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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions Resource Report Resource Website |
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) | HIBACHI, hibachi | simulation software, software application, software resource | Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods. | data, simulation, dataset, compare, machine, evaluate, learning, method | NIAID AI116794; NIDDK DK112217; NLM LM012601 |
PMID:29218887 | Free, Available for download, Freely available | SCR_017140 | SciCrunch Registry | Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions | 2026-10-17 01:29:15 | 0 | |||||||
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GeneTests Resource Report Resource Website 10+ mentions |
GeneTests (RRID:SCR_010725) | GeneTests | analysis service resource, biomaterial analysis service, data or information resource, database, material analysis service, narrative resource, portal, production service resource, service resource, topical portal, training material | The GeneTests Web site, a publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, is available at no cost to all interested persons. By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making. At This Site: * GeneReviews: Expert-authored peer-reviewed disease descriptions * Laboratory Directory: International directory of genetic testing laboratories * Clinic Directory: International directory of genetics and prenatal diagnosis clinics * Educational Materials: Illustrated glossary, information on genetic services, PowerPoint presentations, annotated Internet resources We comply with the HONcode standard for trustworthy health information. |
has parent organization: University of Washington; Seattle; USA has parent organization: NCBI |
NCI ; NHGRI 1 P41 LM/HG 06029; NLM 1 P41 LM/HG 06029; NLM contract N01-LM-4-3505; NLM 5 P41 LM07242; NLM 2 P41 LM 06001; DOE DE-FG03-02ER63301/A00 |
nlx_94696 | SCR_010725 | SciCrunch Registry | GeneTests: Clinical Genetic Information Resource | 2026-10-17 01:27:32 | 12 | ||||||||
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Developmental and Reproductive Toxicology Database Resource Report Resource Website 1+ mentions |
Developmental and Reproductive Toxicology Database (RRID:SCR_002326) | DART | data or information resource, database | Bibliographic database providing references to developmental and reproductive toxicology literature on the National Library of Medicine's Toxicology Data Network. It covers teratology and other aspects of developmental and reproductive toxicology. It contains over 200,000 references to literature published since 1965. DART/ETIC is easily accessible and free of charge. Search by subject terms, title words, chemical name, Chemical Abstracts Service Registry Number (RN), and author. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order, but may be sorted by publication date, author or title. | chemical, developmental, medicine, reproductive, teratology, toxicology, development | has parent organization: National Library of Medicine | U.S. Environmental Protection Agency ; NIEHS ; National Center for Toxicological Research ; NLM |
PMID:24698185 | Free | nif-0000-21110 | SCR_002326 | SciCrunch Registry | 2026-10-17 01:33:04 | 1 | ||||||
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Protein Clusters Resource Report Resource Website 1+ mentions |
Protein Clusters (RRID:SCR_003459) | ProtClustDB | data or information resource, database | Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP | bacteriophage, mitochondrial organelle, chloroplast organelle, plasmid, phylogeny, nucleotide sequence, chloroplast, dna, virus, genome, organelle, gold standard |
is listed by: re3data.org has parent organization: NCBI |
NIH ; Intramural Research Program ; NLM |
PMID:18940865 | Free, Available for download, Freely available | nif-0000-03354, r3d100010861 | https://doi.org/10.17616/R3TS52 | SCR_003459 | SciCrunch Registry | Protein Clusters Database, NCBI Protein Clusters, Entrez Protein Clusters | 2026-10-17 01:32:39 | 4 | ||||
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NCBI BioProject Resource Report Resource Website 10000+ mentions |
NCBI BioProject (RRID:SCR_004801) | data or information resource, database | Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP. | genome sequencing, sequencing, genotype, phenotype, sequence variant, epigenetic, data set, genome, assembly, annotation, mapping, cellular organism, gene mapping, gene expression, biological tag, gene rearrangement, genetic algorithm, genetic code, genetic genealogy, gold standard, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: INSDC has parent organization: NCBI |
NLM | PMID:22139929 | Free, Freely available | r3d100013330, nlx_143909, biotools:bioproject | http://www.ncbi.nlm.nih.gov/genomeprj, https://bio.tools/bioproject, https://doi.org/10.17616/R31NJMS2 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | SCR_004801 | SciCrunch Registry | NCBI BioProject Database, BioProject | 2026-10-17 01:33:01 | 14025 | ||||
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SHRINE Resource Report Resource Website 1+ mentions |
SHRINE (RRID:SCR_006293) | SHRINE | software application, software resource, source code | Software providing a scalable query and aggregation mechanism that enables federated queries across many independently operated patient databases. This platform enables clinical researchers to solve the problem of identifying sufficient numbers of patients to include in their studies by querying across distributed hospital electronic medical record systems. Through the use of a federated network protocol, SHRINE allows investigators to see limited data about patients meeting their study criteria without compromising patient privacy. This software should greatly enable population-based research, assessment of potential clinical trials cohorts, and hypothesis formation for followup study by combining the EHR assets across the hospital system. In order to obtain the maximum number of cases representing the study population, it is useful to aggregate patient facts across as many sites as possible. Cutting across institutional boundaries necessitates that each hospital IRB remain in control, and that their local authority is recognized for each and every request for patient data. The independence, ownership, and legal responsibilities of hospitals predetermines a decentralized technical approach, such as a federated query over locally controlled databases. The application comes with the SHRINE Core Ontology but it can be used with any ontology, even one that is disease specific. The Core Ontology is designed to enable the widest range of studies possible using facts gathered in the EMR during routine patient care. SHRINE allows multiple ontologies to be used for different research purposes on the same installed systems. | software network, clinical database, data sharing, clinical, medical record, federated, platform, network |
is related to: i2b2 Cross-Institutional Clinical Translational Research project is related to: i2b2 Research Data Warehouse has parent organization: Harvard Medical School; Massachusetts; USA |
Informatics for Integrating Biology and the Bedside ; NLM 5 U54 LM008748; NCRR 1 UL1 RR025758-01 |
PMID:19567788 | Available under a BSD3 Open unspecified license Software license. | nlx_151949 | SCR_006293 | SciCrunch Registry | Shared Health Research Informatics NEtwork | 2026-10-17 01:33:16 | 8 | |||||
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Gene Atlas Resource Report Resource Website 10+ mentions |
Gene Atlas (RRID:SCR_008089) | Geneatlas | atlas, data or information resource, database | This website allows visitors to search for genes of interest based on their spatial expression patterns in the Postnatal Day 7 mouse brain. Geneatlas provides two searching tools: A graphical interface for customized spatial queries; A textual interface for querying annotated structures. Geneatlas is the product of a collaboration between researchers at Baylor College of Medicine, Rice University, and University of Houston. | gene, brain, mouse, protein, spatial expression, molecular neuroanatomy resource, FASEB list |
has parent organization: University of Houston; Texas; USA has parent organization: Baylor University; Texas; USA |
Burroughs Wellcome Fund ; NLM 5T15LM07093; NCRR P41RR02250 |
nif-0000-10987 | SCR_008089 | SciCrunch Registry | 2026-10-17 01:34:40 | 47 | ||||||||
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MUMmer Resource Report Resource Website 500+ mentions |
MUMmer (RRID:SCR_018171) | alignment software, data processing software, image analysis software, software application, software resource | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NIAID N01 AI15447; NLM R01 LM06845; NSF IIS 9902923 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | SciCrunch Registry | MUMmer4, MUMmer 3.0 | 2026-10-17 01:29:35 | 547 | |||||
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LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG003749; NIDA U54 DA021519; NIEHS P30 ES06096; NIEHS U01 ES015675; NLM R01 LM008106 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | SciCrunch Registry | 2026-10-17 01:29:42 | 4 | ||||||
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Limitation-Recognizer Resource Report Resource Website |
Limitation-Recognizer (RRID:SCR_018747) | data analysis software, data processing software, software application, software resource | Software tool to recognize self acknowledged limitation sentences in biomedical articles. Automatic recognition of self acknowledged limitations in clinical research literature to support efforts in improving research transparency. | ASWG, automatic recognition, self acknowledged limitation, clinical research literature, research transparency, limitation sentence recognition |
uses: Stanford CoreNLP has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA |
NLM | PMID:29718377 | Free, Freely available | SCR_018748 | SCR_018747 | SciCrunch Registry | limitationrecognizer, limitation recognizer, limitation-recognizer | 2026-10-17 01:29:36 | 0 | ||||||
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ANTIGENpro Resource Report Resource Website 100+ mentions |
ANTIGENpro (RRID:SCR_018779) | data access protocol, service resource, software resource, web service | Web tool as sequence-based, alignment-free and pathogen-independent predictor of protein antigenicity.Predicts likelihood that protein is protective antigen. Integrated in SCRATCH suite of predictors. | Protein antigenicity, sequence based predictior, alignment free predictor, pathogen independent predictor, protein antigenicity predictor, SCRATCH suite, predictor | has parent organization: University of California at Irvine; California; USA | Microsoft Faculty Research Award ; NLM LM 07443; NSF 0513376; NSF EIA 0321390 |
PMID:20934990 | Free, Freely available | SCR_018779 | SciCrunch Registry | 2026-10-17 01:29:37 | 343 | ||||||||
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SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | data processing software, image analysis software, software application, software resource | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | LHNCBC HHSN276201500692P; NIH ; NLM |
Free, Available for download | SCR_016215 | SciCrunch Registry | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-10-17 01:33:10 | 4 | |||||||||
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DeepCell Resource Report Resource Website 10+ mentions |
DeepCell (RRID:SCR_022197) | data processing software, image analysis software, segmentation software, software application, software resource | Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software. | segmenting individual cells, microscopy image, cell segmentation | NIGMS F32 GM119319; NIGMS P50 GM107615; NLM DP1 LM01150; Paul Allen Family Foundation |
DOI:10.1371/journal.pcbi.1005177 | Free, Available for download, Freely available | SCR_022197 | SciCrunch Registry | Deepcell | 2026-10-17 01:31:03 | 14 | ||||||||
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PONDR Resource Report Resource Website 100+ mentions |
PONDR (RRID:SCR_023691) | data access protocol, software resource, web service | Web tool to predict order and disorder from amino acid sequence. Used to predict of natural disordered regions in proteins. | amino acid sequence, predict sequence order and disorder, protein natural disordered regions prediction, protein, | DOE ; MRC of Canada ; NLM R01 LM06916; NSF |
DOI:10.1016/S1093-3263(00)00138-8 | Free, Freely available | SCR_023691 | SciCrunch Registry | Predictor of Natural Disordered Regions | 2026-10-17 01:31:34 | 171 | ||||||||
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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 | Austrian Science Fund ; German Research Foundation ; Korean Government ; Mexican National Council of Science and Technology ; NIAID R01AI167860; NIA U19AG063744; NIDDK T32DK007202; NIDDK U01DK119702; NIDDK U24DK133658; NIGMS 1DP2GM137413; NIGMS 1R01GM132649; NIGMS R01GM107550; NIGMS R35GM142938; NIH Office of the Director S10 OD021750; NLM 1R01LM013115; NSF ; Research Council of Norway ; Sao Paulo Research Foundation |
PMID:37577622 | Free, Freely available, | SCR_024713 | SciCrunch Registry | 2026-10-17 01:32:08 | 7 | ||||||||
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Hanalyzer Resource Report Resource Website |
Hanalyzer (RRID:SCR_000923) | software application, software resource, source code | An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download. | genomic, visualization, reading, reasoning, reporting, throughput analyzer, data network |
has parent organization: University of Colorado Denver; Colorado; USA has parent organization: SourceForge |
NIDCR R01DE15191; NLM R01LM008111; NLM R01LM009254; NIGMS R01GM083649; NLM T15LM009451; NHGRI 5R01HG004483-09 |
PMID:19325874 | nlx_48287 | SCR_000923 | SciCrunch Registry | Hanalyzer: A 3R System | 2026-10-17 01:32:56 | 0 | |||||||
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Clair library Resource Report Resource Website |
Clair library (RRID:SCR_007019) | Clairlib | data analysis software, data processing software, software application, software resource, software toolkit, text extraction software, text-mining software | A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries. | analysis, information, linguistic, module, network, process, retrieval, perl, natural language processing, information retrieval, network analysis |
is listed by: Biositemaps has parent organization: University of Michigan; Ann Arbor; USA |
NSF IIS 0534323; NSF IIS 0329043; NSF BCS 0527513; NLM R01 LM008106; NIDA U54 DA021519 |
Open unspecified license: Content is available under GNU Free Documentation License 1.3 or later. | nif-0000-33210 | SCR_007019 | SciCrunch Registry | Computational Linguistics And Information Retrieval Library | 2026-10-17 01:31:14 | 0 | ||||||
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Pubmed Commons Resource Report Resource Website 1+ mentions |
Pubmed Commons (RRID:SCR_014021) | data or information resource, discussion, forum, narrative resource | A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments. | forum, PubMed, commuication |
is listed by: Connected Researchers is related to: PubMed is related to: Connected Researchers |
NIH ; NLM |
Free, Membership required, The community can contribute to this resource | SCR_014021 | SciCrunch Registry | 2026-10-17 01:31:12 | 3 | |||||||||
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PseudoFuN Resource Report Resource Website 1+ mentions |
PseudoFuN (RRID:SCR_017095) | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families. | gene, pseudogene, sequence, homology, regulatory, network, miRNA, coexpression, noncoding, RNA, TCGA, cancer |
has parent organization: Ohio State University; Ohio; USA has parent organization: Indiana University School of Medicine; Indiana; USA |
NLM T15 LM011270 | Free, Freely available | https://github.com/yanzhanglab/PseudoFuN_app | SCR_017095 | SciCrunch Registry | Pseudogene Functional Networks | 2026-10-17 01:31:39 | 2 | |||||||
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | SciCrunch Registry | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-10-17 01:31:39 | 2 |
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