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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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IBIS: Inferred Biomolecular Interactions Server Resource Report Resource Website 1+ mentions |
IBIS: Inferred Biomolecular Interactions Server (RRID:SCR_004886) | IBIS | data or information resource, database | A web server and database that organizes, analyzes and predicts interactions between proteins and other biomolecules. For a given protein sequence or structure query, it reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined structural biological assemblies. It also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation. | protein interaction, protein protein, protein small molecule, protein nucleic acid, protein ion interaction, interacting partner, binding site, homology, protein complex, structure conservation, nucleic acid, protein dna, protein rna, protein chemical, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: NCBI Structure has parent organization: NCBI |
PMID:22102591 PMID:19843613 |
OMICS_01917, biotools:ibis_ncbi, nlx_85682 | https://bio.tools/ibis_ncbi | SCR_004886 | Inferred Biomolecular Interactions Server, NCBI Inferred Biomolecular Interactions Server | 2026-08-15 11:28:41 | 5 | ||||||
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dbNSFP Resource Report Resource Website 500+ mentions |
dbNSFP (RRID:SCR_005178) | dbNSFP | data or information resource, database | A database for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) in the human genome. Version 2.0 is based on the Gencode release 9 / Ensembl version 64 and includes a total of 87,347,043 nsSNVs and 2,270,742 essential splice site SNVs. It compiles prediction scores from six prediction algorithms (SIFT, Polyphen2, LRT, MutationTaster, MutationAssessor and FATHMM), three conservation scores (PhyloP, GERP++ and SiPhy) and other related information including allele frequencies observed in the 1000 Genomes Project phase 1 data and the NHLBI Exome Sequencing Project, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, etc. Some dbNSFP contents (may not be up-to-date though) can also be accessed through variant tools, ANNOVAR, KGGSeq, UCSC Genome Browser''s Variant Annotation Integrator, Ensembl Variant Effect Predictor and HGMD. | non-synonymous single-nucleotide variant, function, annotation, functional prediction, non-synonymous mutation, splice site mutation, FASEB list |
is used by: Exomiser is listed by: OMICtools has parent organization: University of Texas Health Science Center at Houston; Texas; USA has parent organization: Google Sites |
PMID:23843252 PMID:21520341 |
Acknowledgement requested, Free, Public | OMICS_00172 | SCR_005178 | 2026-08-15 11:28:38 | 708 | |||||||
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SuperCAT Resource Report Resource Website 10+ mentions |
SuperCAT (RRID:SCR_004882) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. SuperCAT hosts typing databases for the Bacillus cereus group of bacteria. The databases contain MultiLocus Sequence Typing (MLST), MultiLocus Enzyme Electrophoresis (MLEE), and Amplified Fragment Length Polymorphism (AFLP) phylogenetic data. multilocus, sequence, Bacillus cereus, bacteria, Genomics, non-vertebrate, taxonomy, identification | bacillus cereus, bacteria, genomics, identification, multilocus, non-vertebrate, sequence, taxonomy | has parent organization: University of Oslo; Oslo; Norway | PMID:29568820 PMID:20651034 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03509 | SCR_004882 | SuperCAT | 2026-08-15 11:28:39 | 15 | |||||||
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CandiSNPer Resource Report Resource Website |
CandiSNPer (RRID:SCR_005173) | CandiSNPer | software resource, service resource, source code | A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region. | single nucleotide polymorphism, gene, plot, linkage disequilibrium, variant, genome-wide association study, genotyping, perl, r |
is listed by: OMICtools is related to: Ensembl has parent organization: Humboldt University of Berlin; Berlin; Germany |
PMID:20172942 | Free for academic use | OMICS_00169 | SCR_005173 | 2026-08-15 11:28:41 | 0 | |||||||
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ScienceBlogs: Medicine and Health Resource Report Resource Website |
ScienceBlogs: Medicine and Health (RRID:SCR_005176) | Sb Medicine & Health, Sb Medicine and Health | data or information resource, blog, narrative resource | ScienceBlogs posts about Medicine & Health. | medicine, health |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: ScienceBlogs |
nlx_144205 | SCR_005176 | ScienceBlogs: Medicine & Health, ScienceBlogs - Medicine and Health, ScienceBlogs: Medicine Health, Sb Medicine Health | 2026-08-15 11:28:43 | 0 | ||||||||
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Wall Street Journal Health Blog Resource Report Resource Website 1+ mentions |
Wall Street Journal Health Blog (RRID:SCR_004914) | WSJ Health Blog | data or information resource, blog, database, narrative resource | Health Blog offers news and analysis on health and the business of health. The blog is written by Katherine Hobson and includes contributions from staffers at The Wall Street Journal, WSJ.com and Dow Jones Newswires. A searchable interface allows the user to find topics of interest. Katherine Hobson has been writing about health and business for more than 15 years, including stints covering cancer, nutrition, exercise science, the U.S. economy and the U.K. beer industry. | health, business | nlx_143942 | SCR_004914 | Health Blog | 2026-08-15 11:28:40 | 1 | |||||||||
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Wisconsin Tissue Bank Resource Report Resource Website |
Wisconsin Tissue Bank (RRID:SCR_004910) | WTB | biomaterial supply resource, tissue bank, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 2,2026. A non-profit program providing tissue procurement services to the state of Wisconsin. The Wisconsin Tissue Bank handles organ donation, works with organ donors, provides organ donation information and organ transplantation. The Wisconsin Tissue Bank staff provides service to hospitals, Medical Examiners/Coroners and Funeral Directors throughout the state of Wisconsin for the recovery of bone, related soft tissue, veins, skin, and cardiovascular tissue for donation and transplantation. The Wisconsin Tissue Bank is dedicated to the education of health care professionals and the public to promote organ and tissue donation. The Wisconsin Tissue Bank promotes an environment sensitive to the physical, emotional, spiritual, social and economic needs of both those served and those who provide the service. | donation, transplantation, organ, tissue, bone, soft tissue, vein, skin, cardiovascular tissue | is listed by: One Mind Biospecimen Bank Listing | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_91313 | http://www.wisconsintissuebank.org | SCR_004910 | 2026-08-15 11:28:41 | 0 | |||||||
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NCI Specimen Resource Locator Resource Report Resource Website |
NCI Specimen Resource Locator (RRID:SCR_004754) | Specimen Resource Locator | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Specimen Resource Locator is a database to help researchers locate human specimens (tissue, serum, DNA/RNA, other specimens) for cancer research. It includes tissue banks and tissue procurement systems with access to normal, benign, precancerous and cancerous human tissue from a variety of organs. Researchers specify the types of specimens, number of cases, preservation methods and associated data they require. The Locator will then search the database and return a list of tissue resources most likely to meet their requirements. When no match is obtained, the researcher is referred to the NCI Tissue Expediter ([email protected]). The Tissue expediter is a scientist who can help researchers identify appropriate resources and/or appropriate collaborators. | tumor, normal, microarray |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Cancer Institute |
NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_80312 | SCR_004754 | 2026-08-15 11:28:41 | 0 | |||||||
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Northwest Tissue Services Resource Report Resource Website |
Northwest Tissue Services (RRID:SCR_004875) | biomaterial supply resource, tissue bank, material resource | Northwest Tissue Services is the only fully accredited non-profit tissue bank in this region. As a non-profit tissue bank, we provide all allograft and tissue products at the lowest possible cost consistent with high quality. Our accreditation by the American Association of Tissue Banks (AATB) is a testament to the quality and safety of tissue we have provided to hospitals and patients in this region for over twenty years. As the most knowledgeable and experienced tissue resource in the Northwest, we work hard every day to provide high quality tissue products and services. |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Puget Sound Blood Center |
nlx_85064 | http://www.nwts.org/ | SCR_004875 | 2026-08-15 11:28:41 | 0 | ||||||||||
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The Guardian: Science Resource Report Resource Website |
The Guardian: Science (RRID:SCR_005166) | Guardian: Science | data or information resource, blog, narrative resource | Latest science news, comment, analysis and features from guardian.co.uk, the world''s leading liberal voice. | science, news, comment, analysis, space, medicine, genetics, medical research |
is used by: NIF Data Federation is used by: Integrated Blogs |
nlx_144198 | SCR_005166 | 2026-08-15 11:28:43 | 0 | |||||||||
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Human Tissue Resource Network Resource Report Resource Website |
Human Tissue Resource Network (RRID:SCR_004785) | HTRN | biomaterial supply resource, tissue bank, material resource | Collect, bank, and distribute human tissue and fluid specimens by uniting tissue-based research resources within the OSU Department of Pathology and promoting collaborative research within the OSU Medical Center and related national human research projects. The HTRN is comprised of the Pathology Core Facility (PCF), Tissue Archive Service (TAS), Tissue Procurement Service (TPS), AIDS and Cancer Specimen Resource (ACSR), the Cancer and Leukemia Group B Pathology Coordinating Office (CALGB - PCO), and an Adenoma Polyp Tissue Bank (APTB). | malignant tissue, normal tissue, tissue, solid tumor, cancer, malignancy, tumor |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Ohio State University College of Medicine; Ohio; USA is parent organization of: Adenoma Polyp Tissue Bank |
AIDS, Cancer, Leukemia, Adenoma polyp, | Restricted | nlx_144405, SCR_005348, nlx_78270 | http://www.pathology.med.ohio-state.edu/HTRN/TPS/tpsr/default.asp | SCR_004785 | Ohio Tissue Procurement Shared Resources | 2026-08-15 11:28:41 | 0 | |||||
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SGN Resource Report Resource Website 1000+ mentions |
SGN (RRID:SCR_004933) | SGN, SGN ref | data or information resource, database | A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions. | database, clade, genomic, sequence, phenotype, pathway, genetic, taxonomy, annotation, blast, plant genome, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: Sol Genomics Network - Bulk download is related to: AmiGO has parent organization: Boyce Thompson Institute for Plant Research |
USDA ; ATC Inc. Advanced Technologies Cambridge ; NSF 0116076; NSF 9872617; NSF 975866; NSF 0421634 |
PMID:20935049 PMID:16010005 |
Public, The community can contribute to this resource | r3d100012078, nlx_89764, biotools:sol_genomics_network | https://bio.tools/sol_genomics_network, https://doi.org/10.17616/R3FS95 | http://www.sgn.cornell.edu/ | SCR_004933 | SGN ref, Sol Genomics Network | 2026-08-15 11:28:40 | 1261 | |||
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SpliceInfo Resource Report Resource Website |
SpliceInfo (RRID:SCR_005100) | data or information resource, database | A database of mRNA alternative splicing in the human genome. Within it, several modes of mRNA alternative splicing, such as exon skipping, alternative 5''-splicing sites, alternative 3''-splicing sites and mutually exclusive exons are computationally derived and extracted. Finally, for each type of alternative splicing, the flanking intronic sequences are collected and then exploited by motif discovery tools. The tissue-specific information and gene functionalities that correspond to the selected regions are also considered. The database provides a means of investigating alternative splicing and can be used for identifying alternative splicing - related motifs, such as the exonic splicing enhancer (ESE), the exonic splicing silencer (ESS) and other intronic splicing motifs. | exon, human genome, intron, mrna alternative splicing, mrna splicing | has parent organization: National Chiao Tung University; Hsinchu; Taiwan | nif-0000-03488 | SCR_005100 | SpliceInfo | 2026-08-15 11:28:41 | 0 | |||||||||
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Integrated Disease Resource Report Resource Website |
Integrated Disease (RRID:SCR_004892) | data or information resource, database | A virtual database currently indexing authoritative information on disease and treatment options from NINDS Disorder List and PubMed Health. | disease, treatment, disorder, health, database |
is used by: NIF Data Federation is related to: NINDS Disorder Index is related to: PubMed Health has parent organization: Integrated |
Data are licensed by their respective owners, Use and distribution is subject to the Terms of Use by the original resource | nlx_86401 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-6 http://neuinfo.org/nif/nifgwt.html?query=nlx_86401, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_86401-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-6 | SCR_004892 | NIF Integrated Disease View, NIF Integrated Disease, Integrated Disease View | 2026-08-15 11:28:39 | 0 | |||||||
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AtProbe Resource Report Resource Website |
AtProbe (RRID:SCR_005412) | AtProbe | data or information resource, database | Arabidopsis thaliana promoter binding element database that focuses on specific binding elements on known genes, found with experimental methods. | gene, binding element |
is listed by: OMICtools has parent organization: Cold Spring Harbor Laboratory |
Free | OMICS_00550 | SCR_005412 | AtProbe: Arabidopsis thaliana Promoter Binding Element Database, Arabidopsis thaliana Promoter Binding Element Database | 2026-08-15 11:28:44 | 0 | |||||||
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DATFAP Resource Report Resource Website |
DATFAP (RRID:SCR_005413) | DATFAP | data or information resource, database | A database of transcription factors from 13 plant species, and PCR primers for around 90% of them. | homolog, sequence, transcription factor |
is listed by: OMICtools is related to: Gene Ontology |
PMID:18366738 | Free | OMICS_00552 | SCR_005413 | Database of transcription factors with alignments and primers | 2026-08-15 11:28:42 | 0 | ||||||
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TFinDIT Resource Report Resource Website |
TFinDIT (RRID:SCR_005411) | TFinDIT | data or information resource, database | A database and web service for structural bioinformatics studies of transcription factor (TF)-DNA interactions. Various datasets can be generated based on one or more search options specified by users. | transcription factor-dna interaction, transcription factor, dna, interaction |
is listed by: OMICtools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of North Carolina at Charlotte; North Carolina; USA |
OMICS_00544 | SCR_005411 | Transcription Factor-DNA Interaction Data Depository, TFinDIT: Transcription Factor-DNA Interaction Data Depository | 2026-08-15 11:28:39 | 0 | ||||||||
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Phenologs Resource Report Resource Website 1+ mentions |
Phenologs (RRID:SCR_005529) | Phenologs | data or information resource, database | Database for identifying orthologous phenotypes (phenologs). Mapping between genotype and phenotype is often non-obvious, complicating prediction of genes underlying specific phenotypes. This problem can be addressed through comparative analyses of phenotypes. We define phenologs based upon overlapping sets of orthologous genes associated with each phenotype. Comparisons of >189,000 human, mouse, yeast, and worm gene-phenotype associations reveal many significant phenologs, including novel non-obvious human disease models. For example, phenologs suggest a yeast model for mammalian angiogenesis defects and an invertebrate model for vertebrate neural tube birth defects. Phenologs thus create a rich framework for comparing mutational phenotypes, identify adaptive reuse of gene systems, and suggest new disease genes. To search for phenologs, go to the basic search page and enter a list of genes in the box provided, using Entrez gene identifiers for mouse/human genes, locus ids for yeast (e.g., YHR200W), or sequence names for worm (e.g., B0205.3). It is expected that this list of genes will all be associated with a particular system, trait, mutational phenotype, or disease. The search will return all identified model organism/human mutational phenotypes that show any overlap with the input set of the genes, ranked according to their hypergeometric probability scores. Clicking on a particular phenolog will result in a list of genes associated with the phenotype, from which potential new candidate genes can identified. Currently known phenotypes in the database are available from the link labeled ''Find phenotypes'', where the associated gene can be submitted as queries, or alternately, can be searched directly from the link provided. | gene, phenotype, ortholog, genotype, human, mouse, yeast, worm | has parent organization: University of Texas at Austin; Texas; USA | Texas Advanced Research Program ; Welch Foundation ; Packard Fellowship ; March of Dimes ; Texas Institute for Drug and Diagnostic Development ; NSF ; NIH ; NIGMS |
PMID:20308572 | nlx_144624 | SCR_005529 | phenologs.org, Phenologs - Systematic discovery of non-obvious disease models and candidate genes | 2026-08-15 11:28:40 | 4 | ||||||
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Oscillatory Thoughts Resource Report Resource Website |
Oscillatory Thoughts (RRID:SCR_005481) | Oscillatory Thoughts | data or information resource, blog, narrative resource | Bradley Voytek''''s blog is where he tries out new ideas. He will often be wrong, but that''''s the point. He is a Neuroscientist studying human cognition, neuroplasticity, and brain computer interfacing. Into really geeky stuff. World zombie neuroscience expert. Also runs brainSCANr.com with his wife, Jessica. | neuroscience, human, cognition, neuroplasticity, brain computer interfacing | is related to: brainSCANr | nlx_144601 | SCR_005481 | Oscillatory Thoughts - Thoughts of a Neuroscientist | 2026-08-15 11:28:43 | 0 | ||||||||
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Boston University Biospecimen Archive Research Core Resource Report Resource Website 1+ mentions |
Boston University Biospecimen Archive Research Core (RRID:SCR_005363) | BU BARC | biomaterial supply resource, tissue bank, material resource | Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org | disease, normal, cancer, tumor, colon, inflammatory bowel disease, rectal cancer, colon cancer, tonsil, obstructive sleep apnea, tonsillitis, parathyroid, parathyroid adenoma, stomach, stomach cancer, prostate, prostate cancer, uterus, uterine cancer, lung, squamous cell carcinoma, adenocarcinoma, ovary, ovarian cancer, thyroid, thyroid papillary carcinoma, kidney, papillary renal cell carcinoma, renal cell carcinoma, clear cell carcinoma, breast, ductal carcinoma in situ, invasive ductal carcinoma, invasive lobular carcinoma, tissue, cancer tissue, colon tissue, tonsil tissue, parathyroid tissue, stomach tissue, prostate tissue, uterine tissue, lung tissue, ovarian tissue, thyroid tissue, kidney tissue, breast tissue, frozen, paraffin block, blood, biopsy, heart disease, diabetes, brain, brain tissue, adrenal, adrenal tissue, parotid, parotid tissue, thymus, pancreas, cervix, esophagus, thymus tissue, pancreatic tissue, cervical tissue, esophageal tissue |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Boston University Medical Campus; Massachusetts; USA has parent organization: Boston University School of Medicine; Massachusetts; USA |
Disease, Cancer, Tumor, Normal, Heart disease, Diabetes, Inflammatory bowel disease, Rectal cancer, Colon cancer, Obstructive sleep apnea, Tonsillitis, Parathyroid adenoma, Stomach cancer, Prostate cancer, Uterine cancer, Squamous cell carcinoma, Adenocarcinoma, Ovarian cancer, Thyroid papillary carcinoma, Papillary renal cell carcinoma, Renal cell carcinoma, Clear cell carcinoma, Ductal carcinoma in situ, Invasive ductal carcinoma, Invasive lobular carcinoma | Public: The mission of the Biospecimen Archive Research Core (BARC) is to collect high quality samples of normal and diseased human material with appropriate clinical annotation and make these materials, Known as biospecimens, Available to qualified researchers while ensuring the informed consent, Safety and anonymity of all providers. | nlx_144430 | SCR_005363 | BU Biospecimen Archive Research Core, Boston University Biospecimen Archive Research Core (BARC), Biospecimen Archive Research Core Boston University Medical Center, Boston University Medical Center Biospecimen Archive Research Core, BUMC BARC, BUMC Biospecimen Archive Research Core | 2026-08-15 11:28:44 | 1 |
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