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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BCO-DMO Resource Report Resource Website 10+ mentions |
BCO-DMO (RRID:SCR_002191) | BCO-DMO | data set, storage service resource, data repository, service resource, data or information resource | Accepts and provides access to marine biogeochemical and ecological data sets from NSF-funded research programs. BCO-DMO is also the data repository for the US GLOBEC and JGOFS programs. | marine, biogeochemical, ecological, ocean, oceanographic, biology, polar |
is listed by: CINERGI has parent organization: Woods Hole Oceanographic Institution; Massachusetts; USA |
NSF | The community can contribute to this resource, For use by the academic and scientific community, Acknowledgement required, See terms of use, Non-commercial, Commercial with written permission | nlx_154701 | SCR_002191 | Biological and Chemical Oceanography Data Management Office, Biological & Chemical Oceanography Data Management Office | 2026-08-04 09:40:35 | 26 | ||||||
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National Center for Earth-Surface Dynamics Resource Report Resource Website |
National Center for Earth-Surface Dynamics (RRID:SCR_002195) | NCED | storage service resource, data repository, service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Field, laboratory, and model data related to earth-surface dynamics created or compiled by NCED-funded scientists. NCED is a Science and Technology Center developed to predict the coupled dynamics and co-evolution of landscapes and their ecosystems in order to transform management and restoration of the Earth-surface environment. | landscape, ecosystem, data set |
is listed by: CINERGI has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
NSF | Free, Freely available | r3d100011295, nlx_154715 | https://doi.org/10.17616/R3XW6D | SCR_002195 | NCED Data Repository | 2026-08-04 09:40:35 | 0 | |||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, software resource, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | NIDDK U24DK133658; NIA U19AG063744; NIGMS 1DP2GM137413; Korean Government ; Austrian Science Fund ; German Research Foundation ; Sao Paulo Research Foundation ; Mexican National Council of Science and Technology ; NIGMS R01GM107550; NSF ; Research Council of Norway ; NIAID R01AI167860; NIDDK T32DK007202; NIGMS 1R01GM132649; NIGMS R35GM142938; NIDDK U01DK119702; NIH Office of the Director S10 OD021750; NLM 1R01LM013115 |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-08-04 09:45:35 | 6 | ||||||||
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Sheep Brain Atlas Resource Report Resource Website 1+ mentions |
Sheep Brain Atlas (RRID:SCR_001752) | portal, atlas, data or information resource | Online portal and image database of coronal sections of the sheep brain. Each image contains stained sections of cell bodies and myelinated fibers; nuclei and tracts are labeled. | sheep brain, atlas, images, coronal section, stain, anatomy |
has parent organization: Michigan State University; Michigan; USA has parent organization: National Science Foundation |
NSF 0131267; NSF 0131826; NSF 0131028 |
Free, Freely available | nif-0000-00102 | https://www.msu.edu/~brains/brains/sheep/index.html | SCR_001752 | Sheep Brain Atlas, The Navigable Atlas of the Sheep Brain | 2026-08-04 09:40:28 | 4 | ||||||
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Dynamic Regulatory Events Miner Resource Report Resource Website 1+ mentions |
Dynamic Regulatory Events Miner (RRID:SCR_003080) | DREM | data processing software, software application, software resource | The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations | transcription, gene regulation, dynamics, time series, gene expression, static, dynamic, transcription factor-gene interaction, chip-chip, transcription factor, regulatory network, hidden markov model, systems biology, gene regulatory network, times series expression data, dynamic network, chip-seq | has parent organization: Carnegie Mellon University; Pennsylvania; USA | NIH ; NIGMS 1RO1 GM085022; NIAID DNO1 AI-5001; NSF 0448453 |
PMID:22897824 | Free, Available for download, Freely available | nif-0000-30478 | SCR_003080 | Dynamic Regulatory Events Miner (DREM) | 2026-08-04 09:40:48 | 5 | |||||
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CINERGI Resource Report Resource Website 1+ mentions |
CINERGI (RRID:SCR_002188) | CINERGI | portal, data or information resource | A project constructing a community inventory and knowledge base on geoscience information resources to meet the challenge of finding resources across disciplines, assessing their fitness for use in specific research scenarios, and providing tools for integrating and re-using data from multiple domains. The project team envisions a comprehensive system linking geoscience resources, users, publications, usage information, and cyberinfrastructure components. This system would serve geoscientists across all domains to efficiently use existing and emerging resources for productive and transformative research. | geoscience |
uses: SciGraph lists: UNAVCO Geodetic Web Services lists: Polar Geospatial Center lists: IRIS DMC Web Services lists: Southern California Earthquake Data Center lists: VentDB lists: IDRISI lists: National Oceanographic Data Center lists: Neotoma Paleoecology Database lists: BCO-DMO lists: Antarctic and Southern Ocean Data Portal lists: Academic Seismic Portal at LDEO lists: National Center for Earth-Surface Dynamics lists: Community Surface Dynamics Modeling System lists: CUAHSI Hydrologic Information System lists: Critical Zone Observatories lists: Incorporated Research Institutions for Seismology lists: Library of Experimental Phase Relations lists: OpenTopography lists: EarthChem lists: MetPetDB lists: PetDB lists: SedDB lists: Polar Rock Repository lists: Antarctic Marine Geology Research Facility lists: National Lacustrine Core Facility lists: Lamont-Doherty Core Repository lists: Smithsonian Mineral Sciences Collections lists: Antarctic Glaciological Data Center lists: National Snow and Ice Data Center lists: U.S. Antarctic Program Data Coordination Center lists: System for Earth Sample Registration lists: QUEST Project lists: PaleoVu lists: ANOVA lists: VS-Lite lists: HIBAL lists: Computational Infrastructure for Geodynamics lists: QuakeML lists: IRIS DMC FDSNWS event Web Service lists: IRIS DMC FDSNWS dataselect Web Service lists: Dryad Digital Repository lists: IRIS DMC FDSNWS station Web Service lists: Global-Multi Resolution Topography Image Service lists: Global-Multi Resolution Topography Grid Service lists: National Geothermal Data System lists: Marine Geosciences Data System MediaBank lists: OBIS lists: Carbon Dioxide Information Analysis Center lists: CCHDO lists: Magnetics Information Consortium lists: National Climatic Data Center lists: GeoStrat lists: National Geophysical Data Center lists: Index to Marine and Lacustrine Geologic Samples lists: World Data Center for Paleoclimatology lists: BCube A Broker Framework for Next Generation Geoscience lists: Academic Seismic Portal at UTIG lists: National Center for Marine Algae and Microbiota lists: Marine Geoscience Data System lists: GenBank lists: UNAVCO |
NSF award 1340233 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154714 | SCR_002188 | Community Inventory of EarthCube Resources for Geosciences Interoperability | 2026-08-04 09:40:35 | 1 | ||||||
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Functional Regression Analysis of DTI Tract Statistics Resource Report Resource Website |
Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) | FRATS | data processing software, software application, software resource, image analysis software | Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles. | computational neuroscience, imaging genomics, magnetic resonance, regression analysis, dti, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NSF BCS-08-26844; NCRR UL1-RR025747-01; NIMH MH086633; NIA AG033387; NIMH MH064065; NICHD HD053000; NIMH MH070890; NINDS R01NS055754; NIBIB U54 EB005149-01 |
PMID:20335089 | Academic Free License | nlx_155629 | SCR_002293 | Functional Regression Analysis of DTI | 2026-08-04 09:40:37 | 0 | |||||
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ImpactStory Resource Report Resource Website 1+ mentions |
ImpactStory (RRID:SCR_002632) | software resource, source code, production service resource, service resource | A 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, wordpress.com, plos, youtube |
is used by: Publons is listed by: FORCE11 is listed by: Connected Researchers is listed by: PLOS Article-Level Metrics is related to: PubMed is related to: GitHub is related to: FigShare is related to: Dryad Digital Repository is related to: Wikipedia is related to: Mendeley |
Alfred P. Sloan Foundation ; NSF ; Open Society Foundation |
Free, Freely available | nlx_156056 | SCR_002632 | ImpactStory | 2026-08-04 09:40:42 | 8 | |||||||
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Short Time-series Expression Miner (STEM) Resource Report Resource Website 50+ mentions |
Short Time-series Expression Miner (STEM) (RRID:SCR_005016) | STEM | data processing software, software application, software resource | The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | statistical analysis, term enrichment, visualization, cluster, compare, short time series, gene expression, microarray, expression profile, gene, gene ontology, gene enrichment analyses, FASEB list |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Carnegie Mellon University; Pennsylvania; USA |
NIAID NO1 AI-5001; NSF 0448453 |
PMID:16597342 PMID:15961453 |
Open unspecified license - Free for academic use | nlx_97053 | SCR_005016 | Short Time-series Expression Miner | 2026-08-04 09:41:16 | 81 | |||||
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Computational Infrastructure for Geodynamics Resource Report Resource Website 10+ mentions |
Computational Infrastructure for Geodynamics (RRID:SCR_003371) | CIG | portal, group, data or information resource | Community-driven organization that develops and disseminates software for geophysics and related fields. They host codes in a wide range of disciplines in geodynamics and computational science including geodynamo, long-term tectonics, magma migration, mantle dynamics, seismology, and short-term crustal dynamics. | geophysics, modeling, computation, computational science, geodynamo, long-term tectonics, magma migration, mantle dynamics, seismology, short term crustal dynamics |
is listed by: CINERGI has parent organization: University of California at Davis; California; USA |
NSF 094946 | Free, Freely available | SciRes_000182 | SCR_003371 | Computational Infrastructure for Geodynamics (CIG) | 2026-08-04 09:40:53 | 11 | ||||||
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Tree of Life: Phylogeny of Spiders Resource Report Resource Website 1+ mentions |
Tree of Life: Phylogeny of Spiders (RRID:SCR_003801) | Phylogeny of Spiders | portal, data or information resource | Project whose aim is to produce a robust phylogeny of all the deepest branches within a mega-diverse group, the spiders, by combining a massive amount of newly generated comparative genomic data with a substantial set of new and re-assessed data on morphology and behavior. They propose to collect a huge amount of genomic information in order to test and improve the results achieved by over 50 detailed morphological cladistic analyses conducted by more than 30 investigators during the past 15 years. The insignificant amount of genomic work to date on spiders has been uncoordinated and of little utility for broad-scale phylogenetic investigation. The advent of high-throughput DNA sequencing, however, makes it feasible to examine substantial parts of the genome across a dense sampling of spider taxa. They propose to sequence at least 50 loci (genome samples of 500-1,000 or more base pairs that can be sequenced as single pieces in both directions simultaneously) for representatives of at least 500 genera of spiders and their closest relatives (the whipscorpion orders Amblypygi, Uropygi, and Schizomida). These genera will be carefully selected by a sampling strategy designed to maximize the resolution of deep branches within spider phylogeny, and will purposefully include all the previously most-favored study organisms of ethologists, ecologists, physiologists, and developmental and molecular biologists, thus integrating and contextualizing their research. Data matrices will be produced that combine the new genomic data with a new, comprehensive survey of morphological and behavioral homologies, offering a unique index to all comparative data on one large group. New computer software, designed in large part by members of their group and using massively parallel processing to achieve supercomputing capability, makes such analyses feasible. | morphology, molecule, phylogeny |
has parent organization: Tree of Life is parent organization of: Spider Ontology |
NSF DEB 0228699 | nlx_158099 | SCR_003801 | ATOL: Phylogeny of Spiders, Assembling the Tree of Life: Phylogeny of Spiders | 2026-08-04 09:40:59 | 1 | |||||||
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Open Science Data Cloud Resource Report Resource Website 1+ mentions |
Open Science Data Cloud (RRID:SCR_003523) | OSDC | data set, software resource, data or information resource, service resource | Service that provides petabyte-scale cloud resources to analyze, manage, and share scientific data. It is designed to serve medium to large sized research projects by managing and operating a secure cloud computing infrastructure that can be shared across a project. This Science as a Service approach to research saves scientists and their funders valuable time and money. All of the software developed is open source and hosted on GitHub. The OSDC also has 1PB of public data in a wide variety of disciplines. The data sets can downloaded over the internet or high performance networks such as Internet2, as well as computed over directly on the OSDC. | cloud | is parent organization of: Bionimbus | Gordon and Betty Moore Foundation ; NSF |
Application required, Purchase | nlx_157679 | SCR_003523 | 2026-08-04 09:40:55 | 3 | |||||||
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Phenoscape Resource Report Resource Website 1+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | portal, data or information resource | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | 2026-08-04 09:40:59 | 8 | |||||||
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Autopack Resource Report Resource Website 1+ mentions |
Autopack (RRID:SCR_006830) | autoPack | data processing software, software application, software resource | An open-source general packing algorithm that packs 3D objects onto surfaces, into volumes, and around volumes. It provides a general architecture to allow various packing algorithms to interoperate efficiently in the same model. autoPack can incorporate any packing solution into its modular python program architecture, but is currently optimized to provide a novel solution to the loose packing problem which places objects of discrete size into place (compared to advancing front, popcorn, or other fast tight-packing solutions that allow objects to scale to arbitrary masses.) Most popular 3D software programs now contain robust physics engines based on Bullet that can separate small collections of overlapping objects or allow volumes to be filled by pouring shapes from generators, but these approaches fails for large complex systems and result in either overlapping geometry, crashed software, or non-random gradients. Most packing algorithms are designed to position objects as efficiently as possible, but autoPack allows the user to select from random loose packing to highly organized packing methods����??even to choose both methods at the same time. autoPack positions 3D geometries into, onto, and around volumes with minimal to zero overlap. autoPack mixes several packing approaches and procedural growth algorithms. autoPack can thus place objects with forces and constraints to allow a high degree of control ranging from completely random distributions to highly ordered structures. * zero to minimal overlaps depending on the method used * accuracy vs speed parameters selected by the user * zero edge effects * complete control, from fully random to fully ordered distributions * agent-based interaction, weighting, and collision control | 3d visualization software, modeling software, 3d packing software, packing, 3d object, surface, volume, algorithm |
is related to: Cellpack has parent organization: Google Code has parent organization: Scripps Research Institute is parent organization of: Cellpack |
QB3 at UCSF Fellowship ; NSF 07576; NCRR P41 RR08605 |
GNU Lesser General Public License | nlx_151791 | https://sites.google.com/site/autofill21/, http://code.google.com/p/autofill/ | SCR_006830 | 2026-08-04 09:41:42 | 3 | ||||||
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Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome Resource Report Resource Website |
Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome (RRID:SCR_003506) | HEFalMp | database, data or information resource, service resource | HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool. | human, map, gene, functional, pathway, disease, genomic, analysis, microarray, dna, protein, sequence | has parent organization: Princeton University; New Jersey; USA | New Jersey Commission on Cancer Research ; PhRMA Foundation 2007RSGl9572; NIGMS R01 GM071966; NSF DBI-0546275; NSF IIS-0513552; NHGRI T32 HG003284; NIGMS P50 GM071508 |
PMID:19246570 | nif-0000-37186 | SCR_003506 | Human Experimental / FunctionAL MaPper, Human Experimental/FunctionAL MaPper | 2026-08-04 09:40:55 | 0 | ||||||
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BioText Search Engine Resource Report Resource Website 1+ mentions |
BioText Search Engine (RRID:SCR_003600) | database, data or information resource | Developed as part of the BioText project at the University of California, Berkeley, the BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. The system indexes all open access articles available at PubMed Central. New articles are indexed daily. The current collection consists of more than 300 journals, 40,000 articles, 100,000 figures, and 60,000 tables. The Full Text & Abstract view searches the full text of articles (in addition to title, author, and abstract information) and returns full-text excerpts that match users' queries. Three selection boxes at the top (ABSTRACTS, FULL-TEXT EXCERPTS and FIGURES allow users to choose what the view displays. The BioText Search Engine allows users to search in tables. When the table view is selected, BioText searches in article titles, table captions, and table contents. The Grid View allows users to search over captions. It returns figures and truncated captions in a grid arrangement. | has parent organization: University of California at Berkeley; Berkeley; USA | NSF DBI-0317510 | PMID:17545178 | nlx_12705 | SCR_003600 | BioText | 2026-08-04 09:40:57 | 8 | ||||||||
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JCVI GenProp Resource Report Resource Website 1+ mentions |
JCVI GenProp (RRID:SCR_004592) | JCVI GenProp | database, data or information resource, service resource | The Genome Properties system consists of a suite of Properties which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. The system has been designed to capture the widest possible range of attributes and currently encompasses taxonomic terms, genometric calculations, metabolic pathways, systems of interacting macromolecular components and quantitative and descriptive experimental observations (phenotypes) from the literature. You may search the Genome Properties Database in 1 of 3 ways: * Search For Predicted Properties in the CMR: The Genome Property Search allows you to search the Genome Property database for state information for selected genomes and properties. * Perform a Keyword Search for a Specific Property: Lists all Genome Properties that match a specific text string. You can choose to search All Fields within a genome property or the Property Name. * Browse Top Level Genome Properties: Click on the properties to see the specific genome property report page. The Genome Properties system presents key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties. | prokaryote, genome, genomics, a | has parent organization: JCVI CMR | NSF DBI-0110270; DOE DE-FG02-01ER63203 |
PMID:15347579 | nlx_58176 | http://www.tigr.org/Genome_Properties | SCR_004592 | Genome Properties, Genome Properties Database, JCVI CMR Genome Properties | 2026-08-04 09:41:10 | 1 | |||||
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PILGRM Resource Report Resource Website 1+ mentions |
PILGRM (RRID:SCR_004749) | PILGRIM | data analysis service, analysis service resource, production service resource, service resource | PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis. | data mining, gene expression, user directed data mining, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Princeton University; New Jersey; USA |
NSF DBI-0546275; NIGMS R01 GM071966; NIGMS P50 GM071508; NCI T32 CA005928 |
PMID:21653547 | nlx_75372, biotools:pilgrm | https://bio.tools/pilgrm | SCR_004749 | Platform for Interactive Learning by Genomics Results Mining | 2026-08-04 09:41:13 | 1 | |||||
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NBC Resource Report Resource Website 1+ mentions |
NBC (RRID:SCR_004772) | NBC | data analysis service, analysis service resource, production service resource, service resource | Webserver for taxonomic classification of metagenomic reads. | metagenome, genome, virus, taxonomy, next-generation sequencing, taxonomic classification, classification |
is listed by: OMICtools has parent organization: Drexel University; Pennsylvania; USA |
NSF DBI-0845827; DOE DE-SC0004335 |
PMID:1062764 PMID:19956701 |
OMICS_01458 | SCR_004772 | Naive Bayes Classification tool, Na����ve Bayesian Classification tool, Naive Bayesian Classification Tool | 2026-08-04 09:41:12 | 3 | ||||||
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G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools Resource Report Resource Website 1+ mentions |
G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools (RRID:SCR_005816) | G-SESAME | data analysis service, analysis service resource, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2,2025. G-SESAME contains a set of tools. They include: tools for measuring the semantic similarity of GO terms; tools for measuring the functional similarity of genes; and tools for clustering genes based on their GO term annotation information. Platform: Online tool, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene ontology, semantic similarity, functional similarity, cluster, gene, annotation, gene annotation |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Clemson University; South Carolina; USA |
NSF DBI-0960586; NSF DBI-0960443 |
PMID:19491312 PMID:17344234 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149313 | SCR_005816 | Gene Semantic Similarity Analysis Measurement Tools, Gene Semantic Similarity Analysis and Measurement Tools | 2026-08-04 09:41:27 | 5 |
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