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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.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
NIF Registry Automated Crawl DataResource, data set, data or information resourceAn automatic pipeline based on an algorithm that identifies new resources in publications every month to assist the efficiency of NIF curators. The pipeline is also able to find the last time the resource's webpage was updated and whether the URL is still valid. This can assist the curator in knowing which resources need attention. Additionally, the pipeline identifies publications that reference existing NIF Registry resources as this is also of interest. These mentions are available through the Data Federation version of the NIF Registry, The RDF is based on an algorithm on how related it is to neuroscience. (hits of neuroscience related terms). Each potential resource gets assigned a score (based on how related it is to neuroscience) and the resources are then ranked and a list is generated.resource, mention, updateSCR_012862(NIF Registry Automated Crawl Data, RRID:SCR_012862)Neuroscience Information Framework NIDA, NIH Blueprint for Neuroscience Research, U.S. Department of Health and Human Servicesrelated to: PubMed Central, Integrated Auto-Extracted Annotation, Integrated Manually Extracted Annotation, PubMed, used by: NIF Data Federation, Integrated DatasetsPMID:22434839Last checked downnlx_144525
Pubmed CommonsResource, narrative resource, discussion, forum, data or information resourceA forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate, PubMed, commuicationSCR_014021(Pubmed Commons, RRID:SCR_014021)NIH, NLMrelated to: PubMed, Connected Researchers, listed by: Connected ResearchersLast checked down
iBIOFindResource, software resource, software application, service resource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles.workflow, model, prediction, research trend, rare disease, resource discovery, biomedicine, genomic, neural network, visualization, reporting, search engine, genetic, neural, clinical translation science award, biomedical resource, funding, gene, protein, neuron, collaborator, publication, trend, grant, funding opportunity, reportSCR_001587(iBIOFind, RRID:SCR_001587)The Cromwell Workshop related to: ModelMaker, Neural Maestro, eNeoTutor, Cytoscape, Biomedical Resource Ontology, PubMedLast checked downnlx_153829
Ensembl VariationResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourcePublic database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population.genome, disease, phenotype, genomic variant, single nucleotide polymorphism nucleotide, insertion, deletion, structural variant, copy number variation, inversion, translocation, somatic variant, allele frequency, genotype, disease phenotype, inherited diseaseSCR_001630(Ensembl Variation, RRID:SCR_001630)Ensembl related to: dbSNP, Database of Genomic Variants Archive, PubMed, Animal QTLdb, OMIA - Online Mendelian Inheritance in Animals, used by: Monarch InitiativeReferences (4)Last checked downnlx_153897
XplorMedResource, analysis service resource, data analysis service, service resource, production service resourceServer 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, literatureSCR_002549(XplorMed, RRID:SCR_002549)University of Ottawa; Ontario; Canada related to: MEDLINE, PubMedReferences (3)Last checked downnif-0000-21425
ImpactStoryResource, software resource, source code, service resource, production service resourceA web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile.altmetrics, metric, citeulike, crossref, scienceseeker, scopus, slideshare, topsy, twitter, vimeo,, plos, youtubeSCR_002632(ImpactStory, RRID:SCR_002632)Alfred P. Sloan Foundation, NSF, Open Society Foundationrelated to: PubMed, GitHub, FigShare, Dryad, Wikipedia, Mendeley, used by: Publons, listed by: FORCE11, Connected Researchers, PLOS Article-Level MetricsLast checked downnlx_156056
EBIMedResource, service resourceA 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, databaseSCR_005314(EBIMed, RRID:SCR_005314)European Bioinformatics Institute related to: MEDLINE, PubMed, Gene Ontology, Universal Protein Resource, NCBI Taxonomy, MedlinePlus, listed by: OMICtoolsLast checked downOMICS_01180
NIF LiteratureResource, narrative resource, data or information resourceSimultaneous search across multiple literature indices, including PubMed and Open Access literature, it is one of the core resources of NIF accessed through the NIF search interface. Literature results are displayed under the Literature tab. Features: * Facet by Year, Author, and / or Journal * Option to search open access literature only * Sort by relevance or year * Snippets from the full text of the paper are included in search results where search term was found * LinkOuts are now provided for some papers. These mean that someone associated a reagent, piece of data, note/blog, etc., with this specific publication. * Searching within sections of articles is now possible within the open access literature. For more info, see, * Annotate papers. Any user can submit a public comment or annotation of an open access paper through the DOMEO tool. For more information, see, journal, pubmed, pubmed central, biomedical, open access, abstract, linkoutSCR_005401(NIF Literature, RRID:SCR_005401)Neuroscience Information Framework NIH Blueprint for Neuroscience Researchrelated to: NeuroMorpho.Org, NIF Web Services, DOMEO, PubMed, PubMed CentralLast checked downnlx_144510*&tab=literature
Integrated Auto-Extracted AnnotationResource, data set, data or information resourceA virtual database that indexes both BioNOT for negation data, and the Resource Discovery Pipeline: an automated resource discovery and semi-automated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. This virtual database currently indexes the following resources: * BioNOT, * Resource Discovery Pipeline,, negative dataSCR_005892(Integrated Auto-Extracted Annotation, RRID:SCR_005892)Integrated NIDA, NIH Blueprint for Neuroscience Researchrelated to: BioNOT, NIF Registry Automated Crawl Data, PubMed, used by: NIF Data FederationPMID:22434839Last checked downnlx_149462
ResearchGateResource, portal, data or information resource, community building portal, databaseA professional, social network and publication database geared to researchers where the latest field specific publications can be read, publications with other specialists can be discussed, and collaboration with colleagues is facilitated. They provide researchers with access to around 40 million abstracts and tens of thousands of Full texts, uploaded by the authors themselves. Researchers can search through 7 of the largest databases simultaneously, such as PubMed, IEEE & network, biology, literature, publication, bibliographic, abstract, collaborate, statistics, citationSCR_006505(ResearchGate, RRID:SCR_006505)related to: PubMed, listed by: FORCE11Last checked downnlx_143849
CBioCResource, software resourceA tool for extraction and collaboration for data curation related to biology. CBioC runs as a web browser extension and allows unobtrusive use of the system during the regular course of research in PubMed. It can also be accessed directly (without having to install a plug-in). Automated text extraction is used as a starting point to bootstrap the database, but then it is up to biologists improve upon the extracted data, ironing out inconsistencies by subsequent edits on a massive scale. * After install, it loads when you visit PubMed. * Gets interactions from PubMed abstracts. * Allows you to vote and modify extracted data. * Also shows data from BIND, DIP, MINT, GRID, IntAct.text extraction, curation, crowd sourcingSCR_008863(CBioC, RRID:SCR_008863)Arizona State University; Arizona; USA Arizona State Universityrelated to: PubMed, listed by: 3DVCPMID:17951840Last checked downnlx_149235
Integrated Manually Extracted AnnotationResource, data set, data or information resourceA virtual database of annotations made by 50 database providers (April 2014) - and growing (see below), that map data to publication information. All NIF Data Federation sources can be part of this virtual database as long as they indicate the publications that correspond to data records. The format that NIF accepts is the PubMed Identifier, category or type of data that is being linked to, and a data record identifier. A subset of this data is passed to NCBI, as LinkOuts (links at the bottom of PubMed abstracts), however due to NCBI policies the full data records are not currently associated with PubMed records. Database providers can use this mechanism to link to other NCBI databases including gene and protein, however these are not included in the current data set at this time. (To view databases available for linking see, ) The categories that NIF uses have been standardized to the following types: * Resource: Registry * Resource: Software * Reagent: Plasmid * Reagent: Antibodies * Data: Clinical Trials * Data: Gene Expression * Data: Drugs * Data: Taxonomy * Data: Images * Data: Animal Model * Data: Microarray * Data: Brain connectivity * Data: Volumetric observation * Data: Value observation * Data: Activation Foci * Data: Neuronal properties * Data: Neuronal reconstruction * Data: Chemosensory receptor * Data: Electrophysiology * Data: Computational model * Data: Brain anatomy * Data: Gene annotation * Data: Disease annotation * Data: Cell Model * Data: Chemical * Data: Pathways For more information refer to Create a LinkOut file, Participating resources ( ): * Addgene * Animal Imaging Database * Antibody Registry * Avian Brain Circuitry Database * BAMS Connectivity * Beta Cell Biology Consortium * bioDBcore * BioGRID * BioNumbers * Brain Architecture Management System * Brede Database * Cell Centered Database * CellML Model Repository * CHEBI * Clinical Trials Network (CTN) Data Share * Comparative Toxicogenomics Database * Coriell Cell Repositories * CRCNS - Collaborative Research in Computational Neuroscience - Data sharing * Drug Related Gene Database * DrugBank * FLYBASE * Gene Expression Omnibus * Gene Ontology Tools * Gene Weaver * GeneDB * Glomerular Activity Response Archive * GO * Internet Brain Volume Database * ModelDB * Mouse Genome Informatics Transgenes * NCBI Taxonomy Browser * NeuroMorpho.Org * NeuronDB * SciCrunch Registry * NIF Registry Automated Crawl Data * NITRC * Nuclear Receptor Signaling Atlas * Olfactory Receptor DataBase * OMIM * OpenfMRI * PeptideAtlas * RGD * SFARI Gene: AutDB * SumsDB * Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat * The Cell: An Image Library * Visiome Platform * WormBase * YPED * ZFIN http://zfin.orgbiomedical, bibliographic, linkout, literatureSCR_008876(Integrated Manually Extracted Annotation, RRID:SCR_008876)Integrated related to: BAMS Connectivity, BioGRID, BioNumbers, PubMed, Brain Architecture Management System, CellML Model Repository, CHEBI, Comparative Toxicogenomics Database, Coriell Cell Repositories, Drug Related Gene Database, DrugBank, Gene Weaver, Internet Brain Volume Database, Cell Centered Database, Brede Database, ModelDB, NeuronDB, NeuroMorpho.Org, Nuclear Receptor Signaling Atlas , Cell Image Library (CIL), Animal Imaging Database, Olfactory Receptor DataBase, Glomerular Activity Response Archive, CRCNS, OMIM, Rat Genome Database (RGD), Visiome Platform, NIDA Data Share, bioDBcore, Addgene, Antibody Registry, Beta Cell Biology Consortium , FlyBase, SumsDB, SciCrunch Registry, Mouse Genome Informatics Transgenes, NCBI Taxonomy, OpenNeuro, PeptideAtlas, Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat, NIF Registry Automated Crawl Data, AutDB, Gene Expression Omnibus, Gene Ontology, Avian Brain Circuitry Database, Zebrafish Information Network, GeneDB, WormBase, YPED, used by: NIF Data Federation, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), Gene Ontology ToolsReferences (2)Last checked downnlx_149407,*&t=indexable&list=cover&nif=nlx_149407-1
DaToResource, data or information resource, databaseA biological database and software tool catalog based on text mined and human annotated url mentions in PubMed abstracts. Data are annotated as to the author''''s country of origin and url status is checked.metadata, catalog, text miningSCR_010280(DaTo, RRID:SCR_010280)Zhejiang University; Zhejiang; China National Natural Science Foundation of Chinarelated to: Cytoscape, PubMedLast checked upnlx_157296
LitInspectorResource, software resource, commercial organizationA literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.gene, signal transduction, pathway, text-miningSCR_011870(LitInspector, RRID:SCR_011870)Genomatix Solutions related to: PubMed, listed by: OMICtoolsPMID:19417065Last checked upOMICS_01187
RefMEDResource, service resource, data or information resource, databaseRelevance Feedback Search Engine for PubMed. When a user enters a keyword in the search box, the PubMed search results will be returned. The user then specifies on a sample of results how much they are relevant to what she intends to find, for example, by specifying whether each article is high relevant, somewhat relevant, or not relevant. Once the user clicks Push Feedback button, the system learns a relevance function from the feedback and returns the top articles ranked highly according to the relevance function. The user can repeat the process until she gets satisfying results.relevance ranking, relevance, relevance feedback, data retrieval, data mining, knowledge discoverySCR_011871(RefMED, RRID:SCR_011871)Pohang University of Science and Technology; Pohang; South Korea Korean Governmentrelated to: PubMed, listed by: OMICtoolsPMID:20406504Last checked upOMICS_01197
Chilibot: Gene and Protein relationships from MEDLINEResource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resourceData analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulationdrug, gene, literature, natural language processing, protein, text-mining, network, keyword, biological concept, graphSCR_001705(Chilibot: Gene and Protein relationships from MEDLINE, RRID:SCR_001705)University of Tennessee Health Science Center; Tennessee; USA PHSrelated to: PubMed, listed by: OMICtools, 3DVCPMID:15473905Last checked upnif-0000-10196, OMICS_01176
MEDLINEResource, data or information resource, bibliography, databaseA 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, biomedicine, gold standardSCR_002185(MEDLINE, RRID:SCR_002185)National Library of Medicine related to: KLEIO, FACTA+., MeSH, XplorMed, MeSH, MuGeX, EBIMed, MEDIE, GREC Corpus, GENIA Project: Mining literature for knowledge in molecular biology, PubMed, Automated recognition of brain region mentions in neuroscience literature., PubMed, PIE the search, Coremine Medical, Whatizit, Cochrane Central Register of Controlled Trials, used by: CoPub, DisGeNET, Molecular Imaging and Contrast Agent Database, listed by: 3DVCLast checked upnlx_53277
Automated recognition of brain region mentions in neuroscience literature.Resource, data set, data or information resourceFreely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.brain region, annotation, journal of comparative neurology, neuroanatomy, brainSCR_002731(Automated recognition of brain region mentions in neuroscience literature., RRID:SCR_002731)University of British Columbia; British Columbia; Canada related to: PubMed, MEDLINE, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:19750194Last checked upnif-0000-24027
Linked Neuron DataResource, data set, data or information resourceNeuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc.neuron, brain, neuroscience, protein, gene, neurotransmitterSCR_003658(Linked Neuron Data, RRID:SCR_003658)Chinese Academy of Sciences; Beijing; China related to: Common Upper Mammalian Brain Ontology, Allen Reference Atlas - Mouse Brain, Neuroscience Information Framework, PubMed, NeuroLex, MeSH, DBpediaLast checked upnlx_157812
PubMed CentralResource, service resource, data or information resource, storage service resource, databaseCollection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.literature, biomedical, life, science, journal, repository, electronic, literature, gold standardSCR_004166(PubMed Central, RRID:SCR_004166)NCBI NIHrelated to: PubMed, JISC Open Citations, Biotea, NIF Registry Automated Crawl Data, NIF Literature, Europe PubMed Central, PubReader, uses: PubReader, listed by: OMICtoolsLast checked upnlx_18862, OMICS_01193
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