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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PONDR Resource Report Resource Website 50+ mentions |
PONDR (RRID:SCR_023691) | data access protocol, software resource, web service | Web tool to predict order and disorder from amino acid sequence. Used to predict of natural disordered regions in proteins. | amino acid sequence, predict sequence order and disorder, protein natural disordered regions prediction, protein, | NLM R01 LM06916; NSF ; DOE ; MRC of Canada |
DOI:10.1016/S1093-3263(00)00138-8 | Free, Freely available | SCR_023691 | Predictor of Natural Disordered Regions | 2026-08-04 09:45:19 | 90 | ||||||||
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Open Tree of Life Resource Report Resource Website 1+ mentions |
Open Tree of Life (RRID:SCR_024603) | portal, web service, software resource, data access protocol, project portal, data or information resource | Project aims to construct comprehensive, dynamic and digitally available tree of life by synthesizing published phylogenetic trees along with taxonomic data. | construct tree of life, digitally available tree of life, published phylogenetic trees, taxonomic data, |
is listed by: DataCite has parent organization: University of California; California; USA |
NSF | Free, Freely available | https://opentreeoflife.github.io/, https://api.datacite.org/dois?prefix=10.48699 | SCR_024603 | 2026-08-04 09:45:33 | 2 | ||||||||
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MCScanX Resource Report Resource Website 100+ mentions |
MCScanX (RRID:SCR_022067) | data processing software, data analysis software, software resource, software application, software toolkit | Software toolkit for detection and evolutionary analysis of gene synteny and collinearity. | gene synteny and collinearity, detection and evolutionary analysis, | NSF DBI 0849896; NSF MCB 0821096; NSF MCB 1021718; NIAID R01 AI068908 |
PMID:22217600 | Free, Available for download, Freely available | SCR_022067 | Multiple Collinearity Scan toolkit X version | 2026-08-04 09:44:56 | 257 | ||||||||
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Polar Rock Repository Resource Report Resource Website |
Polar Rock Repository (RRID:SCR_002212) | PRR | database, data or information resource | National facility for permanent curatorial preservation of rock collections from Antarctica and Southern Ocean. Repository preserves existing rock/dredge/unconsolidated/terrestrial core/photo archive collections for research use. Database allows online requests for sample loans. Mapping tool combines existing PRR database with high resolution satellite images of Antarctica, REMA or USGS topographic layers. PRR created Polar Rock Boxes for educators who are teaching about Earth science and Antarctica. Each Polar Rock Box contains samples with binder full of teaching information about Earth science and Antarctica. These boxes are freely available as short loans to US schools. | Sampling in polar regions, rock, polar, antarctica, dredge, southern ocean, glacial sediment, volcano, metadata |
is listed by: CINERGI has parent organization: Ohio State University; Ohio; USA |
NSF | Free, Freely available | nlx_154740, r3d100011627 | https://doi.org/10.17616/R3JD0W | SCR_002212 | Polar Rock Repository Database, U.S. Polar Rock Repository | 2026-08-04 09:40:35 | 0 | |||||
|
Scholarometer Resource Report Resource Website |
Scholarometer (RRID:SCR_004279) | Scholarometer | source code, data set, web service, software resource, data access protocol, data or information resource | Scholarometer (beta) is a social tool to facilitate citation analysis and help evaluate the impact of an author''s publications. It is a social (crowdsourcing) application that leverages the wisdom of the crowds. Scholarometer makes visualization of author and discipline networks available on the web site. It requires users to tag their queries with one or more discipline names, choosing from predefined ISI subject categories or arbitrary tags. This generates annotations that go into a database, which collects statistics about the various disciplines, such as average number of citations per paper, average number of papers per authors, etc. This data is publicly available. Scholarometer users can save the finding into formats appropriate for local reference management software (e.g., EndNote), or for social publication sharing systems (e.g., BibSonomy). Currently, our system supports the following export formats: BibTex (BIB), RefMan (RIS), EndNote (ENW), comma-separated values (CSV), tab-separated values (XLS), and BibJSON. Export data is dynamically generated in response to any filter, merge or delete actions performed by the user. Since Scholarometer is a browser extension that provides a smart interface for Google Scholar, it does not have the limitations of server based citation analysis tools that sit between the user and Google Scholar. At the same time Scholarometer is not an application, such as Publish or Perish, and therefore it is platform independent and runs on every system that supports the Firefox or the Chrome browser. Still, Scholarometer uses Google Scholar, which provides the most comprehensive source of citation data across the sciences and social sciences. Scholarometer provides a RESTful web API so that other developers can make use of our crowdsourced data. Select the method on the left panel to see corresponding documentation. The extension/add-on code is available in the Mozilla Firefox Add-ons and Google Chrome Extensions repositories. Additional server-side code is not available at this time. | has parent organization: Indiana University Bloomington; Indiana; USA | NSF IIS-0811994 | PMID:22984414 | nlx_29330 | SCR_004279 | 2026-08-04 09:41:06 | 0 | ||||||||
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AntWeb Resource Report Resource Website 100+ mentions |
AntWeb (RRID:SCR_004851) | AntWeb | image repository, storage service resource, data repository, service resource, database, data or information resource | Database of images, specimen records, and natural history information on ants including Search Tools, Regional Lists, In Depth Information, Ant Image Comparison Tool, PDF Field Guides, Maps on AntWeb and Google Earth, and Ant Genera of the World Slideshow. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images. As of February of 2013, AntWeb has 97,814 ant images, of 23,272 specimens representing over 10,549 species. AntWeb provides tools for submitting images, specimen records, annotating species pages, and managing regional species lists. AntWeb contains information on the ant faunas of several areas in the Nearctic and Malagasy biogeographic regions, and global coverage of all ant genera. AntWeb provides tools for exploring the diversity and identification of ants (Hymenoptera: Formicidae). These tools have been developed to encourage the study of ants, to facilitate the use of ants in inventory and monitoring programs, and to provide ant taxonomists with access to images of type specimens. AntWeb illustrates the diversity of ants by providing information and high quality color images of many of the approximately 10,000 known species of ants. AntWeb currently focuses on the species of the Nearctic and Malagasy biogeographic regions, and the ant genera of the world. Over time, the site will grow to describe every species of ant known. | image, FASEB list | has parent organization: California Academy of Sciences | Private donations ; NSF DEB-0344731; NSF EF-0431330 |
nlx_84285 | SCR_004851 | 2026-08-04 09:41:14 | 195 | ||||||||
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DataONE Resource Report Resource Website 10+ mentions |
DataONE (RRID:SCR_003999) | DataONE | portal, database, storage service resource, software resource, data repository, service resource, catalog, data or information resource | A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community. | earth, environment, data sharing, cyberinfrastructure, earth observational data, data management, data set, FASEB list |
uses: DataUp is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of New Mexico; New Mexico; USA |
NSF 0830944; NSF 1430508 |
Acknowledgement requested | DOI:10.25504/FAIRsharing.yyf78h, nlx_158410, DOI:10.17616/R3101G, r3d100010478, DOI:10.2586 | https://doi.org/10.17616/R3101G, https://doi.org/10.17616/r3101g, https://doi.org/10.2586/, https://dx.doi.org/10.2586/, https://fairsharing.org/10.25504/FAIRsharing.yyf78h, https://doi.org/10.17616/R3TG83 | SCR_003999 | Data Observation Network for Earth | 2026-08-04 09:41:02 | 44 | |||||
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Cell Type Ontology Resource Report Resource Website 1+ mentions |
Cell Type Ontology (RRID:SCR_004251) | CL | ontology, data or information resource, controlled vocabulary | Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases. | cell ontology, ontology repository |
is listed by: BioPortal is listed by: Ontology Lookup Service is related to: CELDA Ontology is related to: OBO is related to: Cell Line Knowledge Base |
BBSRC ; MRC ; NIH ; NSF DBI-9978564; NSF PGRP-0321666 |
PMID:15693950 | Free, Freely available | nlx_26501 | http://purl.bioontology.org/ontology/CL | http://cellontology.org, http://www.obofoundry.org/cgi-bin/detail.cgi?id=cell, | SCR_004251 | cellontology.org, Obo-cell-type, Cell Ontology | 2026-08-04 09:41:06 | 6 | |||
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BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | portal, web service, software resource, data access protocol, project portal, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse. | biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standard |
is used by: Blueprint Epigenome is related to: Mouse Genome Informatics (MGI) is related to: biomaRt has parent organization: Ontario Institute for Cancer Research has parent organization: European Bioinformatics Institute |
Wellcome Trust ; Spanish Government ; Sandra Ibarra Foundation for Cancer ; Breast Cancer Campaign Tissue Bank ; U.S. Department of Energy ; NSF NRF 2013M3A6A4043695; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-08-04 09:40:47 | 284 | ||||||
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MOPED - Model Organism Protein Expression Database Resource Report Resource Website 1+ mentions |
MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) | MOPED | data analysis service, resource, analysis service resource, production service resource, service resource, database, data or information resource | An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. | protein expression, gene expression, model organism, gene, protein, pathway, proteomics, transcriptomics, data visualization, overlap plot, heatmap, dot plot, data sharing, protein localization, gene localization |
is related to: GeneCards is related to: UniProt is related to: KEGG is related to: Reactome |
Robert B McMillen Foundation ; NSF DBI0544757; NIGMS 5R01GM076680; NIDDK UO1DK072473; NIDDK 1U01DK089571 |
PMID:24350770 PMID:22139914 |
nlx_151470 | SCR_006065 | Multi-Omics Profiling Expression Database | 2026-08-04 09:41:30 | 2 | ||||||
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CRCNS Resource Report Resource Website 100+ mentions |
CRCNS (RRID:SCR_005608) | CRCNS | funding resource, storage service resource, collaborative tool, data repository, service resource, data or information resource | Website for brain experimental data and other resources such as stimuli and analysis tools. Provides marketplace and discussion forum for sharing tools and data in neuroscience. Data repository and collaborative tool that supports integration of theoretical and experimental neuroscience through collaborative research projects. CRCNS offers funding for new class of proposals focused on data sharing and other resources. | collaborative research, data sharing, computational model, brain, computational neuroscience, data set, FASEB list |
is used by: NIF Data Federation is used by: DataLad is used by: Integrated Datasets is recommended by: National Library of Medicine is listed by: DataCite is related to: Integrated Manually Extracted Annotation has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: University of California; California; USA |
NIH ; NSF IIS-0749049; NSF 0636838 |
PMID:18259695 | Free, Freely available | nif-0000-00255, r3d100011269 | https://api.datacite.org/dois?prefix=10.6080, https://doi.org/10.17616/R31S7P | SCR_005608 | CRCNS Data sharing, Collaborative Research in Computational Neuroscience - Data sharing, Collaborative Research in Computational Neuroscience, CRCNS - Data sharing | 2026-08-04 09:41:23 | 119 | ||||
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Clair library Resource Report Resource Website |
Clair library (RRID:SCR_007019) | Clairlib | data processing software, data analysis software, software resource, text-mining software, text extraction software, software application, software toolkit | A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries. | analysis, information, linguistic, module, network, process, retrieval, perl, natural language processing, information retrieval, network analysis |
is listed by: Biositemaps has parent organization: University of Michigan; Ann Arbor; USA |
NSF IIS 0534323; NSF IIS 0329043; NSF BCS 0527513; NLM R01 LM008106; NIDA U54 DA021519 |
Open unspecified license: Content is available under GNU Free Documentation License 1.3 or later. | nif-0000-33210 | SCR_007019 | Computational Linguistics And Information Retrieval Library | 2026-08-04 09:41:44 | 0 | ||||||
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GIMME Resource Report Resource Website 1+ mentions |
GIMME (RRID:SCR_014115) | GIMME | data processing software, data analysis software, software resource, software application, software toolkit | Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels. | Functional, connectivity, analysis, fMRI, BOLD, signal, predefined, region, pattern, BRAIN Initiative |
uses: MATLAB is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NIBIB EB022904; NIBIB R21 EB015573; NSF 0852147 |
PMID:22732562 | Free, Available for download, Freely available | SCR_014115 | Group Iterative Multiple Model Estimation | 2026-08-04 09:43:20 | 2 | ||||||
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scite Resource Report Resource Website 1+ mentions |
scite (RRID:SCR_018568) | software resource, text extraction software, software application, service resource, data or information resource | Web tool to classify citation statements from scientific articles using deep learning. Used for discovering and evaluating scientific articles via Smart Citations. | Classify citation statement, context, text extraction, deep learning, citation context, cited claim evidence, ASWG | NIDA R44 DA050155; NSF |
Restricted | SCR_018568 | 2026-08-04 09:44:25 | 2 | ||||||||||
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PetaVision Resource Report Resource Website |
PetaVision (RRID:SCR_017451) | OpenPV | simulation software, software application, software resource | Open source software neural simulation toolbox. C++ library for designing and deploying large scale neurally inspired computational models. Object oriented neural simulation toolbox optimized for high performance multi core, multi node computer architectures. | Neural, simulation, computational, model, object, oriented, BRAIN Initiative | is recommended by: BRAIN Initiative | NSF 1734980 | Free, Available for download, Freely available | http://petavision.github.io/ | SCR_017451 | 2026-08-04 09:44:08 | 0 | |||||||
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Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | analysis service resource, web service, software resource, data access protocol, production service resource, service resource | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
NSF GRFP DGE1144152; DOE CSGF fellowship ; NIGMS R01 GM106303 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | EVcouplings | 2026-08-04 09:44:27 | 24 | |||||
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GeoDa Resource Report Resource Website 100+ mentions |
GeoDa (RRID:SCR_018559) | data processing software, data analysis software, software resource, software application, data visualization software | Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression. | Spatial analysis, data analysis, spatial autocorrelation visualization, spatial regression, mapping | NSF BCS 9978058; NCI R01 CA95949 |
DOI:10.1111/j.0016-7363.2005.00671.x | Free, Freely available | SCR_018559 | 2026-08-04 09:44:22 | 192 | |||||||||
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BcForms Resource Report Resource Website |
BcForms (RRID:SCR_018654) | data access protocol, software resource, software toolkit, web service | Software toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. Web tool for describing molecular structure of macromolecular complexes, including non canonical monomeric forms, circular topologies, and crosslinks. Describes semantic meaning of whole cell computational models. | Molecular structure description, molecular complex, atom, bond, protein, complex, modification, crosslinked residue, semantic meaning description, bio.tools |
is used by: BpForms is used by: ObjTables is listed by: Debian is listed by: bio.tools is related to: BpForms |
NIBIB P41 EB023912; NIGMS R35 GM119771; NSF 1649014 |
PMID:32423472 | Free, Freely available | biotools:bcforms | https://bio.tools/bcforms | SCR_018654 | 2026-08-04 09:44:22 | 0 | ||||||
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National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility Resource Report Resource Website 1+ mentions |
National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility (RRID:SCR_017361) | ICR, FT-ICR | access service resource, core facility, service resource | Facility provides service operations for sample analysis that requires ultrahigh resolution and high mass accuracy of Fourier Transform Ion Cyclotron Resonance. Used for research in biomolecular analysis, hydrogen-deuterium exchange and environmental and petrochemical analysis. Four FT-ICR mass spectrometers feature high magnetic fields including the world-record 21 tesla and are compatible with multiple ionization and fragmentation techniques. | FT-ICR, ICR, Ion Cyclotron Resonance, Fourier Transform Ion Cyclotron Resonance, analysis, spectrometer, magnetic, field, tesla, ionization, fragmentation, technique | is related to: Florida State University; Florida; USA | NSF ; NIH ; Department of Defense ; Department of Energy ; Florida State |
Restricted | SCR_017361 | National High Magnetic Field Laboratory Ion Cyclotron Resonance Facility, Ion Cyclotron Resonance Facility, NHMF Laboratory Cyclotron Resonance Facility | 2026-08-04 09:44:08 | 1 | |||||||
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National High Magnetic Field Laboratory Electron Magnetic Resonance Core Facility Resource Report Resource Website 1+ mentions |
National High Magnetic Field Laboratory Electron Magnetic Resonance Core Facility (RRID:SCR_017359) | EMR | access service resource, core facility, service resource | EMR Facility offers home-built, high-frequency and high-field continuous-wave instruments providing frequency coverage from 9 GHz to 1 THz, with additional frequencies available up to 2.5 THz using molecular gas laser. EMR covers variety of magnetic resonance techniques associated with electron like Electron Paramagnetic/Spin Resonance (EPR/ESR). EPR/ESR can be performed on any sample that has unpaired electron spins and used in applications in physics, materials science, chemistry and biology, including studies of impurity states, molecular clusters, antiferromagnetic, ferromagnetic and thin film compounds, natural or induced radicals, optically excited paramagnetic states, electron spin-based quantum information devices, transition-metal based catalysts; and for structural and dynamical studies of metallo-proteins, spin-labeled proteins and other complex bio-molecules and their synthetic models. | Magnet, EMR, Electron Magnetic Resonance, Tallahassee Florida Headquarters, spin, resonance, unpaired, electron, spectrometer | is related to: Florida State University; Florida; USA | NSF ; Florida State ; Department of Defense ; Department of Energy ; NIH |
Restricted | https://nationalmaglab.org/user-facilities/emr, https://nationalmaglab.org/images/users/emr/searchable_docs/epr_news_vol2_n2.pdf | https://nationalmaglab.org/user-facilities/emr/instruments-emr | SCR_017359 | NHMFL EMR facility, EMR Instruments, Electron Magnetic Resonance Facility | 2026-08-04 09:44:09 | 1 |
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