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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Ontology of Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Adverse Events (RRID:SCR_003428) | OAE | ontology, data or information resource, controlled vocabulary | Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles. | adverse event, health, pathological, molecular, cellular, organismal, multi-organismal |
is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology is related to: Ontology of Vaccine Adverse Events has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:25093068 | Free, Freely available | nlx_157522 | http://purl.bioontology.org/ontology/OAE, http://svn.code.sf.net/p/oae/code/trunk/src/ontology/oae.owl | SCR_003428 | 2026-08-08 11:58:00 | 2 | ||||||
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Chung-Ang University; Seoul; South Korea Resource Report Resource Website 1+ mentions |
Chung-Ang University; Seoul; South Korea (RRID:SCR_003547) | university | Private comprehensive research university in South Korea. Starting as a church-run kindergarten in 1918, CAU transformed into a school for female kindergarten teachers in 1922 and was granted university status in 1953. | grid.254224.7, ISNI:0000 0001 0789 9563, Crossref funder ID:501100002460, nlx_10442, Wikidata:Q41790 | https://ror.org/01r024a98 | SCR_003547 | CAU | 2026-08-08 11:58:02 | 2 | ||||||||||
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Mindtouch DekiWiki Resource Report Resource Website 1+ mentions |
Mindtouch DekiWiki (RRID:SCR_003425) | MindTouch | commercial organization, software resource, source code | A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more. | authoring, publishing, standard, web service, cloud |
is listed by: FORCE11 is listed by: Biositemaps has parent organization: University of Wisconsin-Madison; Wisconsin; USA has parent organization: SourceForge |
Free, Freely available | nif-0000-33097 | http://sourceforge.net/projects/dekiwiki/, https://www.force11.org/node/4733 | SCR_003425 | MindTouch Core, DekiWiki, MindTouch Deki Wiki, Deki Wiki, MindTouch (frmly deki wiki) | 2026-08-08 11:57:58 | 2 | ||||||
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nSolver Analysis Software Resource Report Resource Website 100+ mentions |
nSolver Analysis Software (RRID:SCR_003420) | nSolver Analysis Software | software resource, software application, data processing software | Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages. | normalization, analysis, ncounter, os x, windows, quality control | is listed by: OMICtools | Restricted | OMICS_02309 | https://nanostring.app.box.com/v/nSolver-AdvancedAnalysis, https://nanostring.com/products/ncounter-analysis-system/ncounter-analysis-solutions/nsolver-data-analysis-support/ | SCR_003420 | 2026-08-08 11:58:05 | 405 | |||||||
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MiMI Plugin for Cytoscape Resource Report Resource Website 1+ mentions |
MiMI Plugin for Cytoscape (RRID:SCR_003424) | MiMI Plugin | software resource, software application, data visualization software, data processing software | The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways. | protein interaction, network visualization, xquery, interactive database, information refining, molecular interaction, bioinformatics tool, java, protein-protein interaction, interaction network, biological effect, bimolecular, interaction, molecular, network, pathway, protein, visualization, plugin |
is listed by: Biositemaps is related to: Cytoscape is related to: Michigan Molecular Interactions has parent organization: University of Michigan; Ann Arbor; USA has parent organization: National Center for Integrative Biomedical Informatics |
NIH ; NIDA U54 DA021519; NLM R01 LM008106; NCRR P41 RR018627 |
PMID:18812364 | nif-0000-33090 | http://mimiplugin.ncibi.org/index.html | SCR_003424 | Cytoscape Plugin for MiMI, MiMI Plugin - Cytoscape Plugin for MiMI | 2026-08-08 11:58:05 | 1 | |||||
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GraphML Resource Report Resource Website 10+ mentions |
GraphML (RRID:SCR_003545) | GraphML | data or information resource, standard specification, narrative resource, markup language, interchange format | A file format for graphs that consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data. It is based on XML and is ideally suited as a common denominator for all kinds of services generating, archiving, or processing graphs. Its main features include support of * directed, undirected, and mixed graphs, * hypergraphs, * hierarchical graphs, * graphical representations, * references to external data, * application-specific attribute data, and * light-weight parsers. | xml, graph | Creative Commons Attribution License, v3 | nlx_157666 | SCR_003545 | The GraphML File Format | 2026-08-08 11:58:00 | 15 | ||||||||
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MAGENTA Resource Report Resource Website 100+ mentions |
MAGENTA (RRID:SCR_003422) | MAGENTA | software resource | A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input. |
is listed by: OMICtools has parent organization: Broad Institute |
PMID:20714348 | Free, Available for download, Freely available | OMICS_00236 | SCR_003422 | Meta-Analysis Gene-set Enrichment of variaNT Associations | 2026-08-08 11:58:00 | 141 | |||||||
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NAPPA Resource Report Resource Website 10+ mentions |
NAPPA (RRID:SCR_003419) | NAPPA | software resource | Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software. | normalization, processing, nanostring, mirna, mrna, os x, windows | is listed by: OMICtools | GNU General Public License, v3 | OMICS_02310 | SCR_003419 | NAPPA: Performs the processing and normalisation of Nanostring miRNA and mRNA data | 2026-08-08 11:58:00 | 12 | |||||||
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Rat Strain Ontology Resource Report Resource Website 1+ mentions |
Rat Strain Ontology (RRID:SCR_003449) | ontology, data or information resource, controlled vocabulary | Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks. | rat strain, obo, gene, pathway, biological process, metabolic, regulatory, signaling, drug, disease, metabolic pathway, regulatory pathway, signaling pathway, drug pathway, disease pathway, gene |
is listed by: BioPortal is listed by: OBO has parent organization: Rat Genome Database (RGD) |
Free, Freely available | nlx_157569, nlx_157544, SCR_003473 | http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=PW:0000001, http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457, http://purl.bioontology.org/ontology/RS, ftp://rgd.mcw.edu/pub/ontology/rat_strain/rat_strain.obo | SCR_003449 | 2026-08-08 11:57:58 | 1 | ||||||||
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FadE Resource Report Resource Website 10+ mentions |
FadE (RRID:SCR_003448) | FadE | software resource | A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms. |
is listed by: OMICtools has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:22965123 | Free, Available for download, Freely available | OMICS_00599 | https://minituba.hegroup.org/ | SCR_003448 | fade - Estimation of position specific methylation parameters in color or nucleotide space with NR optimization | 2026-08-08 11:58:05 | 35 | ||||||
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Ontology of Vaccine Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Vaccine Adverse Events (RRID:SCR_003442) | OVAE | ontology, data or information resource, controlled vocabulary | A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO). | owl, vaccine adverse event, vaccine, adverse event |
uses: Vaccine Ontology is listed by: BioPortal is listed by: OBO is related to: Ontology of Adverse Events has parent organization: University of Michigan Medical School; Michigan; USA |
PMID:24279920 | Free, Freely available | nlx_157538 | http://purl.bioontology.org/ontology/OVAE, http://ovae.googlecode.com/svn/trunk/src/ontology/ovae.owl | SCR_003442 | 2026-08-08 11:57:58 | 1 | ||||||
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Proteome Commons Tranche repository Resource Report Resource Website 1+ mentions |
Proteome Commons Tranche repository (RRID:SCR_003441) | Tranche | software resource | A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most. | proteome, storage, proteomics, distributed, server, mass spectrometry, protein, peptide, file sharing, security |
is listed by: Biositemaps has parent organization: University of Michigan; Ann Arbor; USA has parent organization: Proteome Commons |
NCI ; Clinical Proteomics Technologies for Cancer ; NCRR P41-RR018627 |
PMID:21063945 PMID:20356086 |
Open unspecified license (Apache v2); registration required . See Terms of Use, Https://proteomecommons.org/terms.jsp | nif-0000-33195 | http://tranche.proteomecommons.org | SCR_003441 | Tranche Project | 2026-08-08 11:58:05 | 8 | ||||
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metagen Resource Report Resource Website 10+ mentions |
metagen (RRID:SCR_003443) | metagen | software resource | Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:17605724 | Free, Available for download, Freely available | OMICS_00238, biotools:metagen | https://www.rdocumentation.org/packages/meta/versions/4.9-6/topics/metagen | SCR_003443 | 2026-08-08 11:58:00 | 21 | ||||||
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Nclamp - data acquisition software for electrophysiology Resource Report Resource Website 1+ mentions |
Nclamp - data acquisition software for electrophysiology (RRID:SCR_003750) | data acquisition software, software resource, software application, data processing software | Data acquisition software that runs in conjunction with neuromatic. configured to work with Igor Pro on PC or Mac, instrutech or national instrument acquisition devices. Funded by The Medical Research Council (UK) Compatibility with WaveMetrics Igor Pro 5 and 6. Compatibility with Mac or PC. NIDAQ interfacing multifunction DAQ boards from National Instruments. Requires Igor NIDAQ Tools MX. ITC interfacing - data acquisition systems from InstruTech / Heka. Requires Igor ITC XOPs. Episodic acquisition (stim and sample). Continuous acquisition (currently for ITC users only). Online analysis, with ability to create your own analysis functions. Notes and Log Files which can be displayed within a table or notebook. Automatic saving of data and log folders to your hard drive. Flexible stimulus pulse generator with ability to use your own pulse waveforms. Instant accessibility to all of NeuroMatics and Igor Pros pre-existing data analysis functions. | nif-0000-00072 | SCR_003750 | Nclamp | 2026-08-08 11:58:05 | 5 | |||||||||||
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Innovative Medicines Initiative Resource Report Resource Website 100+ mentions |
Innovative Medicines Initiative (RRID:SCR_003754) | IMI | organization | Initiative to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. It does this by initiating and managing consortia composed of the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organizations, and medicines regulators. IMI is a public-private partnership between the European Union and the European pharmaceutical industry, represented by the European Federation of Pharmaceutical Industries and Associations (EFPIA), with a timeframe separated into two phases (2008-2013, 2014-2024) that are each defined by unique research agendas. The first phase (2008 2013) had four pillars that defined the focus of its research agenda: * Predicting safety: evaluating the safety of a compound during the pre-clinical phase of the development process and the later phases in clinical development. * Predicting efficacy: improving the ability to predict how a drug will interact in humans and how it may produce a change in function. * Knowledge management: utilization of information and data for predicting safety and efficacy. * Education and training: closing existing training gaps in the drug development process. Some of the consortia managed under IMI focused on specific health issues while others focused on broader challenges in drug development. Additionally, IMI launched a number of education and training projects during its first phases. The goal of the second phase (IMI2, 2014-2024) is to develop next generation vaccines and drugs. The focus is on delivering the right prevention and treatment for the right patient at the right time. There is a strong focus on the development of new medicines with an emphasis on tools and methods that accelerate patient access to new medicines. IMI2's agenda can be defined by four axes of research: * target validation and biomarker research (efficacy and safety) * adoption of innovative clinical trial paradigms * innovative medicines * patient-tailored adherence programs As part of its distinct goals, IMI2 aims to deliver: * 30% better success rate in clinical trials of priority medicines identified by the WHO; clinical proof of concept in immunological, respiratory, neurological and neurodegenerative diseases in five years; * new and approved diagnostic markers for four of these diseases and at least two new medicines which could either be new antibiotics or new therapies for Alzheimer's disease. | drug development, drug, tool development, biomarker, data sharing, target validation, safety, efficacy, clinical trial, medicine, adherence program, vaccine, consortium, diagnostic marker, oncology, drug discovery |
is listed by: Consortia-pedia is related to: AddNeuroMed is related to: European Federation of Pharmaceutical Industries and Associations has parent organization: European Union has parent organization: European Federation of Pharmaceutical Industries and Associations is parent organization of: AddNeuroMed |
European Union FP7 ; Horizon 2020 ; EFPIA ; Other life science industries or organizations |
Wikidata: Q1664196, nlx_157984, grid.454814.8, ISNI: 0000 0004 0577 0821 | https://ror.org/019af4n30 | SCR_003754 | 2026-08-08 11:58:09 | 322 | |||||||
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Global Health Innovative Technology Fund Resource Report Resource Website 10+ mentions |
Global Health Innovative Technology Fund (RRID:SCR_003753) | GHIT Fund, GHIT | institution | A consortium that focuses their efforts on discovering and developing new pharmaceutical drugs, vaccines (both preventive and therapeutic) and diagnostics against the infectious diseases that are prevalent in developing countries. The initial targets are those disorders designated by WHO as neglected tropical diseases prevalent in developing nations. The consortium aims to facilitate international partnerships that enable Japanese technology, innovations, and insights to play a more direct role in improving global health. Another goal of GHIT is to develop a new drug-discovery screening platform to assist the screening of compound libraries housed within Japanese companies and academic institutions. The vision is to have Japanese research organizations donate compounds, with the Fund reimbursing screening costs and leveraging screening programs of existing product-development partners. | global health, health, drug development, biomarker, consortium, drug, vaccine, diagnostics, healthcare, developing country, disease | is listed by: Consortia-pedia | Government of Japan ; Bill and Melinda Gates Foundation ; Pharmaceutical industry |
grid.475132.6, nlx_157983 | https://ror.org/02yfqyv95 | SCR_003753 | 2026-08-08 11:58:05 | 17 | |||||||
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Medical Dictionary for Regulatory Activities Resource Report Resource Website 1+ mentions |
Medical Dictionary for Regulatory Activities (RRID:SCR_003751) | MEDDRA | ontology, data or information resource, controlled vocabulary | Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA) | umls | is listed by: BioPortal | nlx_157471 | SCR_003751 | 2026-08-08 11:58:09 | 4 | |||||||||
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DTU Center for Biological Sequence Analysis Resource Report Resource Website 1000+ mentions |
DTU Center for Biological Sequence Analysis (RRID:SCR_003590) | CBS, DTU CBS | web service, production service resource, software resource, data access protocol, analysis service resource, service resource | Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics. | nucleotide, sequence, amino acid, dna, microarray, molecule, immunology, protein function, protein structure, protein, post-translational, whole genome, sequence analysis |
has parent organization: Technical University of Denmark; Lyngby; Denmark is parent organization of: NESbase is parent organization of: O-GLYCBASE is parent organization of: OligoWiz is parent organization of: SignalP |
Danish National Research Foundation ; Danish Research Councils ; Danish Center for Scientific Computing ; Villum Kann Rasmussen Foundation ; Novo Nordisk Foundation ; European Union ; NIH |
nlx_12329 | http://www.cbs.dtu.dk/index.shtml | SCR_003590 | 2026-08-08 11:58:01 | 1475 | |||||||
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BioVacSafe Resource Report Resource Website 1+ mentions |
BioVacSafe (RRID:SCR_003745) | BioVacSafe | data or information resource, portal, organization portal, consortium | Project focused on developing cutting edge tools to speed up and improve the testing and monitoring of vaccine safety, both before and after release to the market. The three specific objectives of the project are: * the characterization of early inflammation induced by vaccines currently on the market and the identification and validation of biomarkers of early inflammation and allergic responses; * the identification and validation of early biomarkers of autoimmunity and their use to help identifying population at risk of developing autoimmunity; * the analysis of the incidence and epidemiology of autoimmune disease in the general population and the link to genetic background or previous events in the life of patients, including severe effects, such as anaphylactic shock. | safety, biomarker, consortium, clinical trial, inflammation, vaccine, infection, immunosafety, efficacy, autoimmunity, drug development, drug, test, monitor |
is listed by: Consortia-pedia has parent organization: University of Surrey; Surrey; United Kingdom |
Innovative Medicines Initiative 115308 | nlx_157978 | SCR_003745 | Biomarkers for Enhanced Vaccine Safety, Biovacsafe.eu, Biomarkers for enhanced vaccines immunosafety, Biomarkers for Enhanced Vaccine ImmunoSafety, BioVacSafe Project, BioVacSafe - Biomarkers for enhanced vaccines immunosafety | 2026-08-08 11:58:09 | 7 | |||||||
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Coca-Cola Company Resource Report Resource Website 1+ mentions |
Coca-Cola Company (RRID:SCR_003749) | Coca-Cola, KO | commercial organization | An American multinational beverage corporation and manufacturer, retailer and marketer of nonalcoholic beverage concentrates and syrups, which is headquartered in Atlanta, Georgia. (Wikipedia) It is the world's largest beverage company, refreshing consumers with more than 500 sparkling and still brands. | beverage | Crossref funder ID: 100004367, ISNI: 0000 0004 0504 2170, grid.451378.c, Wikidata: Q3295867, nlx_158091 | https://ror.org/00yc8qw13 | SCR_003749 | KO, The Coca-Cola Company, Coca-Cola | 2026-08-08 11:58:02 | 2 |
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