Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MEDLINE Resource Report Resource Website 10000+ mentions |
MEDLINE (RRID:SCR_002185) | MEDLINE | data or information resource, database, bibliography | A premier bibliographic database that contains over 18 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive feature is that the records are indexed with NLM Medical Subject Headings (MeSH). PubMed provides free access to MEDLINE and links to full text articles when possible. The great majority of journals are selected for MEDLINE based on the recommendation of the Literature Selection Technical Review Committee (LSTRC), an NIH-chartered advisory committee of external experts analogous to the committees that review NIH grant applications. Some additional journals and newsletters are selected based on NLM-initiated reviews, e.g., history of medicine, health services research, AIDS, toxicology and environmental health, molecular biology, and complementary medicine, that are special priorities for NLM or other NIH components. These reviews generally also involve consultation with an array of NIH and outside experts or, in some cases, external organizations with which NLM has special collaborative arrangements. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by the NLM National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Time coverage: generally 1946 to the present, with some older material. Source: Currently, citations from approximately 5,516 worldwide journals in 39 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations. | software, biomedicine, gold standard |
is used by: CoPub is used by: DisGeNET is used by: Molecular Imaging and Contrast Agent Database is listed by: 3DVC is related to: KLEIO is related to: FACTA+. is related to: MeSH is related to: XplorMed is related to: MeSH is related to: MuGeX is related to: EBIMed is related to: MEDIE is related to: GREC Corpus is related to: GENIA Project: Mining literature for knowledge in molecular biology is related to: PubMed is related to: Automated recognition of brain region mentions in neuroscience literature. is related to: PubMed is related to: PIE the search is related to: Coremine Medical is related to: Whatizit is related to: Cochrane Central Register of Controlled Trials has parent organization: National Library of Medicine |
nlx_53277 | SCR_002185 | 2026-08-01 12:02:00 | 48375 | |||||||||
|
Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | data analysis service, data access protocol, service resource, production service resource, software resource, analysis service resource, web service | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-08-01 12:02:59 | 8 | |||||||
|
GREC Corpus Resource Report Resource Website 1+ mentions |
GREC Corpus (RRID:SCR_006719) | GREC | training set | A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format | annotation, information extraction, text mining, semantic role, semantic search, gene, computational linguistics, gene regulation |
is listed by: FORCE11 is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:19852798 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, For Copyright of abstracts refer to PubMed. | nif-0000-06688 | SCR_006719 | Gene Event Regulation Corpus | 2026-08-01 12:03:18 | 3 | |||||
|
PubMed Resource Report Resource Website 10000+ mentions |
PubMed (RRID:SCR_004846) | data or information resource, database, bibliography | Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut. | biomedical, literature, publication, open, access, bibliography, gold standard |
is used by: Knowledgebase for Addiction Related Genes is used by: Drug Related Gene Database is used by: ChannelPedia is used by: Molecular Imaging and Contrast Agent Database is used by: Colwiz is used by: Nowomics is used by: PINT is listed by: OMICtools is listed by: FORCE11 is listed by: LabWorm is related to: Chilibot: Gene and Protein relationships from MEDLINE is related to: ImpactStory is related to: Automated recognition of brain region mentions in neuroscience literature. is related to: Information Hyperlinked Over Proteins is related to: PubMed Central is related to: PIE the search is related to: Anne O'Tate is related to: PubBrain is related to: Europe PubMed Central is related to: ResearchGate is related to: CBioC is related to: CiteAb is related to: LitInspector is related to: RefMED is related to: Pubmed Commons is related to: iBIOFind is related to: Ensembl Variation is related to: MEDLINE is related to: XplorMed is related to: Linked Neuron Data is related to: NCBI Structure is related to: MeSH is related to: MEDLINE is related to: EBIMed is related to: Coremine Medical is related to: NIF Literature is related to: GoPubMed is related to: Integrated Auto-Extracted Annotation is related to: Polbase is related to: Integrated Manually Extracted Annotation is related to: DaTo is related to: NIF Registry Automated Crawl Data has parent organization: NCBI works with: Open Regulatory Annotation Database works with: rentrez |
NLM | Free, Freely available | nlx_82958, OMICS_01195 | http://www.force11.org/node/4652, http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed | SCR_004846 | Pub Med | 2026-08-01 12:02:41 | 98390 | ||||||
|
MuGeX Resource Report Resource Website |
MuGeX (RRID:SCR_005306) | MuGeX | service resource | Service that automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease. | disease, gene, mutation |
is listed by: OMICtools is related to: MEDLINE has parent organization: Sabanci University; Istanbul; Turkey |
PMID:18172928 | Acknowledgement requested | OMICS_01189 | SCR_005306 | MuGeX - Mutation Gene Extractor, Mutation Gene Extractor | 2026-08-01 12:02:49 | 0 | ||||||
|
CoPub Resource Report Resource Website 1+ mentions |
CoPub (RRID:SCR_005327) | CoPub | software resource, data access protocol, service resource, web service | Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. | microarray, gene, literature, enrich, annotate, network, database, differential expression, bio.tools |
uses: MEDLINE uses: Gene Ontology is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Netherlands Bioinformatics Centre |
Netherlands Bioinformatics Centre | PMID:18442992 | Free, Public, Acknowledgement requested | OMICS_01178, biotools:copub | https://bio.tools/copub | http://services.nbic.nl/cgi-bin/copub/CoPub.pl | SCR_005327 | 2026-08-01 12:02:50 | 5 | ||||
|
DisGeNET Resource Report Resource Website 1000+ mentions |
DisGeNET (RRID:SCR_006178) | DisGeNET | data or information resource, database | Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature. | gene, disease, gene-disease association, gene-disease ontology, gene-disease text mining, text mining, genotype-phenotype, rdf, genotype, phenotype, gene-disease, variant-disease, FASEB list |
uses: Comparative Toxicogenomics Database (CTD) uses: Genetic Association Database uses: UniProt uses: Mouse Genome Database uses: Reactome uses: Unified Medical Language System uses: Entrez Gene uses: MEDLINE uses: National Center for Biomedical Ontology uses: National Cancer Institute Thesaurus uses: Human Phenotype Ontology uses: Semanticscience Integrated Ontology uses: Cytoscape uses: Literature-derived human gene-disease network uses: Rat Genome Database (RGD) uses: National Library of Medicine uses: PsyGeNET is used by: HmtPhenome is listed by: 3DVC is affiliated with: Gene-Disease Association Type Ontology has parent organization: Pompeu Fabra University; Barcelona; Spain |
EFPIA ; Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regional ; Elixir-Excelerate ; Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Union Horizon 2020 |
PMID:27924018 PMID:25877637 PMID:21695124 PMID:20861032 |
Restricted | nlx_151710, r3d100013301 | https://doi.org/10.17616/R31NJMR9 | SCR_006178 | database of gene disease associations | 2026-08-01 12:09:37 | 2210 | ||||
|
MEDIE Resource Report Resource Website 1+ mentions |
MEDIE (RRID:SCR_006254) | MEDIE | data analysis service, service resource, production service resource, analysis service resource | An intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining techniques. You can find abstracts/sentences in MEDLINE by specifying semantics of correlations; for example, What activates p53 and What causes colon cancer. Semantic search uses a semantic query for finding biomedical correlations. Input a subject, a verb, and an object of a concept (or either of them) into a form. Results of the query will be shown in a second. (E.g., What does p53 activate? (subject=p53, verb=activate)) Reference: Miyao, Yusuke, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya and Jun''''ichi Tsujii (2006) Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. Proceedings COLING-ACL 2006. Sydney, Australia, pp. 1017--1024. | natural language processing, text mining, semantic search, computational linguistics, search engine |
is used by: BioLexicon is listed by: OMICtools is listed by: FORCE11 is related to: MEDLINE has parent organization: University of Tokyo; Tokyo; Japan has parent organization: National Centre for Text Mining |
nif-0000-06682, OMICS_01188 | http://www-tsujii.is.s.u-tokyo.ac.jp/medie/, https://www.force11.org/node/4643 | SCR_006254 | 2026-08-01 12:09:37 | 3 | ||||||||
|
FACTA+. Resource Report Resource Website 1+ mentions |
FACTA+. (RRID:SCR_001767) | FACTA+ | software resource, data access protocol, service resource, web service | Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/ | text mining, gene, protein, disease, symptom, drug, enzyme, compound, biomedical, association, machine learning, chemical, text-mining software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:18772154 | Free, Freely available | biotools:facta_plus, nif-0000-10272, OMICS_01181 | http://refine1-nactem.mc.man.ac.uk/facta/, https://bio.tools/facta_plus | SCR_001767 | Finding Associated Concepts with Text Analysis | 2026-08-01 12:07:31 | 2 | ||||
|
MeSH Resource Report Resource Website 10000+ mentions |
MeSH (RRID:SCR_004750) | MeSH | controlled vocabulary, data or information resource | A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world''''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic. | umls, database, health, thesaurus, medical, gold standard |
is used by: Nowomics is used by: Cytokine Registry is listed by: BioPortal is related to: MEDLINE is related to: Public Health Image Library is related to: MEDLINE is related to: DermAtlas. is related to: Coremine Medical is related to: Unified Medical Language System is related to: I3-CRB: Interoperable IT Infrastructure for Biological Resources Centres / Biobanks - France is related to: Robert Hoehndorf Version of MeSH is related to: PharmGKB Ontology is related to: Linked Neuron Data is related to: PubMed has parent organization: National Library of Medicine |
Free | nlx_75424 | http://purl.bioontology.org/ontology/MESH | SCR_004750 | MeSH (Medical Subject Headings), Medical Subject Headings | 2026-08-01 12:02:40 | 31414 | ||||||
|
GENIA Project: Mining literature for knowledge in molecular biology Resource Report Resource Website 1+ mentions |
GENIA Project: Mining literature for knowledge in molecular biology (RRID:SCR_007990) | GENIA | software resource | Resources and tools from a project to automatically extract useful information from texts written by scientists to help overcome the problems caused by information overload. The primary annotated resource created is the GENIA corpus, a collection of biomedical literature which consists of multiple layers of annotation, encompassing both syntactic and semantic annotation. The project also created or coordinated the annotation of multiple other corpus resources. Additionally, a rich set of automatic tools are available for various annotation tasks, most trained on various parts of the GENIA corpus annotations. The GENIA corpus was developed to provide a reference material for the development of bio-TM systems. The corpus currently contains 1,999 Medline abstracts which were collected using the three MeSH terms, human, blood cells, and transcription factors. The corpus has been annotated with various levels of linguistic and semantic information. The GENIA corpus includes the following: * POS annotation * Treebank * Coreference Annotation * Term annotation * Event annotation * Relation annotation * Cellular localization * Disease-Gene association * Pathway corpus The GENIA Project initiated the BioNLP Shared Task series and has organized a number of tasks in three different shared task events, many using resources based on GENIA Corpus annotations. Tools include: * XConc suite: a collection of XML-based tools which are integrated to support the corpus development and annotation. | annotation, biomedical, computational linguistics, text mining, literature, molecular biology, syntactic annotation, semantic annotation, syntax, semantics, information extraction, blood cell, transcription factor, protein interaction, task |
is listed by: FORCE11 is related to: MEDLINE has parent organization: National Centre for Text Mining has parent organization: University of Tokyo; Tokyo; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japan Science and Technology Agency |
nif-0000-06689 | http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/home/wiki.cgi?page=GENIA+Project | SCR_007990 | 2026-08-01 12:03:35 | 2 | |||||||
|
EBIMed Resource Report Resource Website 1+ mentions |
EBIMed (RRID:SCR_005314) | EBIMed | service resource | A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading. | protein, gene, annotation, drug, specie, association, database |
is listed by: OMICtools is related to: MEDLINE is related to: PubMed is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: MedlinePlus has parent organization: European Bioinformatics Institute |
OMICS_01180 | SCR_005314 | 2026-08-01 12:02:58 | 1 | |||||||||
|
Coremine Medical Resource Report Resource Website 1+ mentions |
Coremine Medical (RRID:SCR_005323) | Coremine Medical | service resource | Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles. | disease, drug, treatment, medical biology, text mining, health, medicine, biology, network, database |
is listed by: OMICtools is related to: MeSH is related to: Entrez Gene is related to: MEDLINE is related to: PubMed is related to: DrugBank is related to: Gene Ontology is related to: UniProt has parent organization: PubGene |
NLM ; European Union FP7 ; Research Council of Norway ; Innovation Norway |
Copyrighted | OMICS_01179 | SCR_005323 | 2026-08-01 12:02:50 | 6 | |||||||
|
Molecular Imaging and Contrast Agent Database Resource Report Resource Website 1+ mentions |
Molecular Imaging and Contrast Agent Database (RRID:SCR_006712) | MICAD | data or information resource, narrative resource, database, data set, book | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Searchable book regarding molecular imaging and contrast agents (under development, in clinical trials or commercially available for medical applications) that have in vivo data (animal or human) published in peer-reviewed scientific journals prior to June 30 of 2013. 1444 agents are currently listed and there will be no more updates. Also available is a downloadable list of FDA approved contrast agents (Latest update: January 2013) and a Molecular Imaging Probes and Contrast Agents List (MIP & CA List) created by the MICAD staff by screening the PubMed / MedLine databases and other appropriate sources of such information. Only agents used in animal or human studies yielding in vivo data were selected for inclusion in the list. The list is by no means considered complete. No one imaging modality has been given preference over the others and the omission of any agent(s) or the introduction of any errors in the list is purely unintentional. The MIP & CA List is subject to the same copyright and disclaimers as the rest of the MICAD content. The database includes, but is not limited to, agents developed for positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), ultrasound (US), computed tomography (CT), optical imaging, planar radiography, and planar gamma imaging. The information on each agent is summarized in a book chapter format containing several sections such as Background, Synthesis, in vitro studies, Animal Studies (with sub-sections: rodents, other non-human primate animals, and human primates), Human Studies, and References. In addition, the references are linked to PubMed for retrieval of the publication abstract. Also, each chapter contains links to resources at the National Center for Biotechnology Information (NCBI) and other relevant databases regarding the target of the imaging probe or contrast agent. | contrast agent, in vitro, in vivo, magnetic resonance imaging, molecular imaging, molecular library, molecular probe, probe, positron emission tomography, single photon emission computed tomography, ultrasound, computed tomography, optical imaging, planar radiography, planar gamma imaging, gold standard |
uses: PubMed uses: MEDLINE has parent organization: NCBI |
NIH Common Fund | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00215 | http://www.ncbi.nlm.nih.gov/books/bookres.fcgi/micad/home.html | SCR_006712 | Molecular Imaging and Contrast Agent Database (MICAD) | 2026-08-01 12:03:12 | 5 | |||||
|
3DVC Resource Report Resource Website |
3DVC (RRID:SCR_001377) | 3DVC | portal, data or information resource, community building portal | THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content. | cell, model, biological structure, molecule |
lists: Albinism database lists: ButterflyBase lists: G2P Knowledge Centre lists: Bio-Job.org lists: RettBASE: IRSF MECP2 Variation Database lists: Resource for Biocomputing Visualization and Informatics lists: National Center for Integrative Biomedical Informatics lists: Genome Network Platform lists: NeuroExplorer lists: Open Provenance Model lists: BarleyBase lists: BioModels lists: Arabidopsis Reactome lists: MEDLINE lists: bioDBcore lists: GermOnline lists: GlycoMapsDB lists: SNPHunter lists: Allen Institute for Brain Science Sleep Study lists: Coddle-Codons Optimized to Discover Deleterious LEsions lists: MicroArray and Gene Expression Markup Language lists: Fungal Genome Initiative lists: EMDataResource.org lists: University of Southern California LONI Software lists: Ontology Development and Information Extraction lists: Software Distribution Sets lists: L-Measure lists: UCSF Chimera lists: Zebrafish Neurophenome Project Database lists: Standards-based Infrastructure with Distributed Resources lists: HapMap 3 and ENCODE 3 lists: NCBI BioProject lists: SEQanswers Wiki lists: NIF Data Federation lists: SMD lists: SoyBase lists: modelcrop.org lists: BiGG Database lists: FSST - Functional Similarity Search Tool lists: LHP LHDL lists: Open Provenance Model Vocabulary lists: DiseaseMeth lists: neuroVIISAS lists: Predictive Networks lists: SitEx lists: NRCAM lists: DisGeNET lists: MCMBB lists: BARD lists: Mouse Genome Informatics (MGI) lists: European Nucleotide Archive (ENA) lists: Comparative Toxicogenomics Database (CTD) lists: PomBase lists: Stanford University HIV Drug Resistance Database lists: Database of Chemical Compounds and Reactions in Biological Pathways lists: UCSD-Nature Signaling Gateway Molecule Pages lists: IntAct lists: The WWW Virtual Library: Model Organisms lists: Helicobacter Pylori Database of Protein Interactomes lists: Genes to Cognition: Neuroscience Research Programme lists: neuroConstruct lists: ModelDB lists: 3DViewnix lists: TMRPres2D lists: Ikaros Project lists: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING lists: Interagency Modeling and Analysis Group lists: Annozilla (Annotea on Mozilla) lists: Artificial Selected Proteins/Peptides Database lists: Cancer Chromosomes lists: CATMA - Complete Arabidopsis Transcriptome MicroArray lists: Combinatorial Extension (CE) lists: ChemDB: The UC Irvine ChemDB lists: CluSTr lists: CTDatabase lists: DRC - Database of Ribosomal Crosslinks lists: Gene Expression in Tooth Database lists: GenoBase lists: GPX-Macrophage lists: Hetero-compound Information Centre- Uppsala lists: IMG lists: InSatDb lists: InterDom lists: IPD-HPA - Human Platelet Antigens lists: Max Planck Unified Proteome Database lists: Molecular Modelling DataBase lists: MegaMotifbase lists: Metalloprotein Site Database lists: MitoDat - Mendelian Inheritance and the Mitochondrion lists: Madison Metabolomics Consortium Database lists: Olfactory Receptor DataBase lists: SUPERFAMILY lists: EyeBrowse lists: Allen Institute Mouse Diversity Study lists: BIRD - Bio Info R and D lists: Bioinformatics Links Directory lists: Electroencephalogram Database: Prediction of Epileptic Seizures lists: Human Protein-Protein Interaction Mining Tool lists: Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki lists: Systems Biology Workbench lists: CellML lists: MathML lists: AraCyc lists: Biochemical Pathways database lists: CellML Model Repository lists: Cytokine Family Database lists: Bacterial Genomes lists: U.S. Pig Genome Project lists: ComBase: A Combined Database For Predictive Microbiology lists: GeneWindow lists: Comprehensive Systems-Biology Database lists: Candidate Genes to Inherited Diseases lists: MeGX lists: Mammalian Phosphorylation Resource lists: Efficient Mixed-Model Association lists: Proteome Analyst PA-GOSUB lists: PubCrawler lists: Conical: The Computational Neuroscience Class Library lists: Gene Expression Profile Analysis Suite lists: Adaptive Poisson-Boltzmann Solver lists: Aggrescan: The Hot Spot Finder lists: Distributed Annotation System lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: DNAWorks at Helix Systems lists: Microarray DB lists: Gene Relationships Across Implicated Loci lists: SEQtools lists: DeRisi Lab lists: Protein Subcellular Location Image Database lists: Open Information Integration lists: Metagenomics Program at JGI lists: BrainPeps lists: EGAN: Exploratory Gene Association Networks lists: CBioC lists: OrChem lists: Generic GO Term Finder lists: G-node portal electrophysiology data sharing lists: LegumeIP lists: Roadmap Epigenomics Project lists: TrakEM2 lists: ATID: Alternative Translational Initiation Database lists: linked life data - a semantic data integration platform for the biomedical domain lists: Crux tandem mass spectrometry analysis software lists: CellProfiler Analyst lists: Scirus - for scientific information only lists: SRS lists: KEGG lists: Antibodypedia lists: SWISS-MODEL Repository lists: BTKbase lists: ExTopoDB lists: MINAS - Metal Ions in Nucleic AcidS lists: Tripod lists: NIH electronic Research Materials catalogue lists: Alliance for Cellular Signaling Molecule Pages Database lists: Death Domain database lists: Cube-DB lists: OntoQuest lists: EASE: the Expression Analysis Systematic Explorer lists: Greglist lists: Chloroplast Genome Database lists: Montage RTS2000 lists: BGI-RISe - Beijing Genomics Institute Rice Information System lists: ApiDB CryptoDB lists: Chilibot: Gene and Protein relationships from MEDLINE lists: AutDB lists: DAVID lists: Dataverse Network Project lists: Binding MOAD lists: Biological Magnetic Resonance Data Bank (BMRB) lists: RNAhybrid lists: RegulonDB lists: Artemis: Genome Browser and Annotation Tool lists: Genomedata lists: CATSS - Child and Adolescent Twin Study in Sweden lists: Viking Viewer for Connectomics lists: SpliceDB lists: Galaxy lists: SPM lists: Hyper Cell Line Database lists: MeGX has parent organization: University of California at San Diego; California; USA |
NSF 1216893 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152536 | http://www.3dvcell.org/conference-toward-3d-virtual-cell | SCR_001377 | 3D Virtual Cell | 2026-08-01 12:01:29 | 0 | |||||
|
KLEIO Resource Report Resource Website 1+ mentions |
KLEIO (RRID:SCR_000698) | KLEIO | service resource | An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008 | semantic search, entity recognition |
is listed by: FORCE11 is listed by: OMICtools is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | Acknowledgement required, See Terms of Use | OMICS_01186, nlx_44954 | http://www.nactem.ac.uk/software/kleio/ | SCR_000698 | 2026-08-01 12:01:29 | 3 | ||||||
|
Cochrane Central Register of Controlled Trials Resource Report Resource Website 10000+ mentions |
Cochrane Central Register of Controlled Trials (RRID:SCR_006576) | CENTRAL, CCRCT | clinical trial, data or information resource, database | A bibliographic database that provides a highly concentrated source of reports of randomized controlled trials. Records contain the list of authors, the title of the article, the source, volume, issue, page numbers, and, in many cases, a summary of the article (abstract). They do not contain the full text of the article. Cochrane Groups maintain and update Specialized Registers, which are collections of controlled trials relevant to the groups. CENTRAL is comprised of these Specialized Registers, relevant records retrieved from MEDLINE and EMBASE, and records retrieved through handsearching (planned manual searching of a journal or conference proceedings to identify all reports of randomized controlled trials and controlled clinical trials). The Cochrane Collaboration contracts a technology company, Metaxis, to merge the records from the sources outlined above and provide a data feed to the publisher. New and changed data are delivered to the publisher on a monthly basis. | controlled trial, bibliography, register, randomized controlled trial, report, FASEB list |
is related to: EMBASE is related to: MEDLINE |
nlx_153928 | SCR_006576 | 2026-08-01 12:03:10 | 12271 | |||||||||
|
National Library of Medicine Resource Report Resource Website 100+ mentions |
National Library of Medicine (RRID:SCR_011446) | NLM | government granting agency | NLM collects, organizes, and makes available biomedical science information to scientists, health professionals, and the public. The Library's Web-based databases, including PubMed/Medline and MedlinePlus, are used extensively around the world. NLM conducts and supports research in biomedical communications; creates information resources for molecular biology, biotechnology, toxicology, and environmental health; and provides grant and contract support for training, medical library resources, and biomedical informatics and communications research. Celebrating its 175th anniversary in 2011, the National Library of Medicine (NLM), in Bethesda, Maryland, is a part of the National Institutes of Health, U.S. Department of Health and Human Services (HHS). Since its founding in 1836 as the library of the U.S. Army Surgeon General, NLM has played a pivotal role in translating biomedical research into practice. It is the world's largest biomedical library and the developer of electronic information services that deliver trillions of bytes of data to millions of users every day. Scientists, health professionals, and the public in the United States and around the globe search the Library's online information resources more than 1 billion times each year. The Library is open to all and has many services and resources for scientists, health professionals, historians, and the general public. NLM has over 17 million books, journals, manuscripts, audiovisuals, and other forms of medical information on its shelves, making it the largest health-science library in the world. In today's increasingly digital world, NLM carries out its mission of enabling biomedical research, supporting health care and public health, and promoting healthy behavior by: * Acquiring, organizing, and preserving the world's scholarly biomedical literature; * Providing access to biomedical and health information across the country in partnership with the 5,800-member National Network of Libraries of Medicine (NN/LM); * Serving as a leading global resource for building, curating and providing sophisticated access to molecular biology and genomic information, including those from the Human Genome Project and NIH Common Fund; * Creating high-quality information services relevant to toxicology and environmental health, health services research, and public health; * Conducting research and development on biomedical communications systems, methods, technologies, and networks and information dissemination and utilization among health professionals, patients, and the general public; * Funding advanced biomedical informatics research and serving as the primary supporter of pre- and post-doctoral research training in biomedical informatics at 18 U.S. universities. |
is used by: DisGeNET recommends: Brain Image Library recommends: Data Archive BRAIN Initiative recommends: OpenNeuro recommends: Brain Observatory Storage Service and Database (BossDB) recommends: CRCNS recommends: NCBI database of Genotypes and Phenotypes (dbGap) recommends: NIMH Data Archive recommends: ENCODE recommends: Genotype-Tissue Expression recommends: HMP Data Analysis and Coordination Center recommends: Illuminating the Druggable Genome recommends: Kids First Data Resource Portal recommends: HMS LINCS Database recommends: Metabolomics Workbench recommends: Patient-Reported Outcomes Measurement Information System recommends: Cancer Nanotechnology Laboratory (caNanoLab) recommends: Cancer Imaging Archive (TCIA) recommends: Network Data Exchange (NDEx) recommends: eyeGENE recommends: National Eye Institute (NEI) Commons recommends: National Sleep Research Resource (NSRR) recommends: CardioVascular Research Grid (CVRG) recommends: AMP-AD Knowledge Portal recommends: National Archive of Computerized Data on Aging (NACDA) recommends: National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) recommends: Immune Tolerance Network TrialShare recommends: The Immunology Database and Analysis Portal (ImmPort) recommends: VectorBase recommends: Virus Pathogen Resource (ViPR) recommends: LONI Image and Data Archive recommends: NeuroImaging Tools and Resources Collaboratory (NITRC) recommends: Child Language Data Exchange System (CHILDES) recommends: Data and Specimen Hub (NICHD DASH) recommends: National Children's Study (NCS) Archive recommends: PhonBank recommends: Archive of Data on Disability to Enable Policy (ADDEP) recommends: National Addiction and HIV Data Archive Program (NAHDAP) recommends: Neuroscience Information Framework recommends: National Institute on Drug Abuse Center for Genetic Studies recommends: NIDA Data Share recommends: AphasiaBank recommends: FluencyBank recommends: NIDDK Central Repository recommends: NIDDK Information Network (dkNET) recommends: Nuclear Receptor Signaling Atlas recommends: Chemical Effects in Biological Systems (CEBS) recommends: Cell Image Library (CIL) recommends: PhysioNet recommends: Transporter Classification Database recommends: Biological General Repository for Interaction Datasets (BioGRID) recommends: Federal Interagency Traumatic Brain Injury Research Informatics System recommends: NeuroMorpho.Org recommends: Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) recommends: The NINDS Human Cell and Data Repository (NHCDR) recommends: ClinicalTrials.gov recommends: dbSNP recommends: dbVar recommends: GenBank recommends: Gene Expression Omnibus (GEO) recommends: NCBI Sequence Read Archive (SRA) recommends: 1000 Functional Connectomes Project recommends: exRNA Atlas recommends: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) recommends: PeptideAtlas recommends: Zebrafish Information Network (ZFIN) recommends: FlyBase recommends: Database of Interacting Proteins (DIP) recommends: Mouse Genome Informatics (MGI) recommends: UniProt recommends: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) recommends: European Nucleotide Archive (ENA) recommends: Analysis, Visualization, and Informatics Lab-space (AnVIL) recommends: DNA DataBank of Japan (DDBJ) recommends: UniProtKB recommends: SPARC Portal is related to: CureHunter is related to: Entrez has parent organization: National Institutes of Health is parent organization of: MalariaWorld is parent organization of: GenNav is parent organization of: NIH Common Data Element Repository is parent organization of: MEDLINE is parent organization of: ClinicalTrials.gov is parent organization of: Developmental and Reproductive Toxicology Database is parent organization of: Directory of Health Organizations Online is parent organization of: Haz-Map: Occupational Exposure to Hazardous Agents is parent organization of: Hazardous Substances Data Bank is parent organization of: Drug Information Portal is parent organization of: NIH Data Sharing Repositories is parent organization of: MeSH is parent organization of: Unified Medical Language System is parent organization of: NCBI is parent organization of: MedlinePlus is parent organization of: RxNorm is parent organization of: Bibliography on Alternatives to the Use of Live Vertebrates in Biomedical Research and Testing is parent organization of: Chemical Carcinogenesis Research Information System is parent organization of: International Toxicity Estimates for Risk is parent organization of: BLAST Assembled RefSeq Genomes is parent organization of: Cross-Sectional and Longitudinal Aging Study is parent organization of: OrbitProject is parent organization of: Household Products Database is parent organization of: Entrez Utilities is parent organization of: Epidemiology of Chronic Disease in the Oldest Old |
nlx_inv_1005117 | SCR_011446 | U.S. National Library of Medicine | 2026-08-01 12:04:09 | 391 | |||||||||
|
PIE the search Resource Report Resource Website 1+ mentions |
PIE the search (RRID:SCR_005296) | PIE | data or information resource, database, service resource | A web service to extract Protein-protein interaction (PPI)-relevant articles from MEDLINE that provides protein interaction information (PPI) articles for biologists, baseline system performance for bio-text mining researchers and a compact PubMed-search environment for PubMed users. It accepts PubMed input formats including All Fields, Author, Journal, MeSH Terms, Publication Date, Title, and Title/Abstract with Boolean operations (AND, OR, and NOT). However, the output is the list of articles prioritized by PPI confidence rates. Some words (mostly gene/protein names) which contributed for PPI prediction are underlined and linked to Entrez or Entrez Gene. Even though our system focuses on a PubMed search environment, it also provides a CGI access for bio-text mining researchers. Using the CGI program, a list of PubMed IDs can be obtained as a query result, thus it can be utilized as a baseline system performance. PIE the search is based on a winning approach in the BioCreative III ACT competition (BC3)1. For input queries, MEDLINE articles are first retrieved through the PubMed service. PPI scores are calculated for the retrieved articles, and the articles are re-ranked based on scores. To effectively capture PPI patterns from biomedical literature, their approach utilizes both word and syntactic features for machine learning classifiers. Dependency parsing, gene mention tagging, and term-based features are utilized along with a Huber classifier. | protein interaction, protein-protein interaction, protein, interaction |
is listed by: OMICtools is related to: PubMed is related to: MEDLINE has parent organization: NCBI |
PMID:22199390 PMID:22151252 |
OMICS_01191 | SCR_005296 | Protein Interaction information Extraction the search | 2026-08-01 12:09:30 | 1 | |||||||
|
XplorMed Resource Report Resource Website 1+ mentions |
XplorMed (RRID:SCR_002549) | data analysis service, service resource, production service resource, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Server that allows you to explore a set of abstracts derived from a MEDLINE search. The system gives you the main associations between the words in groups of abstracts. Then, you can select a subset of your abstracts based on selected groups of related words and iterate your analysis on them. The only input needed is a set of abstracts (in one of the currently accepted input formats) or a definition of how to obtain them. XplorMed is recommended for cases in which you do not know exactly what are you expecting to find. Your interests may be modified by the results obtained, or you may want to inquire new questions as the analysis develops. Also, the results may suggest you additional words that should be used to expand your query in MEDLINE (e.g., unexpected abbreviations of a protein name, or synonyms of a disease). | abstract, literature-research, information retrieval, part-of-speech, bioinformatics, text-mining, literature |
is related to: MEDLINE is related to: PubMed has parent organization: University of Ottawa; Ontario; Canada |
PMID:12532176 PMID:11551795 PMID:12074170 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21425 | http://www.ogic.ca/projects/xplormed/ | SCR_002549 | Xploring Medline abstracts, XplorMed: eXploring Medline abstracts | 2026-08-01 12:09:06 | 1 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
