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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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jmzTab Resource Report Resource Website 1+ mentions |
jmzTab (RRID:SCR_003481) | software resource | A Java interface to the mzTab data exchange format for reporting a summary of proteomics results. | standalone software, mac os x, unix/linux, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:24659499 | Apache License, v2 | OMICS_04542, biotools:jmztab | https://bio.tools/jmztab | SCR_003481 | 2026-09-19 12:50:21 | 1 | |||||||
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National Institute of General Medical Sciences Image Gallery Resource Report Resource Website |
National Institute of General Medical Sciences Image Gallery (RRID:SCR_003480) | NIGMS Image Gallery | data or information resource, image collection, video resource | Database of scientific photos, illustrations, and videos made available by the National Institute of General Medical Sciences. | training material, database, illustration, media, news, photo, research | has parent organization: National Institute of General Medical Sciences | NIGMS | Permission is granted to use these images for educational, News media or research purposes, Provided the source for each image is credited. The material in this database may not be used to promote or endorse commercial products or services. | nif-0000-33708 | SCR_003480 | 2026-09-19 12:50:21 | 0 | |||||||
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MINC Brain Imaging Toolbox Resource Report Resource Website |
MINC Brain Imaging Toolbox (RRID:SCR_003519) | data processing software, image analysis software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.Comprised of a large array of sophisticated programs, this comprehensive software package with tools based around the MINC file format. Utilities are provided for conversion, viewing, editing, registering, segmentation, and a wide array of analysis. Many programs are in Perl. MINC software tools for neurological imaging are free. Input format: Analyze, DICOM, Minc | mri, neuroimaging, pet, registration, segmentation, analysis, neurological imaging | has parent organization: McGill University; Montreal; Canada | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_10430 | http://www.idoimaging.com/cgi-sys/cgiwrap/acrabb/imaging/program.pl?ident=280 | SCR_003519 | 2026-09-19 12:50:22 | 0 | ||||||||
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WikiSurgery - The Free Surgical Encyclopedia Resource Report Resource Website |
WikiSurgery - The Free Surgical Encyclopedia (RRID:SCR_003556) | data or information resource, image, narrative resource, video resource, wiki | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A free surgical encyclopedia for surgeons and their patients. Contributions in the form of new articles and editing can be made by anyone at anytime anywhere in the world. With over 33,000 articles for surgeons and patients, including news, articles, operation scripts, biographies and images. The website is a "wiki" which allows for the collaborative editing and building of content. Contributions in the form of new articles and editing can be made by those who register on the site, confirm their email address and whose application is accepted by an administrator. Wikisurgery is more than just a depot of surgical knowledge, not just articles about facts but also articles about controversy, debates, with none of the usual editorial limits on space. Indeed we hope it will become a record of surgical thought, experience and progression. Key Topics: Operation Scripts, Basic Surgical Skills Training Program, Basic Laparoscopic Training Program, Operative Images, Patient Information; there is also a Featured Videos section. | clinical medicine, surgery | International Journal of Surgery | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_11092 | SCR_003556 | Wikisurgery | 2026-09-19 12:50:22 | 0 | ||||||||
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Ontology of Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Adverse Events (RRID:SCR_003428) | OAE | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-19 12:50:19 | 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 | 2026-09-19 12:50:22 | 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) | 2026-09-19 12:50:20 | 2 | ||||||
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nSolver Analysis Software Resource Report Resource Website 100+ mentions |
nSolver Analysis Software (RRID:SCR_003420) | nSolver Analysis Software | data processing software, software application, software resource | 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 | 2026-09-19 12:50:19 | 405 | |||||||
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MiMI Plugin for Cytoscape Resource Report Resource Website 1+ mentions |
MiMI Plugin for Cytoscape (RRID:SCR_003424) | MiMI Plugin | data processing software, data visualization software, software application, software resource | 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 | 2026-09-19 12:50:19 | 1 | |||||
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GraphML Resource Report Resource Website 10+ mentions |
GraphML (RRID:SCR_003545) | GraphML | data or information resource, interchange format, markup language, narrative resource, standard specification | 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 | 2026-09-19 12:50:22 | 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 | 2026-09-19 12:50:19 | 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 | 2026-09-19 12:50:19 | 12 | |||||||
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HealthGrid Wiki Resource Report Resource Website |
HealthGrid Wiki (RRID:SCR_003572) | data or information resource, narrative resource, wiki | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. HealthGrid is a wiki dedicated to grids for health. It is maintained as a dynamic knowledge resource for the healthgrid community. The HealthGrid community (a world-wide initiative) gathers individuals from the public and private domain world-wide who are actively exploring the beneficial impact of healthgrid technology on healthcare provision and research. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_12797 | SCR_003572 | HealthGrid | 2026-09-19 12:50:22 | 0 | ||||||||||
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Adverse Event Reporting Ontology Resource Report Resource Website 1+ mentions |
Adverse Event Reporting Ontology (RRID:SCR_003571) | AERO | controlled vocabulary, data or information resource, ontology | An ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events. | owl, rdf, aero, bfo, ogms, iao, adverse event, clinician, health |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
New BSD License (code), Creative Commons Attribution License (content) | nlx_11209 | http://bioportal.bioontology.org/ontologies/1580, http://www.obofoundry.org/cgi-bin/detail.cgi?id=AERO, http://purl.obolibrary.org/obo/aero.owl, http://purl.obolibrary.org/obo/aero | SCR_003571 | 2026-09-19 12:50:22 | 1 | |||||||
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GCG/SeqWeb Resource Report Resource Website |
GCG/SeqWeb (RRID:SCR_003454) | GCG SeqWeb, GCG-SeqWeb | availability annotation standard, data analysis software, data or information resource, data processing software, narrative resource, nif annotation standard, software application, software resource, standard specification, text-mining software, this resource is no longer in service | THIS RESOURCE IS NO LONGER IN SERVCE, documented January 28, 2019. Core Facility provides the software and support for computer assisted protein and DNA sequence analysis and database access. The Genetics Computer Group GCG-Wisconsin package is currently available on PBRC's UNIX platform that is accessible via modem or direct connection. The package can be accessed via three interfaces: the command-line interface (UNIX C-shell), the web-based interface (SeqWeb) and the X-Windows based graphics interface (SeqLab). Applications in the package include sequence editing, alignment, comparison, primer design, restriction analysis, mapping, data presentation, database browsing, etc. In addition to local databases, access to remote databases (BLAST) is integrated into the package. The local databases are updated quarterly. Databases available include GenBank, EMBL, PIR-Protein, SWISS-PROT and Restriction Enzymes (REBASE). | bioinformatics, data mining, statistical analysis, dna microarray, molecular modeling, genetic analysis, protein, dna, sequence analysis |
is listed by: Biositemaps has parent organization: University of Hawaii at Manoa |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33361 | http://core.biotech.hawaii.edu/b-gcg.htm | SCR_003454 | SeqWeb GCG, Sequence Analysis Software Package, GCG, Genetics Computer Group | 2026-09-19 12:50:20 | 0 | ||||||
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Rat Strain Ontology Resource Report Resource Website 1+ mentions |
Rat Strain Ontology (RRID:SCR_003449) | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-19 12:50:21 | 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 | 2026-09-19 12:50:20 | 35 | ||||||
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miniTUBA Resource Report Resource Website |
miniTUBA (RRID:SCR_003447) | miniTUBA | analysis service resource, production service resource, service resource, storage service resource | miniTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data. miniTUBA represents in a network view possible influences that occur between time varying variables in your dataset. For these networks of influence, miniTUBA predicts time courses of disease progression or response to therapies. minTUBA offers a probabilistic framework that is suitable for medical inference in datasets that are noisy. It conducts simulations and learning processes for predictive outcomes. The DBN analysis conducted by miniTUBA describes from variables that you specify how multiple measures at different time points in various variables influence each other. The DBN analysis then finds the probability of the model that best fits the data. A DBN analysis runs every combination of all the data; it examines a large space of possible relationships between variables, including linear, non-linear, and multi-state relationships; and it creates chains of causation, suggesting a sequence of events required to produce a particular outcome. Such chains of causation networks - are difficult to extract using other machine learning techniques. DBN then scores the resulting networks and ranks them in terms of how much structured information they contain compared to all possible models of the data. Models that fit well have higher scores. Output of a miniTUBA analysis provides the ten top-scoring networks of interacting influences that may be predictive of both disease progression and the impact of clinical interventions and probability tables for interpreting results. The DBN analysis that miniTUBA provides is especially good for biomedical experiments or clinical studies in which you collect data different time intervals. Applications of miniTUBA to biomedical problems include analyses of biomarkers and clinical datasets and other cases described on the miniTUBA website. To run a DBN with miniTUBA, you can set a number of parameters and constrain results by modifying structural priors (i.e. forcing or forbidding certain connections so that direction of influence reflects actual biological relationships). You can specify how to group variables into bins for analysis (called discretizing) and set the DBN execution time. You can also set and re-set the time lag to use in the analysis between the start of an event and the observation of its effect, and you can select to analyze only particular subsets of variables. | analysis, analyze, bayesian, causation, clinical, linear, medical, structure, temporal, network analysis, network, molecule, information refining, gene expression regulation, bioinformatics, statistical package, interaction network, prediction, pathway, inference, biomedical, intervention |
is listed by: Biositemaps has parent organization: National Center for Integrative Biomedical Informatics has parent organization: University of Michigan; Ann Arbor; USA |
Society of University Surgeons Foundation ; NIDA U54DA021519; NIAID 1R21AI057875-01; NIGMS K08 GM074678-01A1 |
PMID:17644819 | Free, Freely available | nif-0000-33272 | SCR_003447 | miniTUBA - Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool, Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool, Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool (miniTUBA), The Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool | 2026-09-19 12:50:20 | 0 | |||||
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Ontology of Vaccine Adverse Events Resource Report Resource Website 1+ mentions |
Ontology of Vaccine Adverse Events (RRID:SCR_003442) | OVAE | controlled vocabulary, data or information resource, ontology | 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 | 2026-09-19 12:50:21 | 1 | ||||||
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NCI Thesaurus Resource Report Resource Website 10+ mentions |
NCI Thesaurus (RRID:SCR_003563) | NCIt | controlled vocabulary, data or information resource, ontology | A reference terminology and core biomedical ontology for NCI that covers approximately 100,000 key biomedical concepts with terms, codes, definitions, and more than 200,000 inter-concept relationships. It is the reference terminology for NCI, NCI Metathesaurus and NCI informatics infrastructure covering vocabulary for clinical care, translational and basic research, and public information and administrative activities. It includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. NCIt features: * Stable, unique codes for biomedical concepts; * Preferred terms, synonyms, definitions, research codes, external source codes, and other information; * Links to NCI Metathesaurus and other information sources; * Over 200,000 cross-links between concepts, providing formal logic-based definition of many concepts; * Extensive content integrated from NCI and other partners, much available as separate NCIt subsets * Updated frequently by a team of subject matter experts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP). | thesaurus, clinical, treatment, prevention, biomedical, owl, health, drug, chemotherapy |
is listed by: OBO is listed by: BioPortal is related to: NCI Metathesaurus is related to: OnEx - Ontology Evolution Explorer has parent organization: National Cancer Institute |
Cancer | See license, http://evs.nci.nih.gov/ftp1/NCI_Thesaurus/NCI_THESAURUS_license.txt | nlx_157698 | ftp://ftp1.nci.nih.gov/pub/cacore/EVS/, https://cabig.nci.nih.gov/concepts/EVS/, https://wiki.nci.nih.gov/display/EVS/NCI+Thesaurus+%28NCIt%29, http://nciterms.nci.nih.gov, http://purl.bioontology.org/ontology/NCIT | http://ncicb.nci.nih.gov/core/EVS | SCR_003563 | ncithesaurus | 2026-09-19 12:50:22 | 10 |
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