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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform Resource Report Resource Website 500+ mentions |
Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (RRID:SCR_023757) | TCMSP | data or information resource, database | Pharmacology platform of Chinese herbal medicines that captures relationships between drugs, targets and diseases. Database includes chemicals, targets and drug-target networks, and associated drug-target-disease networks, as well as pharmacokinetic properties for natural compounds involving oral bioavailability, drug-likeness, intestinal epithelial permeability, blood-brain-barrier, aqueous solubility. | Pharmacology platform, Chinese herbal medicines, drugs, targets and diseases, drug-target networks, natural compounds, pharmacokinetic properties, | National Natural Science Foundation of China | PMID:24735618 | Free, Freely available | https://tcmsp-e.com/ | SCR_023757 | TCMSP database | 2026-08-21 12:42:51 | 577 | ||||||
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NeuroPep Resource Report Resource Website 10+ mentions |
NeuroPep (RRID:SCR_023102) | data or information resource, database | Comprehensive resource of neuropeptides, which holds non-redundant neuropeptide entries. Data collected from resources including MEDLINE abstracts, full papers, UniProt,database at www.neuropeptides.nl and Neuropedia. Contains detailed annotations for each entry, including source organisms, tissue specificity, families, names, post-translational modifications, 3D structures and literature references. Amino acid compositions, isoelectric points, molecular weight and other physicochemical properties of peptides are also provided. Search database with keywords such as sequence, name, family, etc.,User friendly web tools like browsing, sequence alignment and mapping are also integrated.Users can submit new entries online. Each new entry is validated before incorporating it. | neuropeptide database, neuropeptide, non-redundant neuropeptide, | Fundamental Research Funds for the Central Universities of China ; National Natural Science Foundation of China |
PMID:25931458 | Free, Freely available | SCR_023102 | 2026-08-21 12:42:31 | 10 | |||||||||
|
OncoboxPD Resource Report Resource Website 1+ mentions |
OncoboxPD (RRID:SCR_023723) | data or information resource, database | Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways. | Gene Ontology terms enrichment patterns, human molecular pathways, curated collection, GO terms enrichment patterns, experimental expression data analysis, |
is related to: oncoboxlib is related to: Gene Ontology |
National Natural Science Foundation of China ; Qingdao Key Health Discipline Development Fund ; Qingdao Key Research Project ; Russian Science Foundation |
PMID:35615022 | Free, Freely available | SCR_023723 | Oncobox Pathway Databank | 2026-08-21 12:42:44 | 8 | |||||||
|
Brassicaceae Database Resource Report Resource Website 100+ mentions |
Brassicaceae Database (RRID:SCR_023019) | BRAD | data or information resource, database | Database includes newly released genome sequences of Brassiceae species and published genomic data of most other Brassicaceae species.Data can be browsed in JBrowse or searched in BLAST. Offers service of searching for syntenic genes, which are generated based on their syntenic relationships to genes in Arabidopsis thaliana. Regularly updated with newly released reference genomes. | genome sequences, Brassiceae species, published genomic data, syntenic genes, | National Natural Science Foundation of China ; National Programon Key Research Project |
DOI:10.1093/nar/gkab1057 | Free, Freely available | SCR_023019 | 2026-08-21 12:42:43 | 400 | ||||||||
|
OrthoVenn2 Resource Report Resource Website 100+ mentions |
OrthoVenn2 (RRID:SCR_022504) | data access protocol, software resource, web service | Web server for whole genome comparison and annotation of orthologous clusters across multiple species.Works on any operating system with modern browser and Javascript enabled. Used to identify orthologous gene clusters and supports user define species to upload customized protein sequences. Interactive graphic tool which provides Venn diagram view for comparing multiple species protein sequences. | whole genome comparison and annotation, orthologous clusters across multiple species, identify orthologous gene clusters, comparing multiple species protein sequences | National Natural Science Foundation of China | PMID:31053848 | Free, Freely available | SCR_022504 | 2026-08-21 12:42:26 | 288 | |||||||||
|
Plant mPLoc Resource Report Resource Website 100+ mentions |
Plant mPLoc (RRID:SCR_023014) | data access protocol, software resource, web service | Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization. | Predicting Plant Protein Subcellular Localization, predicting subcellular localization, plant proteins, | National Natural Science Foundation of China ; Science and Technology Commission of Shanghai Municipality ; Shanghai Pujiang Program |
PMID:20596258 | Free, Freely available | SCR_023014 | Plant-mPLoc | 2026-08-21 12:42:34 | 362 | ||||||||
|
KinasePhos 3.0 Resource Report Resource Website 1+ mentions |
KinasePhos 3.0 (RRID:SCR_023595) | simulation software, software application, software resource | Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool. | redesign and expansion of prediction, kinase specific phosphorylation sites, kinase specific phosphorylation site prediction, site prediction, kinase specific phosphorylation, | Ganghong Young Scholar Development Fund ; Guangdong Province Basic and Applied Basic Research Fund ; National Natural Science Foundation of China ; Science ; Technology and Innovation Commission of Shenzhen Municipality ; Warshel Institute for Computational Biology |
PMID:35781048 | Free, Available for download, Freely available | https://github.com/tom-209/KinasePhos-3.0-executable-file | SCR_023595 | 2026-08-21 12:42:42 | 3 | ||||||||
|
Database Commons Resource Report Resource Website 10+ mentions |
Database Commons (RRID:SCR_023661) | catalog, data or information resource, database | Curated catalog of worldwide biological databases to provide landscape of biological databases throughout the world and enable easy retrieval and access to specific collection of databases of interest. Catalog of worldwide biological databases as well as their curated meta information and derived statistics. | Curated catalog, worldwide biological databases, curated meta information, | International Partnership Program of the Chinese Academy of Sciences ; National Natural Science Foundation of China ; Professional Association of the Alliance of International Science Organizations ; Strategic Priority Research Program of the Chinese Academy of Sciences ; Youth Innovation Promotion Association of Chinese Academy of Sciences |
PMID:36572336 PMID:34718731 |
Free, Freely available | SCR_023661 | 2026-08-21 12:42:42 | 28 | |||||||||
|
Beijing: Short TR Study Resource Report Resource Website 1+ mentions |
Beijing: Short TR Study (RRID:SCR_003502) | Beijing Short TR | data or information resource, data set | Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information | nifti, fmri, resting-state fmri, image collection, early adult human, mprage, diffusion tensor imaging, neuroimaging, brain, demographic |
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 2008AA02Z405 |
Creative Commons Attribution-NonCommercial License | nlx_157642 | SCR_003502 | Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Short TR Sample, BNU Short TR Sample | 2026-08-21 12:37:02 | 6 | |||||
|
trRosetta Resource Report Resource Website 100+ mentions |
trRosetta (RRID:SCR_021181) | service resource, simulation software, software application, software resource | Software tool for fast and accurate protein structure prediction. Builds protein structure based on direct energy minimizations with restrained Rosetta. Restraints include inter-residue distance and orientation distributions, predicted by deep residual neural network. Homologous templates are included in network prediction to improve accuracy for easy targets. | protein structure, restraint-guided structure generation, protein structure prediction | uses: Rosetta | China Scholarship Council ; Fok Ying-Tong Education Foundation ; Key Laboratory for Medical Data Analysis and Statistical Research of Tianjin ; National Natural Science Foundation of China ; NIGMS R01 GM092802; NIH Office of the Director DP5 OD026389; Thousand Youth Talents Plan of China |
PMID:31896580 | Free, Freely available | https://github.com/gjoni/trRosetta | SCR_021181 | transformed restrained Rosetta | 2026-08-21 12:41:51 | 100 | ||||||
|
CIRIquant Resource Report Resource Website 1+ mentions |
CIRIquant (RRID:SCR_021661) | data analysis software, data processing software, software application, software resource, software toolkit | Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. | circRNA quantification, differential expression analysis, RNA-Seq data, circular RNA, circular isoform switching events | National Natural Science Foundation of China | DOI:10.1038/s41467-019-13840-9 | Free, Available for download, Freely available | https://sourceforge.net/projects/ciri/files/, https://ciri-cookbook.readthedocs.io/en/latest/CIRIquant_0_home.html# | SCR_021661 | 2026-08-21 12:42:02 | 4 | ||||||||
|
CIRCexplorer2 Resource Report Resource Website 10+ mentions |
CIRCexplorer2 (RRID:SCR_021664) | data analysis software, data processing software, software application, software resource | Software package for comprehensive and integrative circular RNA analysis. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. Used to annotate circRNAs, de novo assemble novel circular RNA transcripts and chracterize various of alternative (back-)splicing events of circular RNAs. | Decipher alternative back splicing, decifer circRNAs splicing pattern, circular RNA analysis, annotate circRNAs | Ministry of Science and Technology of China ; National Natural Science Foundation of China |
PMID:27365365 PMID:30539552 |
Free, Available for download, Freely available | SCR_021664 | 2026-08-21 12:42:03 | 49 | |||||||||
|
CancerMIRNome Resource Report Resource Website 10+ mentions |
CancerMIRNome (RRID:SCR_022092) | data access protocol, data or information resource, database, software resource, web service | Web server for cancer miRNome interactive analysis and visualization based on human miRNome data of cancer types from The Cancer Genome Atlas, and public cancer circulating miRNome profiling datasets from NCBI Gene Expression Omnibus and ArrayExpress. Comprehensive database for interactive analysis and visualization of miRNA expression profiles. | cancer miRNome interactive analysis, human miRNome data, cancer data, miRNA expression profiles |
is related to: The Cancer Genome Atlas is related to: ArrayExpress |
National Natural Science Foundation of China ; Riverside Faculty Start-up Fund ; Science and Technology Project of Guizhou Province ; UC Academic Senate CoR Research Grant ; UC Cancer Research Coordinating Committee Competition Award ; United States Department of Agriculture |
DOI:10.1093/nar/gkab784 | Free, Freely available | SCR_022092 | 2026-08-21 12:42:12 | 48 | ||||||||
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Residue Iteration Decomposition Resource Report Resource Website 1+ mentions |
Residue Iteration Decomposition (RRID:SCR_022174) | RIDE | software resource, software toolkit | Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials. | temporal decomposition of EEG signal, EEG, event related potentials, single trial analysis, event related brain potentials, ERP, ERP decomposition method, ERP reconstruction, Latency variability, residue iteration decomposition, single trial analysis | is related to: MATLAB | Germany Hong Kong Joint Research Scheme ; Hong Kong Baptist University ; Hong Kong Research Grant Council ; National Natural Science Foundation of China |
PMID:25455337 | Free, Available for download, Freely available | SCR_022174 | Residue Iteration DEcomposition | 2026-08-21 12:42:22 | 8 | ||||||
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GetOrganelle Resource Report Resource Website 100+ mentions |
GetOrganelle (RRID:SCR_022963) | software resource, software toolkit | Software toolkit to assembly of organelle genome from genomic skimming data. Used for accurate de novo assembly of organelle genomes. | Organelle genome assembly, genomic skimming data, organelle genomes, de novo assembly | Chinese Academy of Sciences ; National Natural Science Foundation of China |
PMID:32912315 | Free, Available for download, Freely available | SCR_022963 | 2026-08-21 12:42:42 | 256 | |||||||||
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Human Protein-Protein Interaction Mining Tool Resource Report Resource Website 1+ mentions |
Human Protein-Protein Interaction Mining Tool (RRID:SCR_008040) | software application, software resource, text-mining software | Web-based tool used to mine human protein-protein interactions (PPIs) from PubMed abstracts based on their co-occurrences and interaction words, followed by evidencs in human PPI databases and shared terms in GO database. | protein-protein interaction, pubmed, text mining |
is listed by: 3DVC has parent organization: Chinese Academy of Sciences; Beijing; China |
Hi-Tech Research and Development Program of China 2006AA02Z322; National Natural Science Foundation of China 30525007; National Natural Science Foundation of China 30730049; National Basic Research Program of China 2006CB504100; National Basic Research Program of China 2006CB500700; National Basic Research Program of China 2007CB947200 |
nif-0000-10256 | SCR_008040 | PPI Finder | 2026-08-21 12:38:33 | 1 | ||||||||
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ImmuCellAI Resource Report Resource Website 10+ mentions |
ImmuCellAI (RRID:SCR_027645) | software application, software resource, source code | Software tool for comprehensive T‐Cell subsets abundance prediction and its application in cancer immunotherapy. | Cell subsets abundance prediction, predicting immunotherapy response, cancer immunotherapy estimate, immune cells, gene expression dataset, | National Natural Science Foundation of China | PMID:32274301 | Free, Available for download, Freely available | https://github.com/lydiaMyr/ImmuCellAI | SCR_027645 | Immune Cell Abundance Identifier | 2026-08-21 12:43:55 | 12 | |||||||
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PanPep Resource Report Resource Website |
PanPep (RRID:SCR_028580) | software application, software resource, source code | Software framework constructed in three levels for predicting the peptide and TCR binding recognition. Used to recognize TCR–antigen binding, by combining the concepts of meta-learning and the neural Turing machine. | predicting peptide and TCR binding recognition, recognize TCR–antigen binding, | National Key Research and Development Program of China ; National Natural Science Foundation of China ; Shanghai Natural Science Foundation Program |
DOI:10.1038/s42256-023-00619-3 | Free, Available for download, Freely available | SCR_028580 | , Pan-Peptide Meta Learning | 2026-08-21 12:44:03 | 0 | ||||||||
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TCellSI Resource Report Resource Website |
TCellSI (RRID:SCR_028753) | data access protocol, software resource, software toolkit, web service | Software R package and web server for T cell state assessment and its applications in immune environment prediction. | T cell state assessment, immune environment prediction, | National Natural Science Foundation of China | PMID:39429885 | Free, Available for download, Freely available | https://github.com/GuoBioinfoLab/TCellSI | SCR_028753 | T cell state identifier (TCellSI) | 2026-08-21 12:44:15 | 0 | |||||||
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ImmuScope Resource Report Resource Website |
ImmuScope (RRID:SCR_028676) | software application, software resource, source code | Software tool to predict CD4+ T cell epitopes, model MHC-II antigen presentation, and assess immune responses. It helps scientists with vaccine design, cancer neoantigen discovery, and tracking viral mutations. | predict CD4+ T cell epitopes, model MHC-II antigen presentation, assess immune responses, | Monash University ; National Health and Medical Research Council of Australia ; National Natural Science Foundation of China |
DOI:10.1101/2025.02.02.636141 | Free, Available for download, Freely available | SCR_028676 | 2026-08-21 12:44:05 | 0 |
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