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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TAED - The Adaptive Evolution Database Resource Report Resource Website 1+ mentions |
TAED - The Adaptive Evolution Database (RRID:SCR_006930) | TAED | data or information resource, database | A database of sequence alignments and phylogenetic trees for chordates and embryophytes. The Adaptive Evolution Database (TAED) was first presented as a collection of branches from chordate and embryophyte gene families with fast evolutionary rates mapped onto the NCBI taxonomy (1,2). The original gene families were from the Master Catalog and are proprietary (3). A new version of TAED is now presented as a taxonomic shell together with a gene family database. In addition to multiple sequence alignments and phylogenetic trees for all families of chordate and embryophyte sequences, the ratio of non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) is provided for each branch of every phylogenetic tree. This ratio, when significantly greater than 1, is an indicator of positive selection and potentially a change of function of the encoded protein. With a gene tree to species tree mapping, the branches significantly greater than 1 are collated together in a phylogenetic context. The framework is expandable to incorporate other genomic-scale information in a phylogenetic context. Ultimately, the database is designed both to provide high-quality gene families with multiple sequence alignments and phylogenetic trees for chordates and embryophytes, and to enable asking the question, What makes each species unique at the molecular genomic level? | evolution, phylogenetic tree, taxonomy | has parent organization: University of Wyoming; Wyoming; USA | nif-0000-03533, r3d100012568 | https://doi.org/10.17616/R3DF5W | SCR_006930 | The Adaptive Evolution Database | 2026-08-10 09:32:59 | 1 | |||||||
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Potential Drug Target Database Resource Report Resource Website 10+ mentions |
Potential Drug Target Database (RRID:SCR_007069) | PDTD | data or information resource, database | It is a dual function database that associates an informatics database to a structural database of known and potential drug targets. PDTD is a comprehensive, web-accessible database of drug targets, and focuses on those drug targets with known 3D-structures. PDTD contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank (PDB). Drug targets of PDTD were categorized into 15 and 13 types according to two criteria: therapeutic areas and biochemical criteria. The database supports extensive searching function using PDB ID, target name and category, related disease. | drug, biochemical, informatics, protein, structural, therapeutic | nif-0000-20891 | SCR_007069 | Potential Drug Target Database | 2026-08-10 09:33:01 | 19 | |||||||||
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COPE: Cytokines and Cells Online Pathfinder Encyclopaedia Resource Report Resource Website 100+ mentions |
COPE: Cytokines and Cells Online Pathfinder Encyclopaedia (RRID:SCR_007187) | data or information resource, database | COPE is an encyclopedia of cytokines and has fully integrated subdictionaries on Angiogenesis, Apoptosis, Bacterial Modulins, CD Antigens, Cell lines, Eukaryotic cell types, Chemokines, CytokineTopics, Cytokine Concentrations in Body Fluids, Cytokine Inter-Species Reactivities, Dual identity proteins, Hematology, Innate Immunity Defense Proteins, Metalloproteinases, Protein domains, Regulatory peptide factors, Virokines, Viroceptors, and Virulence Factors. Most entries have a description as well as references. | FASEB list | has parent organization: COPE | nif-0000-00783 | SCR_007187 | Cytokines and Cells Online Pathfinder Encyclopedia, COPE | 2026-08-10 09:33:03 | 162 | |||||||||
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Gait in Parkinson's Disease Resource Report Resource Website 1+ mentions |
Gait in Parkinson's Disease (RRID:SCR_006891) | data or information resource, database | Database that contains measures of gait from 93 patients with idiopathic PD (mean age: 66.3 years; 63% men), and 73 healthy controls (mean age: 66.3 years; 55% men). The database includes the vertical ground reaction force records of subjects as they walked at their usual, self-selected pace for approximately 2 minutes on level ground. Underneath each foot were 8 sensors (Ultraflex Computer Dyno Graphy, Infotronic Inc.) that measure force (in Newtons) as a function of time. The output of each of these 16 sensors has been digitized and recorded at 100 samples per second, and the records also include two signals that reflect the sum of the 8 sensor outputs for each foot. This database also includes demographic information, measures of disease severity (i.e., using the Hoehn & Yahr staging and/or the Unified Parkinson's Disease Rating Scale) and other related measures (available in HTML or xls spreadsheet format). A subset of the database includes measures recorded as subjects performed a second task (serial 7 subtractions) while walking, which shows excerpts of swing time series from a patient with PD and a control subject, under usual walking conditions and when performing serial 7 subtractions. Under usual walking conditions, variability is larger in the patient with PD (Coefficient of Variation = 2.7%), compared to the control subject (CV = 1.3%). Variability increases during dual tasking in the subject with PD (CV = 6.5%), but not in the control subject (CV = 1.2%). | gait, speed, treadmill, stride variability |
is used by: NIF Data Federation is used by: Aging Portal has parent organization: Physiobank |
Parkinson's disease | NIH ; National Parkinson's Foundation ; Parkinson's Disease Foundation |
PMID:16053531 | Acknowledgement requested | nif-0000-00248 | SCR_006891 | 2026-08-10 09:33:04 | 1 | ||||||
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SDSC Biology Workbench Resource Report Resource Website 10+ mentions |
SDSC Biology Workbench (RRID:SCR_007188) | data or information resource, database, service resource | The Biology WorkBench is a web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems. Register for a free account. | has parent organization: University of California at San Diego; California; USA | nlx_28496 | SCR_007188 | Biology Workbench | 2026-08-10 09:33:12 | 12 | ||||||||||
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Bath Information and Data Services Resource Report Resource Website 1+ mentions |
Bath Information and Data Services (RRID:SCR_007184) | data or information resource, database | BIDS provided bibliographic database services to the academic community in the UK. Their mission is to provide, on a not-for-profit basis, the highest possible level of service to allow UK Academic institutions and their members access to bibliographic data, scholarly publications and research data. BIDS is believed to have been a world first - a national service providing widespread network access to commercially supplied bibliographic databases, free at the point of delivery. BIDS academic and scholarly journals services are now incorporated into IngentaConnect www.ingentaconnect.com If you are a student, researcher or member of staff at a UK higher or further education institution you can access any of the services to which your institution has subscribed. In addition, there are some services which can be searched without a subscription. These include ingentaJournals and Medline. You can discover which services are available to you by logging in to BIDS with your Athens username and password. All available services will be highlighted in the service selection page. | database, academic, scholarly, journal, education, research | JISC | nif-0000-30162 | SCR_007184 | BIDS | 2026-08-10 09:33:03 | 1 | |||||||||
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Arabidopsis Gene Regulatory Information Server Resource Report Resource Website 50+ mentions |
Arabidopsis Gene Regulatory Information Server (RRID:SCR_006928) | AGRIS | data or information resource, database | An information resource of Arabidopsis promoter sequences, transcription factors and their target genes that contains three databases. *AtcisDB consists of approximately 33,000 upstream regions of annotated Arabidopsis genes (TAIR9 release) with a description of experimentally validated and predicted cis-regulatory elements. *AtTFDB contains information on approximately 1,770 transcription factors (TFs). These TFs are grouped into 50 families, based on the presence of conserved domains. *AtRegNet contains 11,355 direct interactions between TFs and target genes. They provide free download of Arabidopsis thaliana cis-regulatory database (AtcisDB) and transcription factor database (AtTFDB). | gene regulatory, gene, arabidopsis thaliana, promoter sequence, target gene, transcription factor, FASEB list |
is listed by: OMICtools has parent organization: Ohio State University; Ohio; USA |
NSF | PMID:21059685 PMID:16524982 PMID:12820902 |
Free, Acknowledgement requested | OMICS_00548, nif-0000-02540 | SCR_006928 | 2026-08-10 09:32:59 | 53 | ||||||
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EMBRYS Resource Report Resource Website 1+ mentions |
EMBRYS (RRID:SCR_006689) | EMBRYS | data or information resource, database | Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System. | Gene, expression, pattern, mapped, whole mount, mouse, embryo, ICR strain, mid gestational stage, transcription, factor, cofactor, data |
uses: RIKEN uses: MGC uses: PANTHER |
Japanese Ministry of Education Culture Sports Science and Technology MEXT ; Japanese Ministry of Health Labor and Welfare |
Free, Freely available | nlx_153839 | http://embrys.jp/embrys/html/MainMenu.html | SCR_006689 | Embryonic Gene Expression Database for Biomedical Research Source, Embryonic gene expression Database as a Biomedical Research Source | 2026-08-10 09:32:54 | 8 | |||||
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UniSTS Resource Report Resource Website 10+ mentions |
UniSTS (RRID:SCR_006843) | UniSTS | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences. Chromosome maps are labeled by name of the originating organism, the map title, total markers, total UniSTSs and links to view maps as well as research documents available through PubMed, another NCBI database. The search functions within UniSTS allow the user to search by gene marker, chromosome, gene symbol and gene description terms to locate markers on specified genes. A representation of the UniSTS datasets is available by ftp. NOTE: All data from this resource have been moved to the Probe database, http://www.ncbi.nlm.nih.gov/probe. You can retrieve all UniSTS records by searching the probe database using the search term unists(properties). (use brackets insead of parenthesis). Additionally, legacy data remain on the NCBI FTP Site in the UniSTS Repository (ftp://ftp.ncbi.nih.gov/pub/ProbeDB/legacy_unists). | marker, primer sequence, mapping, sequence tagged site, genomic position, gene, sequence, nucleotide, nucleotide sequence, chromosome, gold standard |
is listed by: re3data.org is related to: NCBI Probe has parent organization: NCBI |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03614 | SCR_006843 | UniSTS: Integrating Markers and Maps, NCBI UniSTS, Entrez UniSTS | 2026-08-10 09:32:57 | 41 | |||||||
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COG Resource Report Resource Website 1000+ mentions |
COG (RRID:SCR_007139) | COG, COG Cluster, COG Function, COG Pathway | data or information resource, database | A database for phylogenetic classification for proteins encoded in complete genomes. Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain. Please be aware that COGs hasn't been updated in many years and will not be. | ortholog, protein, cog, conserved protein sequence, unicellular cluster, genome, order, class, phyla, eukaryotic cluster, gold standard |
is listed by: OMICtools is related to: MLTreeMap is related to: ProOpDB is related to: Conserved Domain Database has parent organization: NCBI is parent organization of: Clusters of Orthologous Groups Analysis Ontology |
PMID:12969510 PMID:9381173 |
OMICS_01688, nif-0000-02672 | SCR_007139 | COG Database, Clusters of Orthologous Groups of proteins, COGs, COGs - Clusters of Orthologous Groups of proteins, COGs - Phylogenetic classification of proteins encoded in complete genomes, COG Cluster, COG Pathway, COG Function | 2026-08-10 09:33:02 | 1278 | |||||||
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AnimalDrugsatFDA Resource Report Resource Website |
AnimalDrugsatFDA (RRID:SCR_010257) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of approved veterinary drugs run by the FDA. | has parent organization: U.S. Food and Drug Administration | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156909 | SCR_010257 | animal drugs at FDA, animaldrugs@fda | 2026-08-10 09:33:57 | 0 | |||||||||
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Genetic Alterations in Cancer Resource Report Resource Website |
Genetic Alterations in Cancer (RRID:SCR_010533) | GAC | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The NIEHS Genetic Alterations in Cancer (GAC) knowledgebase is a comprehensive collection of data compiled from studies reported in the published literature on genetic alterations in tumors associated with exposure to specific chemical, physical, or biological agents that can be linked to genes implicated in the development of cancers. GAC provides access to data from peer reviewed journals for hundreds of studies of gene mutations, loss of heterozygosity, and/or chromosome changes in tumors from humans, mice, or rats. Results are summarized in tables and graphic profiles that show the incidence (percent) of tumors with alterations in each gene that has been studied. Detailed data tables display results for each subject studied in the cited reference and the reference ID is hyperlinked to its PubMed abstract for more information. A mutation spectrum for individual genes and links to gene information from The Cancer Genome Anatomy Project and the Rat Genome Database are also provided. | has parent organization: National Institute of Environmental Health Sciences | PMID:16410370 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_23898 | http://www.niehs.nih.gov/research/resources/databases/gac/index.cfm | SCR_010533 | 2026-08-10 09:34:01 | 0 | |||||||
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Brains Lab Resource Report Resource Website |
Brains Lab (RRID:SCR_010534) | Brains Lab | data or information resource, blog, narrative resource | I''m studying how the brain works on various levels; this blog chronicles some of my informal notes along the way. I previously went to Vassar College, majoring in Neuroscience and Behavior with a minor in Math. Now I work at a biology lab in Maryland. I appreciate any feedback that you may have, good or bad. You can email me at amckenz at g mail dot com. What I write on here is obviously my opinion. Everything on the site is filed under a Creative Commons License v. 3.0. That means that you can copy and re-publish this stuff anywhere without my permission. Thanks for reading. Essay titles include: * A Loss of Agency Following Use of ADHD Medications in College Aged Adults * An Evolutionary Account of the Environmentally Programmed Stress Response * Changes in protein structure of myelin sheaths throughout vertebrate evolution * Effect of Glucocorticoids on the Attenuation in Neurogenesis due to Sleep Deprivation * Insulin sensitivity and age-related memory changes due to caloric restriction * Is Neurogenesis in the Hippocampus Linked to Depression? * Novelty-Seeking and Associative Learning of Chemotaxis in C. Elegans * The Effects of D2 Receptors on the Inverted U-Shape Response Curve to Psychostimulants * Three Applications of Optogenetics The author has included some tricks and illusions from around the web that reveal fascinating facets of our thought processes including: The Checker, Sensory Homonculus Picture, A Blindspot Demonstration, A Ball in a Box, Iterated Choices, The Max Plank Institute for Biological Cybernetics, The Motion Aftereffect Illusion, The Phi Phenomenon, The Common Fate Phenomenon, A Double Face, The Troxler Effect | brain imaging, brain-computer interface, cognitive psychology, connectomics, developmental neuroscience, evolutionary biology, molecular neuroscience, neurogenesis, neurogenetics, neuropharmacology, neurotransmitter, theoretical neuroscience, trend, neuroscience, vision, synapse, somata, systems neuroscience | has parent organization: WordPress | Aging | nlx_24102 | SCR_010534 | Brains Lab: Synapses Somata and Systems Neuroscience | 2026-08-10 09:34:01 | 0 | |||||||
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Nomenclature for the description of sequence variants Resource Report Resource Website 100+ mentions |
Nomenclature for the description of sequence variants (RRID:SCR_010261) | MUTNOMEN | data or information resource, database | Database of gene mutation nomenclature. | has parent organization: Human Genome Variation Society | PMID:10612815 | nlx_156915 | SCR_010261 | 2026-08-10 09:33:59 | 460 | |||||||||
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Omixon blog Resource Report Resource Website |
Omixon blog (RRID:SCR_010020) | Omixon blog | data or information resource, blog, narrative resource | We share commentaries, news and announcement that advance our goal of helping clinical labs to adopt next generation sequencing for the analysis of diagnostic gene targets. | is listed by: OMICtools | OMICS_01720 | SCR_010020 | 2026-08-10 09:33:56 | 0 | ||||||||||
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NetAge Database Resource Report Resource Website 1+ mentions |
NetAge Database (RRID:SCR_010224) | NetAge | data or information resource, database | Database that contains gene sets and microRNA-regulated protein-protein interaction networks for longevity, age-related diseases and aging-associated processes. | longevity, protein-protein interaction, mirna-regulated protein-protein interaction network, gene, protein, mirna, biogerontology | has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel | Age-related disease, Aging | PMID:20186480 | Acknowledgement requested, Public | nlx_156769 | SCR_010224 | 2026-08-10 09:33:59 | 6 | ||||||
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SPIKE Resource Report Resource Website 100+ mentions |
SPIKE (RRID:SCR_010466) | SPIKE | data or information resource, database, service resource | Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways | visualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, ear, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: ConsensusPathDB has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Cancer | A-T Children's Project ; Wolfson Foundation ; European Union FP7 ; Israel Science Foundation |
PMID:21097778 PMID:18289391 |
biotools:spike, nlx_157705 | https://bio.tools/spike | SCR_010466 | Signaling Pathway Integrated Knowledge Engine | 2026-08-10 09:34:00 | 131 | ||||
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COVIBD Resource Report Resource Website |
COVIBD (RRID:SCR_009155) | software application, software resource | Software application that refines linkage analysis of affected sibpairs by considering attributes or environmental exposures thought to affect disease liability. This refinement utilizes a mixture model in which a disease mutation segregates in only a fraction of the sibships, with the rest of the sibships unlinked. Covariate information is used to predict membership within the two groups corresponding to the linked and unlinked sibships. The pre-clustering model uses covariate information to first form two probabilistic clusters and then tests for excess IBD-sharing in the clusters. The Cov-IBD model determines probabilistic group membership by joint consideration of covariate and IBD values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154207, nlx_154275, SCR_009109 | SCR_009155 | R/COVIBD | 2026-08-10 09:33:45 | 0 | |||||||||
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METLIN Resource Report Resource Website 1000+ mentions |
METLIN (RRID:SCR_010500) | METLIN | data or information resource, database | A public repository of metabolite information as well as tandem mass spectrometry data is provided to facilitate metabolomics experiments. It contains structures and represents a data management system designed to assist in a broad array of metabolite research and metabolite identification. An annotated list of known metabolites and their mass, chemical formula, and structure are available. Each metabolite is linked to outside resources for further reference and inquiry. MS/MS data is also available on many of the metabolites. | metabolite, tandem, mass spectrometry, metabolomics, mass, chemical formula, structure, FASEB list |
is listed by: NIDDK Information Network (dkNET) is related to: KEGG has parent organization: Scripps Research Institute |
PMID:16404815 | nlx_158116, r3d100012311 | SCR_010500 | Metabolite and Tandem MS Database (METLIN), METLIN Metabolite Database, Metabolite and Tandem MS Database | 2026-08-10 09:34:00 | 2825 | |||||||
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Molecular Modeling DataBase Resource Report Resource Website 10+ mentions |
Molecular Modeling DataBase (RRID:SCR_010623) | MMDB | data or information resource, database | The Molecular Modeling DataBase (MMDB), also known as Entrez Structure, is a database of experimentally determined structures obtained from the RCSB Protein Data Bank (PDB). MMDB is developed by the Structure Group of the NCBI Computational Biology Branch. The data processing procedure at NCBI results in the addition of a number of useful features that facilitate computation on the data and link them to many other data types in the Entrez system. The structure database is considerably smaller than Entrez''s Protein or Nucleotide databases, but a large fraction of all known protein sequences have homologs in this set, and one may often learn more about a protein by examining 3-D structures of its homologs. These are accessible as Related Structures in the Links menu of Entrez Protein sequence records (illustrated example). It is then possible to align the query protein to the structure-based sequence, as shown in the illustration on this page. Additional resources can be used along with MMDB to interactively view the structures, find similar 3D structures, learn about the types of interactions and bound chemicals that have been found to exist among the similar 3D structures, and more. | macromolecule, structure, 3d spatial image, protein structure, gold standard |
is related to: NCBI Structure has parent organization: NCBI |
PMID:17135201 | nlx_56387 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure, http://www.ncbi.nlm.nih.gov/structure | SCR_010623 | Entrez Structure, NCBI Structure, Structure database, Structure (Molecular Modeling Database) | 2026-08-10 09:34:02 | 16 |
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