clinical and biomedical setting. | owl | is listed by: BioPortal | nlx_157337 | SCR_010272 | 2026-09-12 12:57:16 | 1 | |||||||||
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HHpred Resource Report Resource Website 1000+ mentions |
HHpred (RRID:SCR_010276) | data or information resource, database, software resource | The primary aim in developing HHpred was to provide biologists with a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred''s sensitivity is competitive with the most powerful servers for structure prediction currently available. HHpred is the first server that is based on the pairwise comparison of profile hidden Markov models (HMMs). Whereas most conventional sequence search methods search sequence databases such as UniProt or the NR, HHpred searches alignment databases, like Pfam or SMART. This greatly simplifies the list of hits to a number of sequence families instead of a clutter of single sequences. All major publicly available profile and alignment databases are available through HHpred. | nlx_156935 | SCR_010276 | Homology detection & structure prediction by HMM-HMM comparison | 2026-09-12 12:57:16 | 1032 | |||||||||||
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BitSeq Resource Report Resource Website 10+ mentions |
BitSeq (RRID:SCR_009904) | BitSeq | software resource | A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btv483 DOI:10.1093/bioinformatics/bts260 |
, OMICS_01269, biotools:bitseq | https://bio.tools/bitseq, https://sources.debian.org/src/bitseq/, | SCR_009904 | 2026-09-12 12:57:15 | 20 | |||||||
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U.S. Department of Labor Resource Report Resource Website 1+ mentions |
U.S. Department of Labor (RRID:SCR_010157) | DOL | institution | Fosters, promotes, and develops the welfare of the wage earners, job seekers, and retirees of the United States; improves working conditions; advances opportunities for profitable employment; and assures work-related benefits and rights. | grid.420412.1, nlx_151864, ISNI: 0000 0001 2097 824X, Wikidata: Q628807, Crossref funder ID: 100000778 | https://ror.org/05mbkbj54 | SCR_010157 | US Dept. of Labor, US DOL, US Department of Labor, United States Department of Labor | 2026-09-12 12:57:15 | 1 | |||||||||
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BioTop Ontology Resource Report Resource Website 1+ mentions |
BioTop Ontology (RRID:SCR_010039) | BT | controlled vocabulary, data or information resource, ontology | A top-domain ontology that provides definitions for the foundational entities of biomedicine as a basic vocabulary to unambiguously describe facts in this domain. It can furthermore serve as top-level model for creating new ontologies for more specific domains or as aid for aligning or improving existing ones. | owl | is listed by: BioPortal | nlx_157329 | http://purl.org/biotop | SCR_010039 | 2026-09-12 12:57:15 | 1 | ||||||||
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Eligibility Feature Hierarchy Resource Report Resource Website |
Eligibility Feature Hierarchy (RRID:SCR_010314) | ELIG | controlled vocabulary, data or information resource, ontology | A set of 1,437 eligibility features that were organized into a feature hierarchy using 80 breast cancer trials. | owl | is listed by: BioPortal | Breast cancer | nlx_157395 | SCR_010314 | 2026-09-12 12:57:17 | 0 | ||||||||
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Enzyme Mechanism Ontology Resource Report Resource Website 1+ mentions |
Enzyme Mechanism Ontology (RRID:SCR_010315) | EMO | controlled vocabulary, data or information resource, ontology | Ontology to describe the active components of the enzyme''s reactions (cofactors, amino acid residues and cognate ligands) and their roles in the reaction. EMO builds upon this by formalizing key concepts, and the relationships between them, necessary to define enzymes and their functions. This describes not only the general features of an enzyme, including the EC number (catalytic activity), 3D structure and cellular locations, but also allows for the detailed annotation of the mechanism. This mechanistic detail can be either at a gross level (overall reaction only), or the more detailed granularity of the steps and components required to effect the overall chemical transformation. | owl | is listed by: BioPortal | nlx_157397 | SCR_010315 | 2026-09-12 12:57:17 | 1 | |||||||||
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Enzyme Reaction Ontology for partial chemical perspectives Resource Report Resource Website 1+ mentions |
Enzyme Reaction Ontology for partial chemical perspectives (RRID:SCR_010316) | PIERO | controlled vocabulary, data or information resource, ontology | An enzyme ontology that deals with partial reactions (transformations) | owl | is listed by: BioPortal | nlx_157398 | SCR_010316 | 2026-09-12 12:57:17 | 1 | |||||||||
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Epilepsy Ontology Resource Report Resource Website |
Epilepsy Ontology (RRID:SCR_010317) | EPILONT | controlled vocabulary, data or information resource, ontology | Ontology about the epilepsy domain and epileptic seizures. Based on the diagnosis proposed by the International League Against Epilepsy (ILAE). | owl | is listed by: BioPortal | nlx_157399 | SCR_010317 | 2026-09-12 12:57:17 | 0 | |||||||||
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Loggerhead Nesting Ontology Resource Report Resource Website |
Loggerhead Nesting Ontology (RRID:SCR_010318) | LHN | controlled vocabulary, data or information resource, ontology | An ontology for Loggerhead sea turtle (Caretta caretta) nesting behavior, based on the published ethogram of Hailman and Elowson. A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms. | obo | is listed by: BioPortal | nlx_157459 | SCR_010318 | 2026-09-12 12:57:17 | 0 | |||||||||
|
Fire Ontology Resource Report Resource Website |
Fire Ontology (RRID:SCR_010320) | FIRE | controlled vocabulary, data or information resource, ontology | Ontology to represent the set of concepts about the fire occurring in natural vegetation, its characteristics, causes and effects, with focus on Cerrado vegetation domain. The fire plays a determinant role on the structure and composition of Cerrado physiognomies. | owl | is listed by: BioPortal | nlx_157404 | SCR_010320 | 2026-09-12 12:57:17 | 0 | |||||||||
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Flora Phenotype Ontology Resource Report Resource Website |
Flora Phenotype Ontology (RRID:SCR_010321) | FLOPO | controlled vocabulary, data or information resource, ontology | Ontology generated from the Flora Malesiana, Flora Gabon, Flora of Central Africa, and a collection of Kew''s African Floras. Every class in the ontology has at least one taxon annotation. This is the pre-classified version of the ontology; the original OWL file is at http://jagannath.pdn.cam.ac.uk/plant/flopo-unclassified.owl | owl | is listed by: BioPortal | nlx_157406 | http://wiki.pro-ibiosphere.eu/wiki/Traits_Task_Group | SCR_010321 | 2026-09-12 12:57:17 | 0 | ||||||||
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BioModels Ontology Resource Report Resource Website |
BioModels Ontology (RRID:SCR_010125) | BIOMODELS | controlled vocabulary, data or information resource, ontology | OWL Representation of the models in the BioModels repository. | owl | is listed by: BioPortal | nlx_157326 | https://code.google.com/p/sbmlharvester/ | SCR_010125 | 2026-09-12 12:57:15 | 0 | ||||||||
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Johns Hopkins University; Maryland; USA Resource Report Resource Website 10+ mentions |
Johns Hopkins University; Maryland; USA (RRID:SCR_010247) | JHU | university | Johns Hopkins University is private research university in Baltimore, Maryland. Founded in 1876, university was named for its first benefactor, American entrepreneur, abolitionist, and philanthropist Johns Hopkins. | private, university, Baltimore, Maryland |
uses: DIRECT2experts is affiliated with: Diabetes Research Centers is related to: Alzheimers Disease Genetics Consortium is related to: International AMD Genetics Consortium is related to: ABX Guide is related to: Clinical and Translational Science Awards Consortium is parent organization of: SynaptomeDB is parent organization of: Johns Hopkins University School of Medicine; Baltimore, Maryland; USA is parent organization of: sim4cc is parent organization of: MRI Studio is parent organization of: CKID A Prospective Cohort Study of Kidney Disease in Children is parent organization of: Nonalcoholic Steatohepatitis Clinical Research Network is parent organization of: ASprofile is parent organization of: GlimmerHMM is parent organization of: Neurogenetics and Behavior Center is parent organization of: Human Proteinpedia is parent organization of: Schramm Lab Spinal Cord Atlases is parent organization of: NetPath is parent organization of: Academic Drug Discovery Consortium is parent organization of: CardioVascular Research Grid (CVRG) is parent organization of: Johns Hopkins University; Undergraduate Neuroscience Program is parent organization of: Bowtie is parent organization of: FLASH is parent organization of: TMAJ is parent organization of: Gastroparesis Clinical Research Consortium is parent organization of: HPRD - Human Protein Reference Database is parent organization of: Atlweb: Alternatives to Animal Testing is parent organization of: Center for Inherited Disease Research is parent organization of: The Protein Coil Library is parent organization of: HIV Guide is parent organization of: Johns Hopkins School of Medicine Department of Molecular and Comparative Pathobiology is parent organization of: Classic Articles in Visual Perception is parent organization of: Experimental Man Blog is parent organization of: MYC Cancer Gene is parent organization of: JIST: Java Image Science Toolkit is parent organization of: DOTS WM tract segmentation is parent organization of: JHU Proj. in Applied Medical Imaging is parent organization of: LDDMM is parent organization of: Johns Hopkins Bloomberg School of Public Health; Maryland; USA is parent organization of: Genetic Resources Core Facility is parent organization of: LS-SNP/PDB is parent organization of: JHU Deep Sequencing and Microarray Core is parent organization of: Glimmer is parent organization of: Johns Hopkins University Labs and Facilities is parent organization of: CRAVAT is parent organization of: John Hopkins University, In-Vivo Cellular Molecular Imaging Center is parent organization of: RosettaDock is parent organization of: CoGAPS is parent organization of: Blox is parent organization of: National Resource for Quantitative Functional MRI is parent organization of: Myrna is parent organization of: CAWorks is parent organization of: Principal Components Analysis of Scalar, Vector, and Mesh Vertex Data is parent organization of: Longitudinal MS Lesion Imaging Archive is parent organization of: Image Synthesis Tools is parent organization of: Atlases of amygdala and hippocampus for pediatric populations is parent organization of: HISAT2 is parent organization of: neurodata is parent organization of: Johns Hopkins University Integrated Imaging Center Core Facility is parent organization of: Center for Computational Biology at JHU is parent organization of: TopHat is parent organization of: PyRosetta is parent organization of: Ecosystem for Multi-modal Brain-behavior Experimentation and Research is parent organization of: Brain Observatory Storage Service and Database (BossDB) is parent organization of: Johns Hopkins University School of Medicine Genetic Resources Core Facility |
, nlx_97251, Wikidata: Q193727, GRID: grid.21107.35, ISNI: 0000 0001 2171 931, Crossref Funder ID: 100007880 | https://ror.org/00za53h95 | SCR_010247 | 2026-09-12 12:57:16 | 21 | ||||||||
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Autism Spectrum Disorder Phenotype Ontology Resource Report Resource Website |
Autism Spectrum Disorder Phenotype Ontology (RRID:SCR_010006) | ASDPTO | controlled vocabulary, data or information resource, ontology | Ontology that encapsulates the Autism Spectrum Disorder behavioral phenotype, informed by the standard ASD assessment instruments and the currently known characteristics of this disorder. | owl, phenotype, behavior | is listed by: BioPortal | Autism Spectrum Disorder | PMID:24163114 | nlx_157322 | http://purl.bioontology.org/ontology/ASDPTO | SCR_010006 | 2026-09-12 12:57:15 | 0 | ||||||
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UCL Bioinformatics Group Resource Report Resource Website 100+ mentions |
UCL Bioinformatics Group (RRID:SCR_010248) | data or information resource, organization portal, portal, software repository, software resource | Group headed by Professor David Jones, and was originally founded as the Joint Research Council funded Bioinformatics Unit within the Department of Computer Science at University College London. Supports the following tools: Protein Structure Prediction Threading (THREADER) Ab initio folding simulations Secondary structure prediction (PSIPRED) Protein disorder prediction (DISOPRED) Protein domain prediction (DomPred) Database of protein disorder (DisoDB) Protein Sequence Analysis Protein function prediction (ffpred) Metsite: Metal binding residue prediction HSPred : Protein-protein interaction characterisation Amino acid substitution matrices Hidden Markov Models (collaboration with N. Goldman, Cambridge, & J. Thorne, NCSU) Genome Analysis Genomic fold recognition (GenTHREADER) Genome annotation using software agents Protein Structure Classification CATH (collaboration with J. Thornton & C. Orengo, UCL Biochemistry) Transmembrane Protein Modelling MEMSAT & MEMSATSVM Folding In Lipid Membranes (FILM) MEMPACK Biological Applications of Data-mining and Machine Learning Techniques Information extraction for biological research (BioRat) Microarray Analysis Data integration for microarray analysis Data visualization Systems Biology Systems biology applied to stem cells Legacy Services (to be retired shortly) Comparison of structure classifications (CATH/SCOP/FSSP) Genomic Threading Database (GTD) | FASEB list | has parent organization: University College London; London; United Kingdom | nlx_156885 | SCR_010248 | 2026-09-12 12:57:16 | 196 | ||||||||||
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University of Texas El Paso Analytical Cytology Core Facility Resource Report Resource Website |
University of Texas El Paso Analytical Cytology Core Facility (RRID:SCR_010137) | UTEP Analytical Cytology, Analytical Cytology, | access service resource, availability annotation standard, core facility, data or information resource, narrative resource, nif annotation standard, service resource, standard specification, this resource is no longer in service | THIS RESOURCE IS NO LONGER IN SERVCE, documented January 23, 2019. Core facility that provides the following services: Zeiss LD-5 Pascal Scanning Confocal Microscope/Assisted access, Zeiss Axioskop Epifluorescence Microscope/Assisted access, Zeiss EM-10 Transmission Electron Microscope/Assisted access, Microscopy sample preparation, Observation and photography service. The Analytical Cytology Core Facility provides assistance in the designing of protocols and the use of sophisticated, well maintained and supervised equipment. Each microscope is equipped with software for image analysis, image processing and printing of digital images. Service contracts are maintained on each of the microscopes. Computers and software are regularly upgraded. Confocal workshops are held regularly to familiarize users with new techniques and new protocols. The specific aims of the Analytical Cytology Core Facility (ACCF) are: 1. to train users in the design of protocols, the fixations, sectioning, cryofixations, immunolocalizations, the use of the Zeiss EM-10, the Zeiss Axioskop epifluorescence microscope and the Zeiss Pascal scanning confocal microscope with image analysis and image processing, 2. to support new faculty in realizing their research objectives that utilize microscopy, 3. to support the productivity of the Infectious Diseases and Immunology unit, the Toxicology unit, the Neuroscience/Metabolic Disorders unit, the Statistical Consulting Laboratory and the Bioinformatics unit by assisting faculty, undergraduate, masters, doctoral and postdoctoral students in advancing biomedical research, 4. to maintain and upgrade equipment and expertise and; 5. to provide core services anticipating self-sustaining maintenance of the core facility. | confocal microscopy, fluorescent microscopy, transmission electron microscopy, labeling, immunohistochemistry assay, photography |
is listed by: Eagle I has parent organization: University of Texas at El Paso |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156615 | http://science.utep.edu/bbrc/General/analytical-cytology | SCR_010137 | , Cytology, UTEP, Analytical | 2026-09-12 12:57:15 | 0 | ||||||
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International Classification of Primary Care Resource Report Resource Website |
International Classification of Primary Care (RRID:SCR_010262) | ICPC | controlled vocabulary, data or information resource, ontology | Ontology of the international classification of primary care (ICPC). Denmark: World Organisation of Family Doctors, 1993. | umls | is listed by: BioPortal | nlx_157453 | SCR_010262 | 2026-09-12 12:57:16 | 0 | |||||||||
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VassarStats Resource Report Resource Website 1000+ mentions |
VassarStats (RRID:SCR_010263) | software resource | Tools for performing statistical computation including: Clinical Research Calculators Probabilities Distributions Frequency Data Proportions Ordinal Data Correlation & Regression t-Tests & Procedures ANOVA ANCOVA | has parent organization: Vassar College; New York; USA | nlx_156916 | SCR_010263 | VassarStats: Website for Statistical Computation | 2026-09-12 12:57:16 | 1062 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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