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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Antigenix America Resource Report Resource Website 1+ mentions |
Antigenix America (RRID:SCR_005871) | commercial organization | An Antibody supplier | nlx_152276 | SCR_005871 | Antigenix America Inc. | 2026-09-19 12:51:00 | 1 | |||||||||||
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UTRdb/UTRsite Resource Report Resource Website 10+ mentions |
UTRdb/UTRsite (RRID:SCR_005868) | data or information resource, portal, topical portal | UTRdb/UTRsite is a portal to other databases, including Nucleotide Sequence Databases, Protein Sequence Databases, other Sequence databanks, Untranslated Nucleotide Sequence Databases, Mitochondrial Databases, Mutation Databases, and others. The site also allows users to start long-term permanent projects or just to do quick searches, depending on the user''s needs. | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
biotools:utrdb, nif-0000-03619 | https://bio.tools/utrdb | http://bighost.area.ba.cnr.it/srs6/ | SCR_005868 | UTRdb/UTRsite | 2026-09-19 12:51:00 | 41 | |||||||
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ClueGO Resource Report Resource Website 1000+ mentions |
ClueGO (RRID:SCR_005748) | ClueGO | software resource | A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | statistical analysis, function, gene ontology, pathway, annotation, network, plugin, gene |
is listed by: Gene Ontology Tools is listed by: SoftCite is related to: Gene Ontology is related to: Cytoscape is related to: KEGG is related to: BioCarta Pathways has parent organization: National Institute of Health and Medical Research; Rennes; France |
National Institute of Health and Medical Research; Rennes; France ; Ville de Paris ; INCa ; Austrian Ministry for Science and Research ; BINII ; European Union 7FP 202230 |
PMID:19237447 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149209 | SCR_005748 | 2026-09-19 12:50:59 | 2951 | ||||||
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ORNL DAAC Data Product Citation Policy Resource Report Resource Website |
ORNL DAAC Data Product Citation Policy (RRID:SCR_005902) | ORNL DAAC Data Product Citation Policy | data or information resource, narrative resource, standard specification | Data Product Citation Policy of including a bibliographic citation for the products that were used in publications to acknowledge the scientists who have provided archived ORNL DAAC (Oak Ridge National Laboratory Distributed Active Archive Center) data products. Such citations will help others find the products and see how they have been used. Citation information is provided in the documentation that accompanies all data products. ORNL DAAC is operated by the ORNL Environmental Sciences Division and is responsible for data archival, product development and distribution, and user support for biogeochemical and ecological data and models. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemcial dynamics is one of the NASA Earth Observing System Data and Information System (EOSDIS) data centers managed by the Earth Science Data and Information System (ESDIS) Project, which is responsible for providing scientific and other users access to data from NASA''s Earth Science Missions. | data citation, bibliographic citation |
is listed by: FORCE11 has parent organization: Oak Ridge National Laboratory |
nlx_149492 | SCR_005902 | Oak Ridge National Laboratory Distributed Active Archive Center Data Product Citation Policy | 2026-09-19 12:51:01 | 0 | ||||||||
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University of Louisville; Kentucky; USA Resource Report Resource Website 1+ mentions |
University of Louisville; Kentucky; USA (RRID:SCR_005749) | UL | university | Public research university in Louisville, Kentucky. It is part of the Kentucky state university system. |
is parent organization of: University of Louisville Labs and Facilities is parent organization of: University of Louisville Micro/Nano Technology Center is parent organization of: University of Louisville Micro/Nano Technology Center Core Facility is parent organization of: University of Louisville School of Medicine Molecular Modeling Core Facility is parent organization of: University of Louisville Biophysical Core Facility is parent organization of: University of Louisville Medicinal Chemistry Core Facility is parent organization of: University of Louisville Protein Expression and Purification Core Facility is parent organization of: University of Louisville Nuclear Magnetic Resonance Spectroscopy Core Facility is parent organization of: University of Louisville Sequencing Technology Center Genomics Services Core Facility is parent organization of: University of Louisville Proteomics Technology Center PTC Core Facility is parent organization of: University of Louisville KY INBRE Data Science Core Facility is parent organization of: University of Louisville Computing and Research Advanced Computing Core Facility is parent organization of: University of Louisville Micro/Nano Technology Center Bioimaging Core Facility is parent organization of: University of Louisville Micro/Nano Technology Center Imaging and Characterization Core Facility |
Wikidata:Q1317143, grid.266623.5, Crossref funder ID:100007924, nlx_26318, ISNI:0000 0001 2113 1622 | https://ror.org/01ckdn478 | SCR_005749 | UofL, U of L, University of Louisville | 2026-09-19 12:50:59 | 3 | ||||||||
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ESTScan Resource Report Resource Website 100+ mentions |
ESTScan (RRID:SCR_005742) | ESTScan | data analysis software, data processing software, software application, software resource | ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics. | dna, dna sequence, coding region, perl module, c, btlib perl module |
is listed by: Debian is listed by: OMICtools has parent organization: SourceForge |
PMID:10786296 | OMICS_08423, nlx_149202 | https://sources.debian.org/src/estscan/ | SCR_005742 | ESTScan project | 2026-09-19 12:50:59 | 291 | ||||||
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AD Clinical Trials Database Resource Report Resource Website |
AD Clinical Trials Database (RRID:SCR_005863) | clinical database, data or information resource, database | A database of Alzheimer's disease and dementia clinical trials currently in progress at centers throughout the U.S. | alzheimer's disease, cause, clinical trial, cure, dementia, treatment, database, clinical database | has parent organization: Alzheimer's Disease Education and Referral Center | Aging | Public | nif-0000-10344 | SCR_005863 | 2026-09-19 12:51:00 | 0 | ||||||||
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University of Louisiana; Louisiana; USA Resource Report Resource Website |
University of Louisiana; Louisiana; USA (RRID:SCR_005743) | university | Public research university in Lafayette, Louisiana. It has the largest enrollment within the nine-campus University of Louisiana System and the second largest enrollment in Louisiana. | is parent organization of: New Iberia Research Center | Wikidata:Q116485, grid.266621.7, Crossref funder ID:100008520, ISNI:0000 0000 9831 5270, nlx_12312 | https://ror.org/01x8rc503 | SCR_005743 | 2026-09-19 12:50:59 | 0 | ||||||||||
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Andrew W. Mellon Foundation Resource Report Resource Website 10+ mentions |
Andrew W. Mellon Foundation (RRID:SCR_005864) | Andrew W. Mellon Foundation | funding resource | The Andrew W. Mellon Foundation currently makes grants in five core program areas: * Higher Education and Scholarship * Scholarly Communications and Information Technology * Art History, Conservation, and Museums * Performing Arts * Conservation and the Environment Within each of its core programs, the Foundation concentrates most of its grantmaking in a few areas. Institutions and programs receiving support are often leaders in fields of Foundation activity, but they may also be promising newcomers, or in a position to demonstrate new ways of overcoming obstacles to achieve program goals. Our grantmaking philosophy is to build, strengthen and sustain institutions and their core capacities, rather than be a source for narrowly defined projects. As such, we develop thoughtful, long-term collaborations with grant recipients and invest sufficient funds for an extended period to accomplish the purpose at hand and achieve meaningful results. | grant, higher education, scholarship, scholarly communication, information technology, art history, conservation, museum, performing arts, environment | nlx_149404 | SCR_005864 | 2026-09-19 12:51:00 | 13 | ||||||||||
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SIMILE Resource Report Resource Website 1+ mentions |
SIMILE (RRID:SCR_005862) | SIMILE | data or information resource, portal, topical portal | SIMILE, a joint project conducted by the MIT Libraries and MIT CSAIL, was focused on developing robust, open source tools that empower users to access, manage, visualize and reuse digital assets. SIMILE seeks to enhance interoperability among digital assets, schemata/vocabularies/ontologies, metadata, and services. A key challenge is that the collections which must inter-operate are often distributed across individual, community, and institutional stores. We seek to be able to provide end-user services by drawing upon the assets, schemata/vocabularies/ontologies, and metadata held in such stores. SIMILE will leverage and extend DSpace, enhancing its support for arbitrary schemata and metadata, primarily though the application of RDF and semantic web techniques. The project also aims to implement a digital asset dissemination architecture based upon web standards. The dissemination architecture will provide a mechanism to add useful views to a particular digital artifact (i.e. asset, schema, or metadata instance), and bind those views to consuming services. To guide the SIMILE effort we will focus on well-defined, real-world use cases in the libraries domain. Since parallel work is underway to deploy DSpace at a number of leading research libraries, we hope that such an approach will lead to a powerful deployment channel through which the utility and readiness of semantic web tools and techniques can be compellingly demonstrated in a visible and global community. The SIMILE Project and its members are fully committed to the open source principles of software distribution and open development and for this reason, it releases the created intellectual property (both software and reports) under a BSD-style license. The SIMILE Project Team Members gladly welcome community efforts. | semantic, interoperability, metadata, information |
is related to: DSpace has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
Andrew W. Mellon Foundation | Open unspecified license - BSD-style license | nlx_149403 | SCR_005862 | Semantic Interoperability of Metadata and Information in unLike Environments, SIMILE Project | 2026-09-19 12:51:00 | 3 | ||||||
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CLENCH Resource Report Resource Website 1+ mentions |
CLENCH (RRID:SCR_005735) | CLENCH | data processing software, software application, software resource, source code | Cluster Enrichment (CLENCH) allows A. thaliana researchers to perform automated retrieval of GO annotations from TAIR and calculate enrichment of GO terms in gene group with respect to a reference set. Before calculating enrichment, CLENCH allows mapping of the returned annotations to arbitrary coarse levels using GO slim term lists (which can be edited by the user) and a local installation of GO. Platform: Windows compatible, Linux compatible, | gene, microarray, function, functional categorization, statistical analysis, slimmer-type tool, gene ontology, annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: TAIR has parent organization: Stanford Center for Biomedical Informatics Research |
PMID:14764555 | Free for academic use | nlx_149216 | http://www.personal.psu.edu/nhs109/Clench | SCR_005735 | CLENCH - Cluster Enrichment, CLENCH: A program for calculating cluster enrichment using the Gene Ontology, Cluster Enrichment, Cluster Enrichment (CLENCH) | 2026-09-19 12:50:59 | 4 | |||||
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SBUR - Society for Basic Urologic Research Resource Report Resource Website |
SBUR - Society for Basic Urologic Research (RRID:SCR_005856) | SBUR | community building portal, data or information resource, funding resource, meeting resource, portal, topical portal, training resource | The Society for Basic Urologic Research (SBUR) is a society of scientists whose expertise includes the study of urologic cancers (prostate, bladder, kidney, testis, penis), the biology of prostate growth, kidney and bladder function, autoimmune urologic diseases, infectious diseases, neuro-urologic diseases, male reproductive biology, infertility and erectile dysfunction. Members include molecular biologists, immunologists, epidemiologists, oncologists, biochemists and clinical urologic scientists. SBUR members serve on a wide variety of advisory panels, study sections, editorial boards and in the pharmaceutical industry. The SBUR organizes two annual meetings to share new findings at a multidisciplinary level, to promote interaction among members and other interested scientists and to highlight new areas of research and funding opportunities. The Society was organized to address the following: * To provide a forum for the presentation and discussion of basic scientific topics related to urology * To develop educational forums concerning scientific advancements related to the field of urology * To promote collaborative investigations among member scientists with an emphasis on the interchange of expertise among clinical and basic scientists * To promote the communication and interests of urologic disease investigators with national funding agencies, industry representatives and academic institutions with regards to urology related research * To serve as a resource for research information and expertise to clinical urologists through the American Urological Association | urology, prostate, bladder, kidney, testis, penis, award | is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology | Urologic disease, Urologic cancer, Neuro-urologic disease, Infertility, Erectile dysfunction | nlx_149393 | SCR_005856 | Society for Basic Urologic Research (SBUR), Society for Basic Urologic Research | 2026-09-19 12:51:00 | 0 | |||||||
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American Urological Association Resource Report Resource Website 100+ mentions |
American Urological Association (RRID:SCR_005859) | AUA | institution | The American Urological Association (AUA), founded in 1902, is the premier professional association for the advancement of urologic patient care, and works to ensure that its more than 18,000 members are current on the latest research and practices in urology. The AUA also pursues its mission of fostering the highest standards of urologic care by providing a wide range of servicesincluding publications, research, the Annual Meeting, continuing medical education (CME) and the formulation of health policy. | urology, research |
is listed by: Collaborating for the Advancement of Interdisciplinary Research in Benign Urology is parent organization of: AmerUrological's channel - YouTube |
Urologic disease | grid.422576.0, ISNI: 0000 0001 2222 2235, Wikidata: Q4745327, Crossref funder ID: 100006280, nlx_149398 | https://ror.org/00sbaqa70 | SCR_005859 | American Urological Association (AUA) | 2026-09-19 12:51:00 | 270 | ||||||
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DRCAT Resource Catalogue Resource Report Resource Website 1+ mentions |
DRCAT Resource Catalogue (RRID:SCR_005931) | DRCAT | catalog, data or information resource, database | Data resource catalog that collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. An entry includes information such as resource identifier(s), name, description and URL. ''''Query'''' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL). DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including ''''Query'''' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts. | metadata, bioinformatics, database, ontology, taxonomy, registry, annotation, data set |
is related to: EDAM Ontology has parent organization: European Bioinformatics Institute |
Acknowledgement required, See license | nlx_151280 | SCR_005931 | DRCAT (the data resource catalogue), DRCAT Resource Catalogue - Bioinformatics Web-based Data Resources, Data Resource Catalogue | 2026-09-19 12:51:02 | 2 | |||||||
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FAIRSharing Catalogue of Standards Resource Report Resource Website 1+ mentions |
FAIRSharing Catalogue of Standards (RRID:SCR_005926) | Catalogue of Standards | data or information resource, database, narrative resource, registry, standard specification | Catalogue to: 1, centralize community-developed bioscience standards, linking to policies, other portals, open access resources and lists of tools and databases implementing the standards; 2. develop and maintain a set of criteria for assessing the usability and popularity of the standards, also the interoperability and relations among them; 3. foster interoperability, addressing overlaps and duplication of efforts that hamper their wider uptake and interfere with the creation of standards-compliant systems. Research community, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated. Similar trends in both the regulatory arena and commercial science. The BioSharing catalogue classifies standards into three types: * reporting requirements (minimal information checklists to report of the same core set of information) * terminological artifacts (such as controlled vocabularies and ontologies to describe the information) * exchange formats (to communicate the information) You can sort columns and browse the reporting guidelines content, or you can view all the standards, or reporting guidelines, or terminological artifacts or exchange formats only. Contribute and help build the catalogue. | report guideline, exchange format, terminology artifact, terminology, metadata standard, ontology, registry, interoperability, markup |
is listed by: FORCE11 has parent organization: FAIRsharing |
BioMed Central | Creative Commons Attribution License, v3 Unported, The community can contribute to this resource | nlx_149630 | http://www.force11.org/node/4699 | http://www.biosharing.org/standards | SCR_005926 | Catalogue of Domain-specific Data Standards, Catalog of Standards, BioSharing Catalogue of Standards, BioSharing catalogue | 2026-09-19 12:51:01 | 2 | ||||
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LHP LHDL Resource Report Resource Website |
LHP LHDL (RRID:SCR_005928) | LHP, LHDL | data or information resource, simulation software, software application, software resource | Distributed repository of anatomo-functional data and of simulation algorithms, fully integrated into a seamless simulation environment and directly accessible. This infrastructure will be used to create the physiome of the human musculo-skeletal system. | algorithm, anatomo-functional data, human, musculo-skeletal, physiome, repository, simulation, system, training tools | is listed by: 3DVC | European Union | nif-0000-10464 | SCR_005928 | The Living Human Digital Library, The Living Human Project | 2026-09-19 12:51:01 | 0 | |||||||
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Dictyostelium Anatomy Ontology Resource Report Resource Website 1+ mentions |
Dictyostelium Anatomy Ontology (RRID:SCR_005929) | controlled vocabulary, data or information resource, ontology | An ontology to describe Dictyostelium where the structural makeup of Dictyostelium and its composing parts including the different cell types, throughout its life cycle is defined. There are two main goals for this new tool: (1) promote the consistent annotation of Dictyostelium-specific events, such as phenotypes (already in use), and in the future, of gene expression information; and (2) encourage researchers to use the same terms with the same intended meaning. To this end, all terms are defined. The complete ontology can be browsed using EBI''s ontology browser tool. (http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=DDANAT) | stricture, cell type, life cycle, phenotype, gene expression | has parent organization: Dictyostelium discoideum genome database | Wellcome Trust ; NIGMS GM64426; NHGRI HG00022 |
PMID:18366659 | nlx_14988 | SCR_005929 | 2026-09-19 12:51:02 | 1 | ||||||||
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caArray Resource Report Resource Website 10+ mentions |
caArray (RRID:SCR_006053) | caArray | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management. | microarray, gene expression, data sharing, service resource, data management, annotation, interoperability, life sciences |
is listed by: re3data.org is listed by: OMICtools is related to: Cancer Biomedical Informatics Grid is related to: MAGE-TAB has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151452, OMICS_00864, r3d100010573 | https://doi.org/10.17616/R33G76 | SCR_006053 | caArray - Array Data Management System, caArray Data Portal | 2026-09-19 12:51:03 | 35 | |||||
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Read Codes Clinical Terms Version 3 Resource Report Resource Website 1+ mentions |
Read Codes Clinical Terms Version 3 (RRID:SCR_006055) | RCD | controlled vocabulary, data or information resource, ontology | Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre | umls | is listed by: BioPortal | nlx_157570 | SCR_006055 | Read Codes CTV3, Read Codes Clinical Terms Version 3 (CTV3) | 2026-09-19 12:51:04 | 1 | ||||||||
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Genome Research Foundation Resource Report Resource Website 1+ mentions |
Genome Research Foundation (RRID:SCR_006056) | GRF, GF | institution | The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project | bioinformatics, genomics, genome, genome sequencing, personalized medicine, personal genomics, angiogenesis, drug, rna expression, protein structure |
has parent organization: Korean Ministry of Education Science and Technology is parent organization of: MetaBase |
Content is available under BioLicense: the freest license. | grid.410888.d, nlx_151458, Wikidata: Q5533483 | https://ror.org/03khjyh83 | SCR_006056 | Genome Foundation | 2026-09-19 12:51:04 | 1 |
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