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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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go-perl Resource Report Resource Website 10+ mentions |
go-perl (RRID:SCR_005730) | go-perl | software resource | go-perl is a set of Perl modules for parsing, manipulating and exporting ontologies and annotations. It includes parsers for the OBO and GO gene association file formats. It has a graph-based object model with methods for graph traversal. For more details, see the documentation included with the modules. go-perl comes bundled with XSL (Extensible Stylesheet Language) transforms (which can also be used independently of Perl, provided you have files in OBO-XML format), as well as scripts that can be used as standalone tools. Installation should be simple, provided you have some experience with Perl and CPAN; see the INSTALL file for details. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | ontology, annotation, software library, slimmer-type tool, parser |
is listed by: Gene Ontology Tools is related to: OBO is related to: go-moose is related to: go-db-perl has parent organization: Comprehensive Perl Archive Network has parent organization: Gene Ontology |
Free for academic use | nlx_149190 | SCR_005730 | 2026-08-15 11:23:13 | 11 | ||||||||
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GraphProt Resource Report Resource Website 10+ mentions |
GraphProt (RRID:SCR_005842) | GraphProt | software resource | Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete. | sequence-binding preference, structure-binding preference, rna-binding protein, high-throughput sequencing, clip-seq, rnacompete, rna, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Freiburg; Baden-Wurttemberg; Germany |
PMID:24451197 | Free, Public | OMICS_02252, biotools:graphprot | https://bio.tools/graphprot | SCR_005842 | 2026-08-15 11:23:15 | 39 | ||||||
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brain-development.org Resource Report Resource Website 100+ mentions |
brain-development.org (RRID:SCR_005838) | brain-development.org | image analysis software, data processing software, portal, registration software, data or information resource, software application, data set, software resource, atlas | brain-development.org hosts data and resources used in computational analysis of brain development, including MRI data sets of developing human, software tools, atlases, protocols and software. Several different atlas datasets are available including: * Adult * Pediatric * Neonatal (T2 Templates, Probability Maps) * Neonatal (High-definition, T1 and T2 Templates, Probability Maps) * Fetal (High-definition, T2 Templates, Probability Maps) * Atlas software Anatomical segmentation protocols are available, as well as an Image Registration Toolkit. | atlas, data set, software tool, computational analysis, brain development, mri, data set, developing human, protocol, atlas software, adult, pediatric, neonatal, fetal, t1, t2, probability map, brain, image | has parent organization: Imperial College London; London; United Kingdom | nlx_149359 | SCR_005838 | brain-development.org at imperial college | 2026-08-15 11:23:18 | 163 | ||||||||
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IXI dataset Resource Report Resource Website 10+ mentions |
IXI dataset (RRID:SCR_005839) | IXI dataset | data or information resource, data set, portal, project portal | Data set of nearly 600 MR images from normal, healthy subjects, along with demographic characteristics, collected as part of the Information eXtraction from Images (IXI) project available for download. Tar files containing T1, T2, PD, MRA and DTI (15 directions) scans from these subjects are available. The data has been collected at three different hospitals in London: * Hammersmith Hospital using a Philips 3T system * Guy''s Hospital using a Philips 1.5T system * Institute of Psychiatry using a GE 1.5T system | neuroimaging, structural mri assay, magnetic resonance angiography, nifti, t1, t2, pd, dti, demographic, normal, healthy, adult, mri, brain, image collection |
is used by: NIF Data Federation has parent organization: Imperial College London; London; United Kingdom |
Normal, Healthy | EPSRC GR/S21533/02 | Acknowledgement requested | nlx_149360 | http://brain-development.org/ | SCR_005839 | Information eXtraction from Images dataset | 2026-08-15 11:23:15 | 38 | ||||
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AMAT Resource Report Resource Website 10+ mentions |
AMAT (RRID:SCR_005836) | AMAT | data or information resource, database, software resource | AMAT is a Matlab-based, open source interface for searching fMRI coordinates together with a simple database of coordinates. The AMAT database is deliberately designed to be minimal. Effectively, the database reproduces the tables of XYZ coordinates which are common in fMRI papers. Each coordinate is associated with the anatomical label given by the authors of the original paper, a ag for Talaraich or MNI coordinates, a very brief description of the description of the functional task or contrast which activated this coordinate, and the PubMed ID of the published paper. The latter links directly to the abstract in PubMed and allows the user to retrieve the original publication. Anatomical information labeling a coordinate as a particular Brodmann area or functional region is optional, and is normally only included if the authors of the original paper included these labels. No other information is stored. | neuroimaging, fmri |
is related to: NIDAG: Neuroimaging Data Access Group has parent organization: University of Nottingham; Nottingham; United Kingdom |
Autism Speaks ; ESRC RES-061-25-0138 |
PMID:19442743 | nlx_149358 | SCR_005836 | AMAT: A meta-analysis toolbox | 2026-08-15 11:23:15 | 26 | ||||||
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University of Maryland School of Medicine; Maryland; USA Resource Report Resource Website 1+ mentions |
University of Maryland School of Medicine; Maryland; USA (RRID:SCR_005837) | UMSOM | university | Medical school of the University of Maryland, Baltimore and is affiliated with the University of Maryland Medical Center and Medical System. Located in Baltimore City, Maryland, U.S. |
is affiliated with: Integrative Human Microbiome Project has parent organization: University of Maryland; Maryland; USA is parent organization of: ECO is parent organization of: NICHD Brain and Tissue Bank for Developmental Disorders is parent organization of: Maryland Brain Collection is parent organization of: HMP Data Analysis and Coordination Center is parent organization of: Circleator is parent organization of: VIROME is parent organization of: Ergatis is parent organization of: Manatee is parent organization of: Maryland Genetics of Interstitial Cystitis is parent organization of: Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Cell Culture and Engineering is parent organization of: Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Mouse Models and Biobank is parent organization of: Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Antibody Validation and Vector Core is parent organization of: Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center is parent organization of: Baltimore Polycystic Kidney Disease (PKD) Research and Clinical Core Center Clinical and Translational Core Resource is parent organization of: Mid-Atlantic Nutrition Obesity Research Center Molecular Genetics and Nutrigenomics Core is parent organization of: Mid-Atlantic Nutrition Obesity Research Center Biostatistics and Medical Informatics Subcore is parent organization of: Mid-Atlantic Nutrition Obesity Research Center Biological Mechanisms and Functional Genomics Core is parent organization of: Mid-Atlantic Nutrition Obesity Research Center Clinical and Translational Research Core is parent organization of: Mid-Atlantic Nutrition Obesity Research Center is parent organization of: NeMOarchive is parent organization of: gene Expression Analysis Resource is parent organization of: Maryland University School of Medicine Flow Cytometry and Mass Cytometry Core Facility is parent organization of: Human Disease Ontology is parent organization of: University of Maryland School of Medicine Baltimore Electron Microscopy Core Imaging Facility |
nlx_51230 | SCR_005837 | University of Maryland School of Medicine | 2026-08-15 11:23:18 | 2 | |||||||||
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Human Adenovirus Type Classification Resource Report Resource Website 100+ mentions |
Human Adenovirus Type Classification (RRID:SCR_005753) | HAdV Type Classification | service resource, analysis service resource, production service resource, knowledge environment | The Human Adenovirus Type Classification coordinates the naming of candidate new types, prior to manuscript submission for peer review. This resource contains a method of submitting candidate HAdV, criteria for a new HAdV type, and a Serotyping tool, which displays all potential types corresponding to the query serotype entered by a user. The criteria are based on discussions at the International Adenovirus Meeting (Dobog��k, Hungary; 26-30 April, 2009) and the NIH Human Adenovirus Working Group Workshop (Bethesda, MD. USA; 3 February 2011), which are summarized in a Letter to the Editor. | hadv, human adenovirus, adenovirus, classification, serotyping, genotyping, genome, nucleotide sequence, human adenovirus working group, serotype | has parent organization: George Mason University; Virginia; USA | Adenovirus | nlx_149215 | SCR_005753 | 2026-08-15 11:23:18 | 153 | ||||||||
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Crystallography Open Database (COD) Resource Report Resource Website 10+ mentions |
Crystallography Open Database (COD) (RRID:SCR_005874) | COD | database, data repository, storage service resource, data or information resource, service resource | Database of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers. It currently contains ~291204 entries (July 2014) in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality. Deposit your data: An interface allows you to upload, validate and edit CIF files before submitting them for deposition. | inorganic, metal-organic, organic, molecule, structure, small molecule, compound, mineral, crystal structure, crystallography, polymorphism, crystal, organic compound |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org has parent organization: Vilnius University; Vilnius; Lithuania |
Research Council of Lithuania contract MIP-124/2010 | PMID:22070882 PMID:22477773 |
Public domain, The community can contribute to this resource, Acknowledgement requested | r3d100010213, nlx_149430 | https://doi.org/10.17616/R37S31 | SCR_005874 | COD - Crystallography Open Database, Crystallography Open Database, Crystallography Open Database (COD), COD | 2026-08-15 11:23:18 | 23 | ||||
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CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | database, production service resource, data analysis service, data or information resource, service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-08-15 11:23:17 | 20 | ||||||
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National Archive of Computerized Data on Aging (NACDA) Resource Report Resource Website 10+ mentions |
National Archive of Computerized Data on Aging (NACDA) (RRID:SCR_005876) | NACDA | database, topical portal, data repository, storage service resource, portal, data or information resource, service resource | Archive of data relevant to gerontological and aging research. Used to advance research on aging. Subjects include demographic, social, economic, and psychological characteristics of older adults, physical health and functioning of older adults, and health care needs of older adults. NACDA staff represents team of professional researchers, archivists and technicians who work together to obtain, process, distribute, and promote data relevant to aging research. | gerontology, secondary analysis, data set, age, intelligence, life span, productive, late adult human |
is recommended by: National Library of Medicine lists: Social Environment and Biomarkers of Aging Study in Taiwan lists: Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) is listed by: re3data.org is related to: Alameda County Health and Ways of Living Study is related to: Charleston Heart Study is related to: Census Microdata Samples Project is related to: Chinese Longitudinal Healthy Longevity Survey (CLHLS) is related to: Early Indicators of Later Work Levels Disease and Death (EI) - Union Army Samples Public Health and Ecological Datasets is related to: Cross-National Equivalent Files is related to: National Survey of Midlife Development in the United States is related to: Precursors of Premature Disease and Death is related to: New Beneficiary Data System is related to: National Survey of Self-Care and Aging is related to: Aging Status and Sense of Control (ASOC) has parent organization: Inter-university Consortium for Political and Social Research (ICPSR) is parent organization of: Established Populations for Epidemiologic Studies of the Elderly is parent organization of: National Survey of the Japanese Elderly is parent organization of: Piedmont Health Survey of the Elderly is parent organization of: Second Malaysian Family Life Survey is parent organization of: Longitudinal Study of Generations is parent organization of: Longitudinal Study of Elderly Mexican American Health is parent organization of: Matlab Health and Socio-Economic Survey is parent organization of: National Long Term Care Survey is parent organization of: National Nursing Home Survey Follow-Up is parent organization of: National Social Life Health and Aging Project (NSHAP) is parent organization of: National Survey of Families and Households |
Aging | NIA | Restricted | nlx_149438, r3d100010259 | https://www.icpsr.umich.edu/icpsrweb/NACDA/index.jsp, https://doi.org/10.17616/R3Z31W | SCR_005876 | , NACDA, National Archive of Computerized Data on Aging | 2026-08-15 11:23:18 | 21 | ||||
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Antibodies Incorporated Resource Report Resource Website 1+ mentions |
Antibodies Incorporated (RRID:SCR_005877) | commercial organization | An Antibody supplier | nlx_152274 | SCR_005877 | 2026-08-15 11:23:18 | 1 | ||||||||||||
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Dryad Digital Repository Resource Report Resource Website 1000+ mentions |
Dryad Digital Repository (RRID:SCR_005910) | database, data repository, storage service resource, data or information resource, service resource | International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository. | international, digital, repository, curated, data, collection, scientific, medical, publication, dataset, FASEB list |
is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: CINERGI is listed by: re3data.org is listed by: Connected Researchers is listed by: DataCite is listed by: FAIRsharing is related to: ImpactStory is related to: Connected Researchers has parent organization: NESCent - National Evolutionary Synthesis Center has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: University of California; California; USA |
Institute for Museum and Library Services ; JISC ; NSF ; European Commission |
DOI:10.25504/FAIRsharing.wkggtx, DOI:10.5061, r3d100000044, DOI:10.15146, DOI:10.17616/R34S33, nlx_149486 | https://doi.org/10.17616/R34S33, https://doi.org/10.5061/, https://doi.org/10.15146, https://dx.doi.org/10.5061/, https://dx.doi.org/10.15146, https://fairsharing.org/10.25504/FAIRsharing.wkggtx, https://api.datacite.org/dois?prefix=10.18736, https://api.datacite.org/dois?prefix=10.6076, , https://doi.org/10.17616/R34S33 | http://www.datadryad.org/ | SCR_005910 | , The Dryad Digital Repository, Dryad Digital Repository, Dryad | 2026-08-15 11:23:15 | 2790 | ||||||
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Opasnet Resource Report Resource Website 1+ mentions |
Opasnet (RRID:SCR_005751) | Opasnet | database, data or information resource, wiki, knowledge environment, narrative resource | Opasnet is a wiki-based website and workspace for helping societal decision making. The website collects, synthesizes, and distributes people''s values and scientific information. Opasnet welcomes anyone who wants to promote science-based decision-making in any field. The specialty is that the information is structured for both scientific scrutiny and for policy use at the same time. In practice, you can do original research, store data, make models, and perform policy assessments and discuss all of that work in one workspace. Originally, the developers of Opasnet came from the environmental health, i.e. a research field that studies the impacts of environment on human health. We are actively working, among other things, on climate change and air pollution, but you can also start a new assessment about a decision of your own interest, or participate in an existing assessment. Opasnet is a website that has basically two parts. One part is a wiki site (called Opasnet wiki or simply Opasnet) that has descriptive pages with text, figures, and tables; it also contains files. The other part is a database called Opasnet Base that contains quantitative estimates about anything that is described in Opasnet. The majority of information is openly available. However, both Opasnet wiki and Opasnet Base have a protected area for working with material that is non-public for some reason. | decision making, environmental health, climate change, air pollution, problem solve, policy, science, public health, persistent pollutant, pollution, climate, environment | has parent organization: National Institute for Health and Welfare; Helsinki; Finland | National Institute for Health and Welfare; Helsinki; Finland | GNU Free Documentation License | nlx_149211 | SCR_005751 | 2026-08-15 11:23:13 | 4 | |||||||
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Terry Fox Foundation Resource Report Resource Website 1+ mentions |
Terry Fox Foundation (RRID:SCR_005873) | TFF | institution | The Terry Fox Foundation is responsible for supporting close to $20 million in discovery based research each year in Canada - all monies raised outside Canada must be distributed to (a) an institute approved by the Foundation and its advisors or (b) remitted to Canada. The Terry Fox Research Institute (TFRI) is a recipient of TFF funding for translational research. TFRI is an exciting new initiative whose goal is to translate rapidly today''s best science into better cancer treatment and diagnosis for all Canadians. The Institute will bring scientists and clinicians together across the country into a functionally integrated, geographically dispersed Institute with nodes in several provinces. Terry Fox was diagnosed with osteogenic sarcoma (bone cancer) in his right leg in 1977 and had his leg amputated 15 cm (six inches) above the knee. While in hospital, Terry was so overcome by the suffering of other cancer patients that he decided to run across Canada to raise money for cancer research. He called his journey the Marathon of Hope. Terry''s Marathon of Hope took place in 1980 with the simple objective of informing Canadians of the importance of finding a cure for cancer. With fierce determination, he ran an average of 42 kilometres (26 miles) every day for 143 days. Terry was forced to end his run on September 1, 1980 when the cancer spread to his lungs. By February 1, 1981, Terry''s dream of raising $1 for every Canadian was realized - the Terry Fox Marathon of Hope fund totaled $24.17 million. Terry died in June 1981. On May 26, 1988, The Terry Fox Run became a Trust, independent from the Canadian Cancer Society, and received tax-exempt charitable registration as a public foundation. In addition to our signature and long-standing National Terry Fox Run Day in September of each year, The Terry Fox Foundation is proud to include in its events portfolio The National School Run Day. The Foundation recognizes the duality of its mandate. Not only does it raise money for research, but it also continues to share the story of Terry Fox. The Terry Fox Foundation strives to maintain the heroic effort and integrity that Terry embodied. It is a grassroots organization that does not allow the Terry Fox name or likeness to be commercialized or conjoined with other worthy causes. To date, over $600 million has been raised worldwide for cancer research in Terry''s name. | research, cancer | is parent organization of: Terry Fox Research Institute | Cancer | ISNI: 0000 0004 5907 4557, Crossref funder ID: 501100002655, nlx_149429, grid.453650.1 | https://ror.org/05vd00053 | SCR_005873 | 2026-08-15 11:23:18 | 5 | |||||||
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JEPETTO Resource Report Resource Website 10+ mentions |
JEPETTO (RRID:SCR_005909) | JEPETTO | software resource | A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results. | gene set enrichment analysis, topological analysis, interaction network, java, enrichment analysis, functional analysis, gene prioritization, integrated analysis, network analysis, interaction, pathway, process, topology, gene |
is listed by: OMICtools has parent organization: Cytoscape has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom |
PMID:24363376 | GNU General Public License | OMICS_02247 | SCR_005909 | Java Enrichment of Pathways Extended To Topology | 2026-08-15 11:23:18 | 15 | ||||||
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OpenCalais Resource Report Resource Website 1+ mentions |
OpenCalais (RRID:SCR_005906) | Calais | commercial organization, production service resource, data analysis service, software application, software resource, service resource, text-mining software, analysis service resource | Service and open API to tag the people, places, facts and events in your content. You hand the Web Service unstructured text (like news articles, blog postings, your term paper, etc.) and it returns semantic metadata in RDF format. Using natural language processing and machine learning techniques, the Calais Web Service examines your text and locates the entities, facts, and events. Calais then processes the entities, facts and events extracted from the text and returns them to the caller in RDF format. * Calais Tagaroo: If you are on WordPress, this plug-in automatically tags content as you type. It can also fetch images from Flickr and videos from Google Video. * Calais Marmoset: To manipulate your search results appearance in Google and Yahoo!, which is simple javacode you embed in your site pages. It will collect the metadata from your page (in the form of RDFa) and hand it over to Google Rich Snippets> and Yahoo! Search Monkey so that you can customize the way your search results appear. * Semantic Proxy: If you want to extract metadata from Web pages using URLs * Calais Collection: For the open source platform Drupal, you can find a complete Calais Collection of modules for easy integration. * OpenPublish: for building a new site from the ground up, this free Content Management System is based on Drupal. OpenPublish bakes-in OpenCalais from the ground up to semantify your site and automate the creation of ''related reading'' widgets, ''topic hubs'' and more. | categorize, tag, semantics, natural language processing, computational linguistics, text mining | is listed by: FORCE11 | Free, Up to 50, 000 documents per day, For public content only, See Terms of Service, Http://www.opencalais.com/terms | nlx_149478 | SCR_005906 | 2026-08-15 11:23:19 | 5 | ||||||||
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PASSion Resource Report Resource Website 10+ mentions |
PASSion (RRID:SCR_005867) | PASSion | software resource | A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data. |
is listed by: OMICtools has parent organization: Netherlands Bioinformatics Centre |
OMICS_01246 | SCR_005867 | 2026-08-15 11:23:18 | 11 | ||||||||||
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Hvidovre Hospital; Hvidovre; Denmark Resource Report Resource Website 1+ mentions |
Hvidovre Hospital; Hvidovre; Denmark (RRID:SCR_005747) | hospital |
is related to: European Gram Negative AntiBacterial Engine has parent organization: University of Copenhagen; Copenhagen; Denmark |
SCR_005747 | Hvidovre Hospital | 2026-08-15 11:23:13 | 1 | ||||||||||||
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Europe PubMed Central Resource Report Resource Website 500+ mentions |
Europe PubMed Central (RRID:SCR_005901) | Europe PMC, UKPMC | database, bibliography, web service, data or information resource, data access protocol, software resource | Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts. | biomedical, literature, publication, health, life science, patent, clinical guideline, grant, text mining, author identification, archiving, open access, gold standard, bio.tools, bio.tools, FASEB list |
uses: EvidenceFinder uses: BioLexicon is listed by: FORCE11 is listed by: Debian is listed by: bio.tools is related to: PubMed is related to: PubMed Central is related to: AGRICOLA is related to: ORCID - Open Researcher and Contributor ID is related to: EvidenceFinder has parent organization: European Bioinformatics Institute has parent organization: Mimas has parent organization: National Centre for Text Mining is parent organization of: EvidenceFinder |
Wellcome Trust WT098231 | PMID:21062818 | Free, The community can contribute to this resource | nlx_149472, biotools:europe_pmc, biotools:ukpmc | https://bio.tools/ukpmc, https://bio.tools/europe_pmc | http://ukpmc.ac.uk/ | SCR_005901 | UK PubMed Central | 2026-08-15 11:23:19 | 517 | |||
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TrED Resource Report Resource Website 1+ mentions |
TrED (RRID:SCR_005869) | TrED | database, data processing software, data or information resource, data analysis software, software application, software resource | TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes. | expressed sequence tag, transcriptional profile, fungal pathogen, bmu01672, chuv862.00, mya-3108, cdna, pathway, microarray, classification, blast, unisequence, peptide, annotation |
is related to: Gene Ontology is related to: KEGG is related to: GenBank is related to: Pfam |
Ministry of Science and Technology of China 2006AA020504 | PMID:17650345 | nlx_149408 | SCR_005869 | TrED - T. rubrum Expression Database, Trichophyton rubrum Expression Database, Trichophyton rubrum Expression Database (TrED) | 2026-08-15 11:23:18 | 5 |
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