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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Protege Resource Report Resource Website 100+ mentions |
Protege (RRID:SCR_003299) | Protege | software resource, authoring tool, software application | Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the W3C's Web Ontology Language (OWL). An OWL ontology may include descriptions of classes, properties and their instances. Given such an ontology, the OWL formal semantics specifies how to derive its logical consequences, i.e. facts not literally present in the ontology, but entailed by the semantics. These entailments may be based on a single document or multiple distributed documents that have been combined using defined OWL mechanisms (see the OWL Web Ontology Language Guide). Protege is based on Java, is extensible, and provides a plug-and-play environment that makes it a flexible base for rapid prototyping and application development. | ontology, java, develop, manage, edit, plug-in, FASEB list |
is listed by: Biositemaps is related to: National Center for Biomedical Ontology is related to: Jambalaya has parent organization: Stanford University School of Medicine; California; USA has parent organization: Stanford Center for Biomedical Informatics Research |
Defense Advanced Research Projects Agency ; eBay ; NCI ; NIST - National Institute of Standards and Technology ; National Centers for Biomedical Computing ; NSF ; Neural ElectroMagnetic Ontologies NEMO ; Pfizer ; NLM LM007885 |
PMID:17687607 | Free, download Freely available | nif-0000-31708 | SCR_003299 | Protégé, Protege Project | 2026-02-14 02:00:25 | 147 | |||||
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Structural Biology Grid Resource Report Resource Website 50+ mentions |
Structural Biology Grid (RRID:SCR_003511) | SBGrid | data repository, storage service resource, computational hosting, data set, data or information resource, service resource | Computing resources structural biologists need to discover the shapes of the molecules of life, it provides access to web-enabled structural biology applications, data sharing facilities, biological data sets, and other resources valuable to the computational structural biology community. Consortium includes X-ray crystallography, NMR and electron microscopy laboratories worldwide.SBGrid Service Center is located at Harvard Medical School.SBGrid's NIH-compliant Service Center supports SBGrid operations and provides members with access to Software Maintenance, Computing Access, and Training. Consortium benefits include: * remote management of your customized collection of structural biology applications on Linux and Mac workstations; * access to commercial applications exclusively licensed to members of the Consortium, such as NMRPipe, Schrodinger Suite (limited tokens) and the Incentive version of Pymol; remote management of supporting scientific applications (e.g., bioinformatics, computational chemistry and utilities); * access to SBGrid seminars and events; and * advice about hardware configurations, operating system installations and high performance computing. Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, tomography and other experimental structural biology technologies in their research. Most new members are fully integrated with SBGrid within 2 weeks of the initial application. | structure, x-ray crystallography, nuclear magnetic resonance, electron microscopy, structural biology, software application, computation, chemistry, meeting, software service, molecule, data sharing, biomedical |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has parent organization: Harvard Medical School; Massachusetts; USA |
NSF | PMID:22514186 | Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, Tomography and other experimental structural biology technologies in their research., The community can contribute to this resource | nif-0000-37641, r3d100010234 | https://doi.org/10.17616/R3NS3R | http://sbgrid.org/index.php | SCR_003511 | SBGrid Software Consortium, SBGrid Science Portal, SBGrid Consortium | 2026-02-14 02:00:51 | 56 | |||
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Michigan Molecular Interactions Resource Report Resource Website 1+ mentions |
Michigan Molecular Interactions (RRID:SCR_003521) | MiMI | web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database | 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 | 2026-02-14 02:00:50 | 5 | |||||||
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Karma Resource Report Resource Website 50+ mentions |
Karma (RRID:SCR_003732) | Karma | data management software, software resource, software application | An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database. | integration, FASEB list |
is related to: GitHub has parent organization: University of Southern California; Los Angeles; USA |
Air Force Research Laboratory FA8750-14-C-0240; NCRR 1 U24 RR025736-01; NCRR 1 UL1 RR031986-01; NSF IIS-1117913; NSF CMMI-0753124 |
PMID:15215426 | Apache License, v2 | nlx_157923 | https://github.com/InformationIntegrationGroup/Web-Karma | SCR_003732 | Karma A Data Integration Tool, Karma - A Data Integration Tool | 2026-02-14 02:00:30 | 83 | ||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data analysis software, software resource, data processing software, software application | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/ https://bio.tools/gasv |
SCR_000061 | Geometric Analysis of Structural Variants | 2026-02-14 01:59:36 | 4 | ||||
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SiPhy Resource Report Resource Website 1+ mentions |
SiPhy (RRID:SCR_000564) | SiPhy | sequence analysis resource | Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions. | java, mutation, phylogeny, substitution pattern, mutation rate |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI ; NSF |
PMID:19478016 | Free, Available for download, Freely available, | OMICS_00183 | SCR_000564 | 2026-02-14 01:59:46 | 6 | ||||||
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forqs Resource Report Resource Website |
forqs (RRID:SCR_000643) | forqs | software resource, simulation software, software application | Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits. | c++, linux, osx, windows, command line, simulation, recombination, quantitative trait, selection, haplotype pattern |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA has parent organization: Bitbucket |
NHGRI HG002536; NHGRI R01 HG007089; NSF EF-0928690 |
PMID:24336146 | Free, Available for download, Freely available | OMICS_02196 | SCR_000643 | Forward-in-time simulation of Recombination, and Selection, Quantitative traits | 2026-02-14 01:59:46 | 0 | |||||
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HapCompass Resource Report Resource Website 1+ mentions |
HapCompass (RRID:SCR_000942) | algorithm | Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings. | algorithm, haplotype, sequence, genome, dna, rna, snp |
is listed by: OMICtools has parent organization: Brown University; Rhode Island; USA |
NSF 1048831; NSF 1321000 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00197 | SCR_000942 | 2026-02-14 01:59:52 | 1 | ||||||||
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sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | data processing software, alignment software, software application, software resource, image analysis software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-02-14 01:59:57 | 0 | ||||||
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Dataverse Network Project Resource Report Resource Website 10+ mentions |
Dataverse Network Project (RRID:SCR_001997) | Dataverse | data repository, storage service resource, portal, catalog, data or information resource, service resource, database, project portal | Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization. | data, repository, collection, publishing, citing, sharing, discovering, research, community, connection |
is used by: UCSF DataShare is used by: Agri-environmental Research Data Repository is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is related to: PROMIS 2 MY Health has parent organization: Harvard University; Cambridge; United States is parent organization of: Universal Numerical Fingerprint is parent organization of: Agri-environmental Research Data Repository |
Alfred P. Sloan Foundation ; NSF ; Microsoft Research |
Free, Available for download, Freely available | r3d100010051, nif-0000-00316 | https://doi.org/10.17616/R3C880 | http://thedata.org/ | SCR_001997 | Harvard Dataverse, The Dataverse Project, Dataverse, Dataverse Network, Dataverse Network Project, Dataverse Project | 2026-02-14 02:00:16 | 12 | ||||
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Incorporated Research Institutions for Seismology Resource Report Resource Website 500+ mentions |
Incorporated Research Institutions for Seismology (RRID:SCR_002201) | IRIS | portal, consortium, data or information resource, organization portal, institution | Passive and active source waveform data, event (earthquake) catalog, channel response data is available. This comprehensive data store of raw geophysical time-series data is collected from a large variety of sensors, courtesy of a vast array of US and International scientific networks, including seismometers (permanent and temporary), tilt and strain meters, infrasound, temperature, atmospheric pressure and gravimeters, to support basic research aimed at imaging the Earth's interior. IRIS also provides data and software for educational purposes. This consortium of over 100 US universities is dedicated to the operation of science facilities for the acquisition, management, and distribution of seismological data. IRIS programs contribute to scholarly research, education, earthquake hazard mitigation, and verification of the Comprehensive Nuclear-Test-Ban Treaty. Data is stored at the IRIS Data Management Center in Seattle, Washington. They currently manage a large archive from over tens of thousands of seismic stations and ship hundreds of terabytes of data yearly. | seismology, geophysics, earth science, earthquake, seismic, time series, metadata, channel response, waveform |
is listed by: CINERGI is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing is parent organization of: IRIS DMC Web Services |
NSF | Free, Freely available | nlx_154710, DOI:10.25504/FAIRsharing.x9rqf7, grid.300201.0, Wikidata: Q16074398, ISNI: 0000 0004 6078 0424, DOI:10.17616/R3X607, DOI:10.7914, DOI:10.17611 | https://ror.org/05xkn9s74 https://doi.org/10.17616/R3X607 https://doi.org/10.17616/r3X607 https://doi.org/10.7914/ https://doi.org/10.17611/ https://dx.doi.org/10.7914/ https://dx.doi.org/10.17611 https://fairsharing.org/10.25504/FAIRsharing.x9rqf7 |
SCR_002201 | IRIS Consortium, Incorporated Research Institutions for Seismology | 2026-02-14 02:00:20 | 540 | |||||
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U.S. Antarctic Program Data Coordination Center Resource Report Resource Website 1+ mentions |
U.S. Antarctic Program Data Coordination Center (RRID:SCR_002221) | USAP-DCC | data repository, storage service resource, data or information resource, service resource, database | Assists scientists in finding Antarctic scientific data of interest and submitting data for long-term preservation in accordance with their obligations under the National Science Foundation (NSF) Office of Polar Programs (OPP) Data Policy. | antarctica, southern ocean, polar |
is listed by: CINERGI has parent organization: Marine Geoscience Data System |
NSF | Free, Freely available | r3d100010660, nlx_154744 | https://doi.org/10.17616/R31898 | http://www.usap-data.org/ | SCR_002221 | 2026-02-14 02:00:20 | 5 | |||||
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EarthChem Resource Report Resource Website 10+ mentions |
EarthChem (RRID:SCR_002207) | EarthChem | data repository, storage service resource, data or information resource, service resource, database | Accepts and makes available geochemical, geochronlogical, and petrological data (analytical and synthesis) through this community-driven effort to facilitate the preservation, discovery, access and visualization of data generated. * PetDB holds geochemical data from sub-oceanic igneous and metamorphic rocks generated at mid-ocean ridges including back-arc basins, young seamounts, and old oceanic crust. Data are compiled primarily from the published literature. * SedDB integrates marine and terrestrial sediment geochemical data compiled primarily from the published literature. * Deep Lithosphere Data Set contains geochemical and petrological data from lower crust and upper mantle xenoliths. (more info) * VentDB contains hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. * NAVDAT - The Western North American Volcanic and Intrusive Rock Database * Geochron is an application that helps with the onerous task of data management for geochronological and thermochronological studies. * EarthChemPortal is the one-stop-shop for geochemical data that gives users the ability to search federated databases PetDB, NAVDAT, and GEOROC simultaneously, integrated into a common output format. (more info) * The EarthChem Library is a repository for geochemical datasets (analytical data, experimental data, synthesis databases) and other digital resources relevant to the field of geochemistry, contributed by the geochemistry community. * SESAR - System for Earth SAmple Registration | geochemical, geochronological, petrological |
is listed by: CINERGI has parent organization: Columbia University; New York; USA is parent organization of: VentDB is parent organization of: PetDB is parent organization of: SedDB is parent organization of: System for Earth Sample Registration |
NSF | Free, Available for download, Freely available | nlx_154721, r3d100011538 | https://doi.org/10.17616/R3V644 | SCR_002207 | IEDA: EarthChem | 2026-02-14 02:00:15 | 24 | |||||
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MetPetDB Resource Report Resource Website 1+ mentions |
MetPetDB (RRID:SCR_002208) | MetPetDB | data repository, storage service resource, data or information resource, service resource, database | Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative. | metamorphic, petrology, geology, geochemistry |
is listed by: CINERGI has parent organization: Rensselaer Polytechnic Institute; New York; USA |
NSF EAR 0949318 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154722 | SCR_002208 | 2026-02-14 02:00:20 | 1 | |||||||
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National Center for Marine Algae and Microbiota Resource Report Resource Website 50+ mentions |
National Center for Marine Algae and Microbiota (RRID:SCR_002120) | NCMA | biomaterial supply resource, organism supplier, material resource | National marine phytoplankton collection, maintaining over 2700 strains from around the world, most are marine phytoplankton but they also have benthic, macrophytic, freshwater and heterotrophic organisms - now incorporating bacteria and viruses. Strain records have (when available): * collection and isolation information * culturing medium recipes and growth conditions * photographs * GenBank accession link * collection site map * link to the taxonomic database Micro*scope The deposition of new strains are welcome if the strains are a valuable addition to the collection. Examples include strains that are referred to in publications, contain interesting molecular, biochemical or physiological properties, are the basis for taxonomic descriptions, are important for aquaculture, or are from an unusual geographical location or ecological habitat. The NCMA offers a course in phytoplankton culturing techniques and facilities for visiting scientists are available at the new laboratories in East Boothbay, Maine. Services include: Mass Culturing DNA and RNA, Purification, Private Holdings, Culture Techniques Course, Visiting Scientists, Single Cell Genomics, Flow Cytometry, Corporate Alliances and Technology Transfer. | marine phytoplankton, marine, phytoplankton, virus, benthic, macrophytic, freshwater, heterotrophic, microbiota, seawater, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is listed by: CINERGI |
NSF | Restricted | nlx_154729 | SCR_002120 | Provasoli-Guillard National Center for Culture of Marine Phytoplankton, Provasoli-Guillard National Center for Marine Algae and Microbiota, CCMP | 2026-02-14 02:00:18 | 53 | ||||||
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Community Surface Dynamics Modeling System Resource Report Resource Website |
Community Surface Dynamics Modeling System (RRID:SCR_002196) | CSDMS | data repository, storage service resource, computational hosting, data set, data or information resource, service resource, software resource | Model repository and data related to earth-surface dynamics modeling. The CSDMS Modeling Tool (CMT) allows you to run and couple CSDMS model components on the CSDMS supercomputer in a user-friendly software environment. Components in the CMT are based on models, originally submitted to the CSDMS model repository, and now adapted to communicate with other models. The CMT tool is the environment in which you can link these components together to run new simulations. The CMT software runs on your own computer; but it communicates with the CSDMS HPCC, to perform the simulations. Thus, the CMT also offers you a relatively easy way of using the CSDMS supercomputer for model experiments. CSDMS deals with the Earth's surface - the ever-changing, dynamic interface between lithosphere, hydrosphere, cryosphere, and atmosphere. They are a diverse community of experts promoting the modeling of earth surface processes by developing, supporting, and disseminating integrated software modules that predict the movement of fluids, and the flux (production, erosion, transport, and deposition) of sediment and solutes in landscapes and their sedimentary basins. CSDMS: * Produces protocols for community-generated, continuously evolving, open software * Distributes software tools and models * Provides cyber-infrastructure to promote the quantitative modeling of earth surface processes * Addresses the challenging problems of surface-dynamic systems: self-organization, localization, thresholds, strong linkages, scale invariance, and interwoven biology & geochemistry * Enables the rapid development and application of linked dynamic models tailored to specific landscape basin evolution (LBE) problems at specific temporal and spatial scales * Partners with related computational and scientific programs to eliminate duplication of effort and to provide an intellectually stimulating environment * Supports a strong linkage between what is predicted by CSDMS codes and what is observed, both in nature and in physical experiments * Supports the imperatives in Earth Science research | model, earth, surface, surface dynamics |
is listed by: CINERGI has parent organization: University of Colorado Boulder; Colorado; USA |
NSF | PMID:17406970 | Free, Freely available | r3d100012544, nlx_154705 | https://doi.org/10.17616/R3051W | SCR_002196 | 2026-02-14 02:00:15 | 0 | |||||
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Neotoma Paleoecology Database Resource Report Resource Website 10+ mentions |
Neotoma Paleoecology Database (RRID:SCR_002190) | Neotoma | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Paleoecology database for plio-pleistocene to holocene fossil data with a centralized structure for interdisciplinary, multiproxy analyses and common tool development; discipline-specific data can also be easily accessed. Data currently include North American Pollen (NAPD) and fossil mammals (FAUNMAP). Other proxies (plant macrofossils, beetles, ostracodes, diatoms, etc.) and geographic areas (Europe, Latin America, etc.) will be added in the near future. Data are derived from sites from the last 5 million years. | data sharing, paleoecology, plio-pleistocene, holocene, fossil |
is listed by: CINERGI has parent organization: Pennsylvania State University |
NSF | Free, Available for download, Freely available | nlx_154700 | SCR_002190 | NeotomaDB, Neotoma DB | 2026-02-14 02:00:20 | 31 | ||||||
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VS-Lite Resource Report Resource Website 1+ mentions |
VS-Lite (RRID:SCR_002431) | VS-Lite | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation. | model, mathematical model, tree ring, dendrochronology, tree ring width, tree, ring, ring growth model |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
NOAA ; NSF 0724802 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000128 | SCR_002431 | Vaganov-Shashkin-Lite, Vaganov-Shashkin-Lite Model of Tree-Ring Width | 2026-02-14 02:00:24 | 2 | ||||||
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Farsight Toolkit Resource Report Resource Website 1+ mentions |
Farsight Toolkit (RRID:SCR_001728) | FARSIGHT | data processing software, software toolkit, software application, image processing software, software resource, image analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules. | editing, 2d, 3d, algorithm, analysis, bio-format, computational, data, graphical, inspection, metadata, microscopy, morphological, morphology, pixel, processing, segmentation, taxonomy, image | has parent organization: University of Houston; Texas; USA | NIBIB R01-EB005157; NSF EEC-9986821; NIBIB R01EB005157 |
PMID:24808857 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10227 | SCR_001728 | FARSIGHTWiki | 2026-02-14 02:00:09 | 2 | |||||
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Ribosomal Mutation Database Resource Report Resource Website 1+ mentions |
Ribosomal Mutation Database (RRID:SCR_001677) | Ribosomal Mutation Database | data repository, storage service resource, data or information resource, service resource, database | This is a database of 16S and 23S ribosomal RNA mutations reported in literature, expanded to include mutations in ribosomal proteins and ribosomal factors. Access to the expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases has been improved to permit searches of the lists of alterations for all the data from (1) one specific organism, (2) one specific nucleotide position, (3) one specific phenotype, or (4) a particular author. Please send bibliographic citations for published work to be included in The Ribosomal Mutation Database to the curator via email. The database currently consists of 1024 records, including 485 16S rRNA records from Escherichia coli, 37 16S-like rRNA records from other organisms, 421 23S rRNA records from E. coli, and 81 23S-like records from other organisms. The numbering of positions in all records corresponds to the numbering in E. coli. We welcome any suggested revisions to the database, as well as information about newly characterized 16S or 23S rRNA mutations. The expanded database will be renamed to The Ribosomal Mutation Database and will include mutations in ribosomal proteins and ribosomal factors. | escherichia coli, mutation, nucleotide, phenotype, ribosomal factor, ribosomal protein, ribosomal rna, rna, rna sequence, rrna, rrna 16s, rrna 23s | has parent organization: Franklin and Marshall College; Pennsylvania; USA | NSF MCB-9726951 | PMID:8594571 PMID:8594570 |
Free, Available for download, Freely available | nif-0000-02522 | SCR_001677 | The Ribosomal Mutation Database | 2026-02-14 02:00:08 | 2 |
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