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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GOHyperGAll Resource Report Resource Website 1+ mentions |
GOHyperGAll (RRID:SCR_005766) | GOHyperGAll | data analysis software, data processing software, software application, software resource | To test a sample population of genes for overrepresentation of GO terms, the R/BioC function GOHyperGAll computes for all GO nodes a hypergeometric distribution test and returns the corresponding p-values. A subsequent filter function performs a GO Slim analysis using default or custom GO Slim categories. Basic knowledge about R and BioConductor is required for using this tool. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, gene ontology, annotation, statistical analysis, slimmer-type tool |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of California at Riverside; California; USA |
PMID:18354039 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149267 | SCR_005766 | 2026-09-12 12:56:31 | 4 | |||||||
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GlycoPeptideSearch Resource Report Resource Website |
GlycoPeptideSearch (RRID:SCR_005767) | GPS | software resource | GlycoPeptideSearch (GPS) simplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra. Results are tabulated in Excel format. Accelerate and simplify interpretation of N-glycopeptide CID MS/MS spectra using GlycoPeptideSearch (GPS). This tool is designed for tandem mass-spectra acquired from proteolytic digests of purified glycoproteins modified with N-glycans and analyzed by LC-MS/MS and CID. The search yields an Excel spreadsheet of N-glycopeptide matches consistent with the spectra. GPS requires two files as input - an mzXML (or other open spectral format) file of glycopeptide CID tandem mass-spectra and a text file (.txt) of peptide sequences containing the N-linked glycosylation motif NXS/T. Spectral datafiles must be converted from raw vendor formats, such as .RAW or .wiff, to an open peak list format (mzXML preferred). In addition to these two input files, the user must specify one or more glycan databases (provided in the software package). The database(s) selected by the user will be used to match glycan structures in the glycopeptide spectra. The output is an Excel spreadsheet with one or more rows for spectra within the dataset that contain evidence of glycoprotein fragmentation, paired with one or more proposed glycopeptide matches for each spectrum. Glycopeptide matches consist of a peptide-glycan pair, with the peptide drawn from the user-supplied peptide file, and the glycan selected from a glycan database(s). The human subset of the GlycomeDB glycan database is provided, and N-linked glycans are automatically selected from it. GPS interprets glycopeptide CID MS/MS spectra by first requiring MS/MS spectra contain evidence of glycopeptide fragmentation - the oxonium ion peaks (m/z 204 - Hex, m/z 366 - HexNAc), and N-glycopeptide core specific peaks (peptide, peptide + HexNAc, peptide + HexNAc-HexNAc, peptide + HexNAc-HexNAc-Hex). For spectra that meet these initial criteria, for a particular peptide, a mass-based search of one or more glycan databases looks for glycans which capture the remaining mass of the spectral precursor. Additional spectral information may be used to narrow the number of matches, and equivalent glycan topologies may be collapsed to a single peptide-glycan pair. GPS also provides N-glycan compositions with the necessary additional mass, even if no glycan with the composition is present in the glycan database(s). GPS can either be run from the command-line or by using its graphical user interface. We recommend the msconvert (or MSConvertGUI) software from the ProteoWizard project to convert spectral datafiles from vendor formats such as .wiff and .RAW into mzXML. | peptide, glyopeptide, glycoprotein, mass-spectra, ms/ms spectra | has parent organization: Edwards Lab | PMID:22239659 | nlx_149231 | SCR_005767 | 2026-09-12 12:56:31 | 0 | ||||||||
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Expression Atlas of the Marmoset Resource Report Resource Website 1+ mentions |
Expression Atlas of the Marmoset (RRID:SCR_005760) | Marmoset Expression Atlas, RIKEN Marmoset Expression Atlas | atlas, data or information resource, data set, expression atlas | Database of gene expression in the marmoset brain.Comparative anatomy of marmoset and mouse cortex from genomic expression. Atlas comparing brain of neonatal marmoset with mouse using in situ hybridization. | gene, marmoset, gene expression, neonatal, brain, in situ hybridization, gene, cortex, thalamus, dorsal nucleus of lateral geniculate body, dlgn, subplate, hippocampus, primary somatosensory cortex, btbd3, cdh6, cdh8, cplx3, ctgf, epha4, epha5, epha6, epha7, efna5, er81, foxp2, gfralpha1, kitl, lhx9, nr1d1, nr4a2, ntng2, relin, roralpha, satb2, sema6a, tbr1, tcf7l2, zic1, zic4, genomic expression |
is used by: NIF Data Federation has parent organization: RIKEN Brain Science Institute |
RIKEN Brain Science Institute ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Funding Program for World-Leading Innovative RD on Science and Technology |
PMID:22496550 | nlx_149225 | http://mmtd.brain.riken.jp/P0marmoset/ | SCR_005760 | Marmoset Gene List, Comparative Anatomy of Marmoset and Mouse Cortex from Genomic Expression, Comparative Anatomy of Marmoset Mouse Cortex from Genomic Expression | 2026-09-12 12:56:31 | 5 | |||||
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Finnish Cancer Registry Resource Report Resource Website 1+ mentions |
Finnish Cancer Registry (RRID:SCR_005881) | Finnish Cancer Registry | institution | The Finnish Cancer Registry maintains a nation-wide database on all cancer cases in Finland going back to 1953. It is also an internationally active institute for statistical and epidemiological cancer research. The Mass Screening Registry is a department of the Finnish Cancer Registry, and is responsible of planning and evaluating national cancer screening programs in Finland. The site contains information on cancer research and up to date statistics on the prevalence of different types of cancer in Finland, the Nordic countries and on a global level. The web pages include information for participants in cancer screening and for professionals involved in organizing such screening. | Cancer | Cancer Society of Finland | grid.424339.b, nlx_149446, ISNI: 0000 0000 8634 0612 | https://ror.org/00j15sg62 | SCR_005881 | 2026-09-12 12:56:32 | 8 | ||||||||
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ScyTek Laboratories Resource Report Resource Website 100+ mentions |
ScyTek Laboratories (RRID:SCR_005919) | commercial organization | An Antibody supplier | nlx_152455 | SCR_005919 | 2026-09-12 12:56:33 | 109 | ||||||||||||
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VectorBase Resource Report Resource Website 500+ mentions |
VectorBase (RRID:SCR_005917) | VectorBase | data or information resource, data repository, database, service resource, storage service resource | Bioinformatics Resource Center for invertebrate vectors. Provides web-based resources to scientific community conducting basic and applied research on organisms considered potential agents of biowarfare or bioterrorism or causing emerging or re-emerging diseases. | blast, clustalw, hmmer, vector, genomics, genome, sequence, population, insecticide resistance, annotation, microarray, gene expression, anatomy, pathogen, human, transcript, transcriptome, protein, proteome, mitochondria sequence, bioinformatics resource center, pathogen, arthropoda, vector control, ontology, software, source code, mitochondrial sequence, data analysis service, image collection, FASEB list |
is recommended by: National Library of Medicine is listed by: re3data.org is related to: Clustal W2 is related to: AnoBase: An Anopheles database is related to: Hmmer has parent organization: European Bioinformatics Institute has parent organization: University of Notre Dame; Indiana; USA |
European Union ; Evimalar network of excellence 242095; INFRAVEC 228421; NIAID |
PMID:22135296 PMID:19028744 PMID:18262474 PMID:18237287 PMID:17145709 |
Restricted | nif-0000-03624, r3d100010880 | https://doi.org/10.17616/R3CK6B | SCR_005917 | VectorBase - Bioinformatics Resource for Invertebrate Vectors of Human Pathogens, VectorBase, vector base | 2026-09-12 12:56:33 | 881 | ||||
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MAGMA Resource Report Resource Website 100+ mentions |
MAGMA (RRID:SCR_005757) | MAGMA | software resource | Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem. | gene, genetic mapping, algorithm, genomics, single nucleotide polymorphism, population study, haplotype-block elucidation, java | has parent organization: SourceForge | Juvenile Diabetes Research Foundation | PMID:12875658 | Open unspecified license | nlx_149220 | SCR_005757 | Multiobjective Analyzer for Genetic Marker Acquisition, MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition | 2026-09-12 12:56:31 | 495 | |||||
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North Texas Traumatic Brain Injury Model System Resource Report Resource Website |
North Texas Traumatic Brain Injury Model System (RRID:SCR_005879) | NT-TBIMS | data or information resource, portal, topical portal | The 16 affiliated Model System centers throughout the United States are responsible for gathering and submitting the core data set to the national database as well as conducting research studies on traumatic brain injury (TBI) both in collaboration with the other centers and within our own site. Through our research we hope to learn more about TBI and about the issues and concerns of people with TBI. Our goals are to improve the outcome and quality of life for people who have had brain injuries and for those who are caring for the person with a TBI. The North Texas Traumatic Brain Injury Model System (NT-TBIMS) pools the efforts and talents of individuals from the Departments of Neurosurgery, Neurology, Physical Medicine and Rehabilitation, Psychiatry (Neuropsychiatry), and Neuroradiology of the two leading medical institutions in the North Texas region. To be a patient involved in the research being conducted by the North Texas Traumatic Brain Injury Model System you must have suffered a TBI, be at least 16 years of age, have received initial treatment for the TBI at either Parkland Health and Hospital System or Baylor University Medical Center and then have received rehabilitative care at either Parkland, University Hospital Zale-Lipshy, or Baylor Institute for Rehabilitation. The patient must also be able to understand and sign an informed consent to participate or, if unable, have a family member or a legal guardian who understands the form sign the informed consent for the patient. | brain injury, brain, injury, traumatic brain injury, clinical, research | has parent organization: University of Texas Southwestern Medical Center; Texas; USA | Traumatic Brain Injury | National Institute on Disability and Rehabilitation Research H133A070027 | nlx_149440 | SCR_005879 | North Texas TBI Model System, North Texas Traumatic Brain Injury Model System (NT-TBIMS) | 2026-09-12 12:56:32 | 0 | ||||||
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Universal Numerical Fingerprint Resource Report Resource Website |
Universal Numerical Fingerprint (RRID:SCR_005912) | UNF | data or information resource, narrative resource, standard specification | Citation standard that offers proper recognition to authors as well as permanent identification through the use of global, persistent identifiers in place of URLs, which can change frequently. Use of universal numerical fingerprints (UNFs) guarantees to the scholarly community that future researchers will be able to verify that data retrieved is identical to that used in a publication decades earlier, even if it has changed storage media, operating systems, hardware, and statistical program format. | identifier, universal numerical fingerprint, data citation |
is listed by: FORCE11 has parent organization: Dataverse Network Project |
nlx_149488 | SCR_005912 | Standard: Universal Numerical Fingerprint, The Standard: Universal Numerical Fingerprint | 2026-09-12 12:56:33 | 0 | ||||||||
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AIDA Toolkit Resource Report Resource Website 1+ mentions |
AIDA Toolkit (RRID:SCR_005914) | data access protocol, software resource, software toolkit, web service | A generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model learning. | software toolkit, web service, search, learning, storage, workflow, text indexing, text statistics, metadata storage, metadata querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, model learning | is related to: Taverna | Open source, Available as a web service, Available for download | nlx_149497 | http://adaptivedisclosure.org/aida/ | SCR_005914 | Adaptive Information Disclosure Application Toolkit | 2026-09-12 12:56:33 | 1 | |||||||
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Icahn School of Medicine at Mount Sinai; New York; USA Resource Report Resource Website 10+ mentions |
Icahn School of Medicine at Mount Sinai; New York; USA (RRID:SCR_005793) | ISMMS, MSSM | university | Icahn School of Medicine at Mount Sinai, formerly Mount Sinai School of Medicine, is graduate medical school in Manhattan, New York City. Leader in medical and scientific training and education, biomedical research and patient care. | medicine, medical, school, university, doctorate, phd |
uses: Scizzle is affiliated with: BioJupies is related to: Alzheimers Disease Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: proMODMatcher is parent organization of: Enrichr is parent organization of: Neuropathology of CTE and Delayed Effects of TBI: Toward In-Vivo Diagnostics is parent organization of: NeuronStudio is parent organization of: Rayburst Open-Source Code is parent organization of: Volume Integration and Alignment System is parent organization of: Volume Integration and Alignment System Source Code is parent organization of: NeuroGL is parent organization of: TIFF Stack Sub-Sampler is parent organization of: Cre-X-Mice: A Database of Cre Transgenic Lines is parent organization of: Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory is parent organization of: Mount Sinai Biobank is parent organization of: ChEA is parent organization of: Kismeth is parent organization of: Lists2Networks is parent organization of: Mount Sianai Department of Neuroscience is parent organization of: NetworKIN is parent organization of: Mount Sinai Alzheimer's Disease Research Center is parent organization of: Manhattan HIV Brain Bank is parent organization of: Computational Neurobiology and Imaging Center is parent organization of: L1000 Characteristic Direction Signature Search Engine is parent organization of: L1000 Fireworks Display is parent organization of: Drug Gene Budger is parent organization of: COVID-19 Crowd Generated Gene and Drug Set Library is parent organization of: GeneOverlap is parent organization of: Datanator is parent organization of: BioSimulations is parent organization of: DE-Sim is parent organization of: Appyters is parent organization of: ezTrack project is parent organization of: Minian is parent organization of: TargetRanger is parent organization of: GeneRanger is parent organization of: Kinase Enrichment Analysis 3 is parent organization of: X2K Web is parent organization of: Diabetes Data and Hypothesis Hub is parent organization of: Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Transgenic and Genome Editing Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Metabolomics Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank and Research CoRE Facility is parent organization of: Icahn School of Medicine at Mount Sinai RNA Nanocore Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Biorepository and Pathology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Mount Sinai Cryo-EM CoRE Core Facility |
nlx_55912, grid.59734.3c, Crossref funder ID:100007277, ISNI:0000 0001 0670 2351, Wikidata:Q1950740 | https://ror.org/04a9tmd77 | SCR_005793 | Mount Sinai School of Medicine, Icahn School of Medicine, Icahn School of Medicine at Mount Sinai | 2026-09-12 12:56:31 | 12 | |||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
Biotechnology and Biological Sciences Research Council ; EMBL ; European Union |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-09-12 12:56:32 | 7512 | |||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-09-12 12:56:31 | 8 | |||||||
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SPLINTER Resource Report Resource Website 10+ mentions |
SPLINTER (RRID:SCR_005826) | SPLINTER | software resource | Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples. |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
Cancer | Free for academic / non-profit use, Commercial use requires license | OMICS_00100 | SCR_005826 | Short IN/DEL Prediction by Large deviation Inference and Non-linear True frequency Estimation by Recursion | 2026-09-12 12:56:32 | 13 | |||||||
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UM-BBD Resource Report Resource Website 1+ mentions |
UM-BBD (RRID:SCR_005787) | UM-BBD, UM-BBD enzymeID, UM-BBD pathwayID, UM-BBD reactionID, UM-BBD ruleID | analysis service resource, data analysis service, data or information resource, data set, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2014. Database containing information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. Its goal is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. The present database has been successfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students, and is being expanded primarily with the help of such students. In addition to reactions and pathways, this database also contains Biochemical Periodic Tables and a Pathway Prediction System. * Search the UM-BBD for compound, enzyme, microorganism, pathway, or BT rule name; chemical formula; chemical structure; CAS Registry Number; or EC code. * Go to Pathways and Metapathways in the UM-BBD * Lists of 203 pathways; 1400 reactions; 1296 compounds; 916 enzymes; 510 microorganism entries; 245 biotransformation rules; 50 organic functional groups; 76 reactions of naphthalene 1,2-dioxygenase; 109 reactions of toluene dioxygenase; Graphical UM-BBD Overview; and Other Graphics (Metapathway and Pathway Maps and Reaction Mechanisms). | enzyme, biocatalysis, biodegredation, chemical, pathway, reaction, microorganism, image, chemical compound, gene, enzymology | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Minnesota Supercomputing Institute ; Lhasa Limited ; University of Minnesota; Minnesota; USA ; European Union FP6 ALARM project ; NIH ; NSF 0543416; DOE DE-FG02-01ER63268; NIGMS R01GM56529; NSF 9630427 |
PMID:19767608 PMID:16381924 PMID:12519997 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03607, r3d100011317 | https://doi.org/10.17616/R33D0V | SCR_005787 | UM-BBD pathwayID, University of Minnesota Biocatalysis and Biodegradation Database, UM-BBD reactionID, Biocatalysis/Biodegradation Database, University of Minnesota Biocatalysis/Biodegradation Database, UM-BBD ruleID, Univeristy of Minnesota Biocatalysis/Biodegradation Database, UM-BBD enzymeID | 2026-09-12 12:56:31 | 9 | ||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | data or information resource, database, portal, project portal, service resource | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase works with: bedGraphToBigWig |
Alfred P. Sloan Foundation ; CISI ; David and Lucille Packard Foundation ; DOE ; HHMI ; NHGRI ; NIGMS GM52848; NIH ; NSF DBI 9809007; UC BIOTEuropean UnionH |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu, https://doi.org/10.17616/R3RK5C | SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-09-12 12:56:31 | 11041 | ||||||
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OMGN Resource Report Resource Website |
OMGN (RRID:SCR_005781) | OMGN | community building portal, data or information resource, portal, training resource | The Oomycete Molecular Genetics Research Collaboration Network (OMGN) is a network for research collaboration for investigators interested in oomycete molecular genetics and genomics. The goals of the OMGN is to facilitate the integration of these investigators into the community and to further strengthen the cooperative culture of this community. A particular emphasis is placed on training and integrating junior faculty and faculty from institutions under-represented in the U.S. research infrastructure. Because of their economic impact as plant pathogens, molecular, genetic and genomics studies are well advanced in many oomycete species. These organisms have served as lead species for the entire Stramenopiles lineage, a major radiation of crown eukaryotes, distinct from plants, animals and fungi. The oomycete molecular genetics community has a strong culture of collaboration and communication, and sharing of techniques and resources. With the recent blossoming of genetic and genomic tools for oomycetes, many new investigators, from a variety of backgrounds, have become interested in oomycete molecular genetics and genomics. The proposed network is open to all researchers with an interest in oomycete molecular genetics and genomics, either at an experimental or a computational level. Investigators new to the field are always welcome, especially those interested in saprophytes and animal pathogens. Goals of OMGN # Provide training to o��mycete molecular genetics researchers, especially those from smaller institutions, in the use of bioinformatics and genomics resources. # Promote the entry, participation and training of new investigators into the field of o��mycete genomics, particularly junior faculty and faculty from institutions under-represented in the U.S. research infrastructure. # Promote communication and collaboration, and minimize duplication of effort, within the worldwide o��mycete genomics community. # Support an O��mycete Genomics Resources Center to maintain and distribute training and research materials produced by community genomics projects. The network''s activities have been supported by two grants from the NSF Research Collaboration Networks in Biology program. | oomycete, molecular genetics, genomics, saprophyte, animal, pathogen, stramenopile | has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA | NSF EF 0130263 | nlx_149251 | SCR_005781 | OMGN - Oomycete Molecular Genetics Research Collaboration Network, Oomycete Molecular Genetics Research Collaboration Network | 2026-09-12 12:56:31 | 0 | |||||||
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GOEx - Gene Ontology Explorer Resource Report Resource Website 10+ mentions |
GOEx - Gene Ontology Explorer (RRID:SCR_005779) | GOEx | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. Gene Ontology Explorer (GOEx) combines data from protein fold changes with GO over-representation statistics to help draw conclusions in proteomic experiments. It is tightly integrated within the PatternLab for Proteomics project and, thus, lies within a complete computational environment that provides parsers and pattern recognition tools designed for spectral counting. GOEx offers three independent methods to query data: an interactive directed acyclic graph, a specialist mode where key words can be searched, and an automatic search. A recent hack included in GOEx is to load the sparse matrix index file directly into GOEx, instead of going through the report generation using the AC/T-fold methods. This makes it easy for GOEx to analyze any list of proteins as long as the list follows the index file format (described in manuscript) . Please note that if using this alternative strategy, there will be no protein fold information. Platform: Windows compatible | proteomics, visualization, statistical analysis, gene ontology, parse, pattern recognition, spectral counting, analysis, protein fold |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Scripps Research Institute |
CNPq ; CAPES ; FAPERJ BBP grant ; PAPES ; PDTIS ; Ary Frauzino Foundation ; NIAID ; NIH ; genesis molecular biology laboratory ; Fiocruz-INCA collaboration ; NIAID UCSD/MCB0237059; NCRR P41RR011823; NIMH 5R01 MH067880 |
PMID:19239707 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149249 | http://pcarvalho.com/patternlab/goex.shtml | SCR_005779 | Gene Ontology Explorer, GO Explorer | 2026-09-12 12:56:31 | 32 | ||||
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AppliChem Resource Report Resource Website 1000+ mentions |
AppliChem (RRID:SCR_005814) | commercial organization | An Antibody supplier | nlx_152277 | SCR_005814 | PanReac AppliChem, AppliChem GmbH | 2026-09-12 12:56:31 | 4849 | |||||||||||
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OWLTools Resource Report Resource Website 10+ mentions |
OWLTools (RRID:SCR_005732) | OWLTools | software resource | OWLTools (aka OWL2LS - OWL2 Life Sciences) is a java API for accessing ontologies in either OBO or OWL. OWLTools provides a bio-ontologies friendly wrapper on top of the Manchester OWL API. It provides many features, including: * convenience methods for OBO-like properties such as synonyms, textual definitions, obsoletion, replaced_by * simple graph-like operations over ontologies * visualization using the QuickGO graphs libraries Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, ontology |
is listed by: Gene Ontology Tools is related to: OBO has parent organization: Gene Ontology has parent organization: Google Project Hosting is parent organization of: OwlSim |
Open unspecified license - Free for academic use | nlx_149192 | SCR_005732 | OWL2LS - OWL2 Life Sciences, OWL Tools | 2026-09-12 12:56:30 | 18 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
