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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-07-25 12:06:10 | 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 | 2026-07-25 12:06:11 | 18 | |||||||
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Blip: Biomedical Logic Programming Resource Report Resource Website 1+ mentions |
Blip: Biomedical Logic Programming (RRID:SCR_005733) | Blip, blipkit | software resource | Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog''''s excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | biology, biomedical, ontology, annotation, software library, bioinformatics, module |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Berkeley Bioinformatics Open-Source Projects |
GNU Lesser General Public License | nlx_149193 | SCR_005733 | Blip - Biomedical Logic Programming, Biomedical Logical Programming (Blip), Biomedical Logic Programming | 2026-07-25 12:06:08 | 2 | |||||||
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University of Neuchatel; Neuchatel; Switzerland Resource Report Resource Website |
University of Neuchatel; Neuchatel; Switzerland (RRID:SCR_005875) | UniNE | university | French-speaking university based in Neuchâtel, Switzerland. The university has four faculties and more than a dozen institutes, including arts and human sciences, natural sciences, law and economics. | is related to: Pharma-Planta Consortium | grid.10711.36, nlx_158304, ISNI:0000 0001 2297 7718, Crossref funder ID:501100005353, Wikidata:Q541548 | https://ror.org/00vasag41 | SCR_005875 | University of Neuchatel, Universite de Neuchatel, University of Neuch�tel, Universit� de Neuch�tel | 2026-07-25 12:06:11 | 0 | ||||||||
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American Cancer Society Resource Report Resource Website 100+ mentions |
American Cancer Society (RRID:SCR_005756) | ACS | non profit organization | The American Cancer Society is the nationwide, community-based, voluntary health organization dedicated to eliminating cancer as a major health problem by preventing cancer, saving lives, and diminishing suffering from cancer, through research, education, advocacy, and service. Together with our millions of supporters, the American Cancer Society (ACS) saves lives and creates a world with less cancer and more birthdays by helping people stay well, helping people get well, by finding cures, and by fighting back. Headquartered in Atlanta, Georgia, the ACS has 12 chartered Divisions, more than 900 local offices nationwide, and a presence in more than 5,100 communities. | cancer, breast cancer, colon, lung, prostate, skin, breast | Cancer | grid.422418.9, Wikidata: Q463665, nlx_149219, ISNI: 0000 0004 0371 6485, Crossref funder ID: 100000048 | https://ror.org/02e463172 | SCR_005756 | American Cancer Society - The Official Sponsor of Birthdays | 2026-07-25 12:06:09 | 476 | |||||||
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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. | 2026-07-25 12:06:11 | 1 | |||||||||||
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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 | 2026-07-25 12:06:11 | 2943 | ||||||
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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 | 2026-07-25 12:06:08 | 1 | ||||||||
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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 | 2026-07-25 12:06:08 | 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 | 2026-07-25 12:06:13 | 13 | ||||||||||
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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) | 2026-07-25 12:06:10 | 252 | ||||||
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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 | 2026-07-25 12:06:14 | 1 | ||||||
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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 | 2026-07-25 12:06:11 | 109 | ||||||||||||
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MetaQC Resource Report Resource Website 10+ mentions |
MetaQC (RRID:SCR_006000) | software resource | Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision. | standalone software, mac os x, unix/linux, windows, r, FASEB list |
is listed by: OMICtools has parent organization: CRAN |
PMID:22116060 | GNU General Public License, v2 | OMICS_04032 | https://github.com/donkang34/MetaQC | SCR_006000 | MetaQC: Objective Quality Control and Inclusion/Exclusion Criteria for Genomic Meta-Analysis, MetaQC: Objective Quality Control and Inclusion / Exclusion Criteria for Genomic Meta-Analysis | 2026-07-25 12:06:15 | 40 | ||||||
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Quantum Dot Corporation Resource Report Resource Website |
Quantum Dot Corporation (RRID:SCR_005941) | commercial organization |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 15, 2017.\\\\\\ \\\\\\ An Antibody supplier |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152443 | SCR_005941 | 2026-07-25 12:06:14 | 0 | |||||||||||
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ProQuest Dissertation Publishing Resource Report Resource Website |
ProQuest Dissertation Publishing (RRID:SCR_006075) | ProQuest Dissertation Publishing | service resource | ProQuest Dissertation Publishing has been publishing dissertations and theses since 1938. In that time, we have published over 2 million graduate works from graduate schools around the world. We have over 700 active university publishing partners, and publish more than 70,000 new graduate works each year. In addition to publishing, we provide access to graduate works for thousands of libraries around the world. Based on your interests, you should find the information you need below: * Authors - Information for authors on why and how to publish their graduate work with us. * Grad Schools & Libraries - Learn about the benefits of publishing, and why to submit online. * Researchers - We can help you find the dissertation or thesis you need. | dissertation, publishing, thesis, graduate, library, research, author |
is related to: ProQuest Dissertations and Theses Global has parent organization: ProQuest |
nlx_151558 | SCR_006075 | 2026-07-25 12:06:14 | 0 | |||||||||
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Workflow4Ever Resource Report Resource Website 1+ mentions |
Workflow4Ever (RRID:SCR_005939) | Wf4Ever | knowledge environment | Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment. | preservation, workflow, provenance, archive, research object, workflow model, management, experimental method |
is listed by: FORCE11 is related to: myExperiment is related to: RightField |
European Union | nlx_151286 | SCR_005939 | 2026-07-25 12:06:12 | 1 | ||||||||
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University of North Texas; Texas; USA Resource Report Resource Website |
University of North Texas; Texas; USA (RRID:SCR_005935) | UNT | university | Public research university in Denton, Texas. | is related to: Alzheimers Disease Genetics Consortium | grid.266869.5, nlx_157964, Wikidata:Q860527, ISNI:0000 0001 1008 957X, Crossref funder ID:100008973 | https://ror.org/00v97ad02 | SCR_005935 | University of North Texas | 2026-07-25 12:06:12 | 0 | ||||||||
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ReproCELL Incorporated Resource Report Resource Website |
ReproCELL Incorporated (RRID:SCR_005973) | commercial organization | An Antibody supplier | nlx_152450 | SCR_005973 | 2026-07-25 12:06:12 | 0 | ||||||||||||
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BASH4RfMRI Resource Report Resource Website |
BASH4RfMRI (RRID:SCR_005970) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI. | algorithm or reusable library, information theory, spectral analysis, correlation, multivariate analysis, platform or development environment, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL is related to: Analysis of Functional NeuroImages is related to: FreeSurfer is related to: 1000 Functional Connectomes Project |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151343 | SCR_005970 | BASH Scripts, bash-rs-fcmri | 2026-07-25 12:06:12 | 0 |
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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."
