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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Database of Arabidopsis Transcription Factors Resource Report Resource Website 10+ mentions |
Database of Arabidopsis Transcription Factors (RRID:SCR_007101) | DATF | data or information resource, database | Database that collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. It uses not only locus (gene), but also gene model (transcript, protein) and the detail information is for each gene model not for locus. It adds multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Rice Transcription Factors (DRTF). It also keeps old information items such as the unique cloned and sequenced information of about 1200 transcription factors, protein domains, 3D structure information with BLAST hits against PDB, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference. | gene, alignment, arabidopsis, binding, clone, dna, domain, locus, phylogenetic tree, transcription, chromosome, transcription factor, blast, family, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
State Key Laboratory of Protein and Plant Gene Research ; National Natural Science Foundation of China 31470330; China 863 Programs 2006AA02Z334; China Postdoctoral Science Foundation Grant 2014M560017 |
PMID:15731212 | Free | nif-0000-21112, OMICS_00551, biotools:datf | https://bio.tools/datf | SCR_007101 | 2026-02-11 10:57:32 | 36 | |||||
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iNPS Resource Report Resource Website 10+ mentions |
iNPS (RRID:SCR_015750) | software resource, algorithm resource | Software for nucleosome detection that builds on the NPS software. Its application to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nucleosome, detection, nps, sequencing data, nucleosome positioning | is related to: NPS | National Natural Science Foundation of China 31210103916; National Natural Science Foundation of China 91019019; Chinese Ministry of Science and Technology 2011CB504206; Chinese Academy of Sciences KSCX2-EW-R-02; Chinese Academy of Sciences KSCX2-EW-J-15; Chinese Academy of Sciences YZ201243; Stem Cell Leading Project XDA01010303; Shanghai Academic Leader Project 11XD1405700; Fundamental Research Funds for the Central Universities 2014JBZ005 |
PMID:25233085 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015750 | iNPS: An improved algorithm for accurate nucleosome positioning from sequencing data | 2026-02-11 10:59:22 | 25 | |||||||
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Beijing: Eyes Open Eyes Closed Study Resource Report Resource Website |
Beijing: Eyes Open Eyes Closed Study (RRID:SCR_001507) | Beijing EOEC | data or information resource, data set | Data set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed. | early adult human, resting state, fmri, diffusion tensor imaging, resting state fmri, eyes open, eyes closed, neuroimaging, mprage, image collection, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China has parent organization: 1000 Functional Connectomes Project |
Healthy | National Natural Science Foundation of China 30770594; National High Technology Program of China (863) 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_152810 | SCR_001507 | Beijing Eyes Open Eyes Closed Study, Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Eyes Open Eyes Closed Sample, Eyes Open Eyes Closed Sample, BNU Eyes Open Eyes Closed Sample | 2026-02-11 10:56:14 | 0 | |||||
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Human Potential Tumor Associated Antigen database Resource Report Resource Website 1+ mentions |
Human Potential Tumor Associated Antigen database (RRID:SCR_002938) | data or information resource, database | To accelerate the process of tumor antigen discovery, we generated a publicly available Human Potential Tumor Associated Antigen database (HPtaa) with pTAAs identified by insilico computing. 3518 potential targets have been included in the database, which is freely available to academic users. It successfully screened out 41 of 82 known Cancer-Testis antigens, 6 of 18 differentiation antigen, 2 of 2 oncofetal antigen, and 7 of 12 FDA approved cancer markers that have Gene ID, therefore will provide a good platform for identification of cancer target genes. This database utilizes expression data from various expression platforms, including carefully chosen publicly available microarray expression data, GEO SAGE data, Unigene expression data. In addition, other relevant databases required for TAA discovery such as CGAP, CCDS, gene ontology database etc, were also incorporated. In order to integrate different expression platforms together, various strategies and algorithms have been developed. Known tumor antigens are gathered from literature and serve as training sets. A total tumor specificity penalty was computed from positive clue penalty for differential expression in human cancers, the corresponding differential ratio, and normal tissue restriction penalty for each gene. We hope this database will help with the process of cancer immunome identification, thus help with improving the diagnosis and treatment of human carcinomas. | cancer, tumor, tumor-associated antigen | has parent organization: Chinese Academy of Sciences; Beijing; China | National 863 program in China 2001AA215411; National Natural Science Foundation of China 30531160045; National Natural Science Foundation of China 30570393; Ludwig Institute for Cancer Research KSP 003 |
PMID:16381942 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02987 | http://www.hptaa.org | SCR_002938 | HPtaa Database | 2026-02-11 10:56:40 | 1 | |||||
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Arabidopsis Hormone Database Resource Report Resource Website 10+ mentions |
Arabidopsis Hormone Database (RRID:SCR_001792) | AHD, AHD2.0 | data repository, service resource, storage service resource, database, data or information resource, ontology, controlled vocabulary | Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions. | arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis service |
is related to: Gene Ontology has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 30625003; National Natural Science Foundation of China 30730011; Ministry of Science and Technology of China 2009CB119101; Ministry of Education of China ED20060047 |
PMID:21045062 PMID:19015126 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02559 | SCR_001792 | Arabidopsis Hormone Database 2.0 | 2026-02-12 09:43:14 | 28 | |||||
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Cancer Treatment Response gene signature DataBase Resource Report Resource Website |
Cancer Treatment Response gene signature DataBase (RRID:SCR_027950) | CTR_DB | data or information resource, database | Data resource for clinical transcriptomes with cancer treatment response, and meanwhile supports various data analysis functions, providing insights into the molecular determinants of drug resistance. CTR-DB 2.0 is updated cancer clinical transcriptome resource, expanding primary drug resistance and newly adding acquired resistance datasets and enhancing the discovery and validation of predictive biomarkers. | clinical transcriptomes, cancer treatment response, primary drug resistance, predictive biomarkers, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:39494527 | Free, Freely available, | SCR_027950 | , CTR-DB 1.0, CTR-DB 2.0 | 2026-02-11 11:01:38 | 0 | |||||||
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Spatial DB Resource Report Resource Website 1+ mentions |
Spatial DB (RRID:SCR_026135) | data or information resource, database | Database for spatially resolved transcriptomes. Provides curated spatially resolved transcriptomic data from published papers, aiming to provide comprehensive and accurate resource of spatial gene expression profiles in tissues. Allows users to browse spatial gene expression profile and compare spatial gene expression profile of any two datasets generated by same or different techniques side by side. | Spatially resolved transcriptomics, gene expression profiles, positional information, disease pathology, spatial gene expression profiles in tissues, curated data, | National Natural Science Foundation of China | PMID:31713629 | Free, Freely available | SCR_026135 | 2026-02-11 11:01:14 | 5 | |||||||||
|
HERB Resource Report Resource Website 50+ mentions |
HERB (RRID:SCR_026468) | data or information resource, database | High-throughput experiment- and reference-guided database of traditional Chinese medicine. | traditional Chinese medicine, experiment- and reference-guided database, | National Natural Science Foundation of China ; Zhejiang Provincial Natural Science Foundation of China ; China Postdoctoral Innovative Talent Foundation |
PMID:33264402 | Free, Freely available, | SCR_026468 | 2026-02-11 11:01:12 | 78 | |||||||||
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FerrDb Resource Report Resource Website 50+ mentions |
FerrDb (RRID:SCR_026852) | data or information resource, database | Manually curated database of ferroptosis regulators and ferroptosis-disease associations. There are two secondary categories of ferroptosis regulators: (1) genes and (2) substances. Gene regulators include driver, suppressor, marker, and unclassified regulator. Substances cover range of chemical entities, including pure substances (e.g., iron, erastin) and mixtures (e.g., herbal extracts). Substance regulators include inducers and inhibitors. FerrDb V2 is updated database. | Manually curated database, ferroptosis regulators, ferroptosis-disease associations, | Guangzhou Municipal Psychiatric Disease Clinical Transformation Laboratory ; Guangzhou Municipal Key Discipline in Medicin ; National Natural Science Foundation of China |
PMID:36305834 PMID:32219413 |
Free, Freely available | SCR_026852 | FerrDb V2 | 2026-02-11 11:01:14 | 65 | ||||||||
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RNAPhaSep Resource Report Resource Website |
RNAPhaSep (RRID:SCR_024958) | data or information resource, database | Database that collects phase separation related RNAs manually curated from publication and public databases. | phase separation related RNAs, publication and public databases data collection, manually curated, | National Key Research and Development Project of China ; National Natural Science Foundation of China ; Fujian Medical University Research Foundation of Talented Scholars ; Guangdong Basic and Applied Basic Research Foundation ; China Postdoctoral Science Foundation |
PMID:34718740 | Free, Freely available | SCR_024958 | 2026-02-11 11:00:57 | 0 | |||||||||
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LLPSDB Resource Report Resource Website 1+ mentions |
LLPSDB (RRID:SCR_024966) | data or information resource, database | Database of proteins undergoing liquid–liquid phase separation in vitro. Contains LLPS related proteins together with the corresponding phase separation conditions validated by experiments. | proteins, liquid–liquid phase separation in vitro, LLPS, Liquid Liquid Phase Separation related proteins, | National Natural Science Foundation of China | DOI:10.1093/nar/gkz778 | Free, Freely available | SCR_024966 | Liquid Liquid Phase Separation DataBase | 2026-02-11 11:00:57 | 3 | ||||||||
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PBmice Resource Report Resource Website 1+ mentions |
PBmice (RRID:SCR_006978) | PBmice | source code, software resource, data repository, service resource, storage service resource, database, data or information resource | Database for storing, retrieving, and displaying the information derived from piggyBac (PB) insertions (Insert) and their characterizations in the mouse genome with piggyBac transposon system. Quick Search and Advanced Search tools have been provided to find information in the PBmice database, the result is centered on Inserts and provides information related to the Inserts. A mapping database is linked to PBmice too. This mapping database allows row experiment data to be inputted in. All the mature data can be allowed publish to PBmice. PBmice Source Code is available with a License Agreement. | c57bl/6j, insertional mutation, mutagenesis, piggybac, transposon, insert, mutation | has parent organization: Fudan University; Shanghai; China | Program for New Century Excellent Talents in University ; Chinese Key Projects for Basic Research 2006CB806700; Chinese Key Projects for Basic Research 2005CB321905; Chinese Key Projects for Basic Research 2002CB512801; Hi-tech Research and Development Project 2007AA022012; National Natural Science Foundation of China 60473124; Shanghai Pujiang Program 05PJ14024 |
PMID:17932058 | nlx_97993 | http://www.scbit.org/PBmice/, http://www.idmshanghai.cn/PBmice/ | SCR_006978 | PiggyBac Mutagenesis Information CEnter, PBmice: PiggyBac Mutagenesis Information CEnter | 2026-02-12 09:44:26 | 1 | |||||
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IPEV Resource Report Resource Website 1+ mentions |
IPEV (RRID:SCR_023702) | software resource, software application, data analysis software, data processing software | Software tool to identify of Prokaryotic and Eukaryotic virus derived sequences in virome using deep learning. Used to calculate set of scores that reflect probability that input sequence fragments are prokaryotic and eukaryotic viral sequences. | Prokaryotic and Eukaryotic virus derived sequences, identify sequences, virome, eukaryotic viral sequences, prokaryotic viral sequences, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
DOI:10.1101/2023.05.28.541705 | Free, Available for download, Freely available | SCR_023702 | Identification of Prokaryotic and Eukaryotic Virus | 2026-02-12 09:47:59 | 1 | ||||||||
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RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | software resource, web service, data access protocol | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/ http://www.rnalocate.org/ |
SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-02-12 09:48:16 | 12 | ||||||
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PopLDdecay Resource Report Resource Website 100+ mentions |
PopLDdecay (RRID:SCR_022509) | software resource, software application, data analysis software, data processing software | Software tool for linkage disequilibrium decay analysis based on variant call format files. | linkage disequilibrium decay analysis, variant call format, VCF) files | National Natural Science Foundation of China ; China Postdoctoral Science Foundation |
PMID:30321304 | Free, Available for download, Freely available | SCR_022509 | 2026-02-12 09:47:24 | 117 | |||||||||
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PharmMapper Resource Report Resource Website 50+ mentions |
PharmMapper (RRID:SCR_022604) | software resource, web service, data access protocol | Web server for potential drug target identification using pharmacophore mapping approach.Designed to identify potential target candidates for given probe small molecules including drugs, natural products, or other newly discovered compounds with binding targets unidentified using pharmacophore mapping approach. Used for potential drug target identification with comprehensive target pharmacophore database. | potential drug target identification, given probe small molecules, identify potential target candidates, binding targets unidentified, pharmacophore mapping approach, drug target identification, target pharmacophore database | National Natural Science Foundation of China ; Shanghai Committee of Science and Technology ; Major National Scientific and Technological Project of China |
PMID:20430828 PMID:28472422 |
Free, Freely available | SCR_022604 | PharmMapper 2017 | 2026-02-12 09:47:37 | 97 | ||||||||
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TAM Resource Report Resource Website 1+ mentions |
TAM (RRID:SCR_023800) | software resource, web service, data access protocol | Web server for miRNA set enrichment analysis. TAM 2.0 is updated version of this web server. Allows to test functional and disease annotations of miRNAs by overrepresentation analysis and to compare input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis. | miRNA set enrichment analysis, functional and disease annotations testing, miRNAs, overrepresentation analysis, | National Natural Science Foundation of China ; Fundamental Research Funds for Central Universities of China ; Natural Science Foundation of Hebei Province ; Doctoral Fund of Ministry of Education of China |
PMID:29878154 PMID:20696049 |
Free, Freely available | SCR_023800 | TAM 2.0 | 2026-02-12 09:48:06 | 2 | ||||||||
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miRBaseConverter Resource Report Resource Website 1+ mentions |
miRBaseConverter (RRID:SCR_023873) | software resource, software application, data analysis software, data processing software | Software R package for converting and retrieving information of miRNAs in different miRBase versions. Used for converting and retrieving miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. Can process huge number of miRNAs in short time without other depends. | converting and retrieving miRNAs information, miRNAs information, different miRBase versions, miRNA Name, miRNA Accession, miRNA Sequence, miRNA Version, miRNA History, miRNA Family, miRNA | Australian Research Council Discovery Project ; National Health and Medical Research council ; Presidential Foundation of Hefei Institutes of Physical Science ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; Applied Basic Research Foundation of Science and Technology of Yunnan Province ; Shanghai Key Laboratory of Intelligent Information Processing China |
PMID:30598108 | Free, Available for download, Freely available | https://github.com/taoshengxu/miRBaseConverter | SCR_023873 | 2026-02-12 09:47:45 | 3 | ||||||||
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CLEAR Resource Report Resource Website 10+ mentions |
CLEAR (RRID:SCR_021663) | software resource, software application, data analysis software, data processing software | Software tool as computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq. CIRCexplorer3-CLEAR is CLEAR pipeline for direct comparison of circular and linear RNA expression. | Strategic Priority Research Program of Chinese Academy of Sciences ; National Natural Science Foundation of China ; Howard Hughes Medical Institute International Program |
PMID:31904419 DOI:10.1101/668657 |
Free, Available for download, Freely available | SCR_021663 | CLEAR/circExplorer3, Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq, CIRCexplorer3-CLEAR | 2026-02-12 09:47:51 | 15 | |||||||||
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HPEPDOCK Server Resource Report Resource Website 10+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | analysis service resource, software resource, data access protocol, service resource, web service, production service resource | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; Huazhong University of Science and Technology |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-02-12 09:47:04 | 46 |
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