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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Plant Environmental Conditions Resource Report Resource Website |
Plant Environmental Conditions (RRID:SCR_003460) | PECO, EO | controlled vocabulary, data or information resource | A structured controlled vocabulary for the representation of plant environmental conditions. | obo, environment, gene expression, phenotype |
is listed by: BioPortal is listed by: OBO has parent organization: Gramene |
nlx_157554 | http://purl.bioontology.org/ontology/PECO, http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/environment_ontology.obo, http://www.gramene.org/plant_ontology/index.html#eo | SCR_003460 | 2026-09-12 12:55:58 | 0 | ||||||||
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Eton Bioscience Resource Report Resource Website 50+ mentions |
Eton Bioscience (RRID:SCR_003533) | data or information resource, department portal, organization portal, portal | An Antibody supplier | nlx_152359 | SCR_003533 | Eton Bioscience Inc. | 2026-09-12 12:55:59 | 87 | |||||||||||
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MultiPhen Resource Report Resource Website 10+ mentions |
MultiPhen (RRID:SCR_003498) | software resource | Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model). | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:22567092 | GNU General Public License, v2 | biotools:multiphen, OMICS_04397 | https://bio.tools/multiphen | SCR_003498 | MultiPhen: a package for the genetic association testing of multiple phenotypes | 2026-09-12 12:55:59 | 31 | ||||||
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EBSeq Resource Report Resource Website 500+ mentions |
EBSeq (RRID:SCR_003526) | EBSeq | software resource | Software R package for RNA-Seq Differential Expression Analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:23428641 DOI:10.1093/bioinformatics/btt087 |
biotools:ebseq, OMICS_01307 | https://bio.tools/ebseq, https://sources.debian.org/src/r-bioc-ebseq/ | SCR_003526 | 2026-09-12 12:55:59 | 590 | |||||||
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Human Physiology Resource Report Resource Website |
Human Physiology (RRID:SCR_003525) | Human Physiology | book, data or information resource, narrative resource, wiki | Human Physiology is a featured book on Wikibooks because it contains substantial content, it is well-formatted, and the Wikibooks community has decided to feature it on the main page or in other places. Please continue to improve it and thanks for the great work so far! A printable and PDF version are available. You can edit its advertisement template. Contents: 1. Homeostasis 2. Cell Physiology 3. Integumentary System 4. The Nervous System 5. Senses 6. The Muscular System 7. Blood Physiology 8. The Cardiovascular System 9. The Immune System 10. The Urinary System 11. The Respiratory System 12. The Gastrointestinal System 13. Nutrition 14. The Endocrine System 15. The Male Reproductive System 16. The Female Reproductive System 17. Pregnancy and Birth 18. Genetics and Inheritance 19. Development: Birth through Death 20. Appendix 1: Answers to Review Questions 21. Authors 22. Further Reading | anatomy, human, physiology, image | has parent organization: Wikibooks | nlx_10645 | SCR_003525 | 2026-09-12 12:55:59 | 0 | |||||||||
|
PharmGKB Ontology Resource Report Resource Website |
PharmGKB Ontology (RRID:SCR_003529) | pharmgkb-owl | controlled vocabulary, data or information resource, ontology | An OWL representation of the data in PharmGKB, Comparative Toxicogenomics Database (CTD) and DrugBank and linked to related ontologies: ChEBI ontology, the Human Disease Ontology (DO), the Anatomical Therapeutic Chemical Classification System (ATC) and the Medical Subject Headings Thesaurus (MESH). The combined knowledge base can be exploited using the ELK reasoner. | owl, medical, drug |
is listed by: BioPortal is related to: Comparative Toxicogenomics Database (CTD) is related to: DrugBank is related to: MeSH is related to: Human Disease Ontology has parent organization: PharmGKB |
PMID:11928517 | New BSD License | nlx_157636 | SCR_003529 | 2026-09-12 12:55:59 | 0 | |||||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
European Molecular Biology Laboratory ; European Union FP6 ENFIN LSHG-CT-2005-518254; NHGRI P41 HG003751; NIGMS GM080223; NIGMS R01 GM100039; Ontario Research Fund |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-09-12 12:55:59 | 4810 | |||||
|
MetaSKAT Resource Report Resource Website 10+ mentions |
MetaSKAT (RRID:SCR_003489) | MetaSKAT | software resource | A R package for multiple marker meta-analysis. |
is listed by: OMICtools has parent organization: Harvard T.H. Chan School of Public Health |
PMID:23768515 | Free | OMICS_00241 | SCR_003489 | 2026-09-12 12:55:59 | 36 | ||||||||
|
Savant Resource Report Resource Website 50+ mentions |
Savant (RRID:SCR_003488) | Savant | software resource | Next-generation genome browser software designed for the latest generation of genome data. |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
Free, Available for download, Freely available | OMICS_00923 | https://github.com/compbio-UofT/savant | SCR_003488 | 2026-09-12 12:55:59 | 64 | ||||||||
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Michigan Molecular Interactions Resource Report Resource Website 1+ mentions |
Michigan Molecular Interactions (RRID:SCR_003521) | MiMI | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu. | gene, interaction, molecule, protein, protein interaction, protein-protein interaction |
is related to: MiMI Plugin for Cytoscape has parent organization: National Center for Integrative Biomedical Informatics |
Michigan Center for Biological Information ; National Center for Integrative Biomedical Informatics ; Pfizer ; Medical and Academic Partnerships ; Howard Hughes Medical Institute ; Microsoft Corporation ; NLM R01 LM008106; NIDA U54 DA021519; NSF IIS 0219513 |
PMID:18978014 PMID:17130145 |
nif-0000-00214 | SCR_003521 | 2026-09-12 12:55:59 | 5 | |||||||
|
L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | data processing software, image analysis software, image processing software, service resource, software application, software resource | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure, https://bio.tools/l-measure | SCR_003487 | 2026-09-12 12:55:59 | 30 | |||||
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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 | 2026-09-12 12:55:59 | 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 | 2026-09-12 12:55:59 | 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 | 2026-09-12 12:55:59 | 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 | 2026-09-12 12:56:00 | 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 | 2026-09-12 12:55:58 | 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 | 2026-09-12 12:55:59 | 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) | 2026-09-12 12:55:58 | 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 | 2026-09-12 12:55:58 | 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 | 2026-09-12 12:55:58 | 1 |
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