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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Interolog/Regulog Database Resource Report Resource Website 1+ mentions |
Interolog/Regulog Database (RRID:SCR_000755) | data or information resource, database | Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins. | interacting, interolog, protein, regulog, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:15173116 | nif-0000-20863, biotools:interolog | https://bio.tools/interolog | SCR_000755 | Interolog | 2026-08-10 09:31:15 | 2 | |||||||
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Collecting Duct Database Resource Report Resource Website |
Collecting Duct Database (RRID:SCR_000759) | CDDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This database is intended to serve as a learning tool to obtain curated information for the design of microarray targets to scan collecting duct tissues (human, rat, mouse). The database focuses on regulatory and transporter proteins expressed in the collecting duct, but when collecting duct proteins are a member of a larger family of proteins, common additional members of the family are included even if they have not been demonstrated to be expressed in the collecting duct. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones. CDDB is a database that organizes lists of genes found in collecting duct tissues from three mammalian species: human, rat, and mouse. Proteins are divided into categories by family relationships and functional classification, and each category is assigned a section in the database. Each section includes links to the literature and to sequence information for genes, proteins, expressed sequence tags, and related information. The user can peruse a section or use a search engine at the bottom of the web page to search the database for a name or abbreviation or for a link to a sequence. Each entry in the database includes links to relevant papers in the kidney and collecting duct literature. It uses links to PubMed to generate MEDLINE searches for retrieval of references. In addition, each entry includes links to curated sequence data available in LocusLink. Individual links are made to sequence and protein data for human, rat, and mouse. Links are then added as curated sequences become available for proteins identified in the renal collecting duct and for proteins identified in kidney and similar in function or homologous to proteins identified in the collecting duct. | expressed sequence tag, expression, family, functional, gene, aquaporin, array, cdna, classification, collecting duct, homologous, human, kidney, literature, mammal, mammalian, microarray, mouse, protein, protein localization and targeting databases, rat, receptor, regulatory, relationship, scan, serial analysis, specie, target, tissue, transporter, vasopressin, water channel protein | has parent organization: National Institutes of Health | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21078 | SCR_000759 | Collecting Duct Database | 2026-08-10 09:31:15 | 0 | |||||||
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QTL Matchmaker Resource Report Resource Website |
QTL Matchmaker (RRID:SCR_000741) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database used for high throughput mapping of genes to QTL and comparative genome analysis between different humans, mice, and rats. This database is designed for the analysis of larger sets of data using genome-scale experimental approaches, and to organize information from various websites and publications. | qtl, comparative genome analysis, genome scale experimental, data organization | has parent organization: Yeshiva University; New York; USA | PMID:16381937 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03382 | SCR_000741 | QTL Matchmaker | 2026-08-10 09:31:14 | 0 | |||||||
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Retinoblastoma Genetics Resource Report Resource Website 1+ mentions |
Retinoblastoma Genetics (RRID:SCR_000742) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A website that provides access to a database, nomenclature, fac sheets, downloadable slides, and other information regarding RB1 gene mutations. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03389 | http://www.verandi.de/joomla/ | SCR_000742 | Retinoblastoma Genetics | 2026-08-10 09:31:14 | 3 | |||||||||
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VectorDB- Molecular Biology Vector Sequence Database Resource Report Resource Website |
VectorDB- Molecular Biology Vector Sequence Database (RRID:SCR_000745) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. A database with information about a variety of vectors, including phage, plasmid, phagemid, phasmid, cosmid, virus and YAC vectors. It also contains information on drosophilia, C. elegans, yeast and drosophilia vectors, including vector functions, hosts and copy number. | vector, yeast, phage, plasmid, phagemid, phasmid, cosmid, virus, yac, drosophilia, yeast, fly | has parent organization: Stanford University; Stanford; California | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03625 | http://www.yeastgenome.org/ | http://seq.yeastgenome.org/vectordb/ | SCR_000745 | vectorDB | 2026-08-10 09:31:14 | 0 | ||||||
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Ridom SpaServer Resource Report Resource Website 100+ mentions |
Ridom SpaServer (RRID:SCR_001460) | data or information resource, database | Database of information of spa-typing of MRSA, or Staphylococcus aureus, that can be used to collate and harmonize data from various geographic regions. | database, information, staphylococcus aureus, bacteria, mrsa, FASEB list | PMID:14662923 | Free, Available for download, Freely available | nif-0000-08852 | SCR_001460 | SpaServer | 2026-08-10 09:31:26 | 322 | ||||||||
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MAboya Gene Expression Patterns and Sequence Tags Resource Report Resource Website 1+ mentions |
MAboya Gene Expression Patterns and Sequence Tags (RRID:SCR_000763) | MAGEST | data or information resource, database | A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future. | ascidia, sea squirt, development, maternal, dna, rna, genetic, chordate, vertebrae, gene, expression | has parent organization: University of Tokyo; Tokyo; Japan | Ministry of Education Science Sports and Culture Japan 1016821; Ministry of Education Science Sports and Culture Japan 11149212; Research for the Future Program from the Japan Society for the promotion of Science 96L00404 |
PMID:11752271 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21247 | http://www.genome.ad.jp/magest | SCR_000763 | MAboya Gene Expression Patterns and Sequence Tags (MAGEST) | 2026-08-10 09:31:16 | 7 | ||||
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Neurospora crassa Database Resource Report Resource Website 1+ mentions |
Neurospora crassa Database (RRID:SCR_001372) | NCD | data or information resource, database | It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available. | gene, annotation, compendium, contig, distance, drosophila, genome, mitochondrial, neurospora crassa, plasmid, region, rrna, sequence, trna, untranslated | Free, Freely available, | nif-0000-20965 | http://www.broadinstitute.org/annotation/genome/neurospora/Home.html | SCR_001372 | Neurospora crassa Database | 2026-08-10 09:31:24 | 4 | |||||||
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MINT Resource Report Resource Website 1000+ mentions |
MINT (RRID:SCR_001523) | MINT | data or information resource, database | A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them. | protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, ortholog, FASEB list |
uses: IntAct uses: PSI-MI is listed by: re3data.org is affiliated with: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: VirusMINT is related to: PSICQUIC Registry is related to: Agile Protein Interactomes DataServer has parent organization: University of Rome Tor Vergata; Rome; Italy works with: IMEx - The International Molecular Exchange Consortium |
European Union ; ENFIN ; Interaction Proteome Project ; IMEx - The International Molecular Exchange Consortium ; HUPO Proteomics Standards Initiative ; AIRC Associazione Italiana per la Ricerca sul Cancro |
PMID:22096227 PMID:24234451 PMID:19897547 PMID:18592188 PMID:18551417 PMID:18428712 PMID:17135203 PMID:11911893 |
nlx_152821, r3d100010414 | https://doi.org/10.17616/R38S3B | SCR_001523 | MINT, the Molecular INTeraction database, Molecular Interactions Database, Molecular INTeraction database, MINT - the Molecular INTeraction database | 2026-08-10 09:31:27 | 1141 | |||||
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PREFAB Resource Report Resource Website 1+ mentions |
PREFAB (RRID:SCR_001009) | PREFAB | data or information resource, database | Downloadable data designed for testing multiple sequence alignment methods. | database, downloadable data, sequence alignment, sequence alignment method |
is listed by: OMICtools is listed by: SoftCite is related to: MUSCLE |
PMID:15034147 | Free, Available for download, Freely available | OMICS_00984 | SCR_001009 | PREFAB - Protein Reference Alignment Benchmark, Protein Reference Alignment Benchmark | 2026-08-10 09:31:18 | 1 | ||||||
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IFPMA Clinical Trials Portal Resource Report Resource Website |
IFPMA Clinical Trials Portal (RRID:SCR_000791) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. IFPMA Clinical Trials Portal is brought to you by IFPMA on behalf of its Member Companies and Associations. IFPMA Clinical Trials Portal ensures: a free and easy-to-use interface for patients and health professionals alike to ongoing clinical trials, clinical trial results and complementary information on related issues; non-promotional and reliable information; industry's commitment to the transparency of clinical trials. * Search by Medical Condition and Drug Name * Language Interfaces (En, Es, Fr, De, Jp) * Glossary and Easy Explanation of Medical Expressions * Geographical Search | clinical, clinical trial, pediatric, disease, cancer, hiv, aids, diabetes, heart disease | has parent organization: IFPMA - International Federation of Pharmaceutical Manufacturers and Associations | IFPMA - International Federation of Pharmaceutical Manufacturers and Associations | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31391 | SCR_000791 | International Federation of Pharmaceutical Manufacturers and Associations Clinical Trials Portal | 2026-08-10 09:31:15 | 0 | |||||||
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Integrated Models Resource Report Resource Website |
Integrated Models (RRID:SCR_001481) | Integrated Models | data or information resource, database | A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun. | model, integrated, database, nif |
is used by: NIF Data Federation lists: Simtk.org lists: ModelDB lists: Open Source Brain lists: CellML Model Repository has parent organization: Integrated |
Free, Freely available | nlx_152726 | https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-12 https://neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_152726-1, https://neuinfo.org/mynif/search.php?q=*&t=indexable&list=cover&nif=nlx_154697-12 | SCR_001481 | Integrated Model View, NIF Integrated Models, NIF Models, NIF Integrated Models View, Integrated Model, NIF Integrated Model | 2026-08-10 09:31:27 | 0 | ||||||
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Ronald M. Davis Tobacco Deposition and Trial Testimony Archive Resource Report Resource Website 1+ mentions |
Ronald M. Davis Tobacco Deposition and Trial Testimony Archive (RRID:SCR_000795) | data or information resource, database | A database of information from the Center for Tobacco Use Prevention and Research. Materials include depositions, trial testimony and opening and closing statements, expert reports, jury instructs, and verdicts. Some transcripts are rough copies and others may be marked as confidential although they no longer retain that status. This resource is in French. | tobacco, legal, testimony, trial, deposition, expert report, jury, verdicts, transcripts, center for tobacco use prevention and research, cigarettes, french | In order to access documents in this collection, users agree to certain conditions. | nif-0000-31469 | SCR_000795 | Tobacco DATTA | 2026-08-10 09:31:15 | 1 | |||||||||
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NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study I Resource Report Resource Website |
NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study I (RRID:SCR_001153) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, futility study of minocycline and creatine in subjects with early untreated Parkinson's Disease (PD) or FS-I (Futility Study I). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. A Multicenter, Double-Blind, Futility Study of Minocycline and Creatine in subjects with early untreated Parkinson's Disease (PD) (FS-1).The primary objective of the study was to assess the impact of minocycline and creatine on the progression of PD in order to assess whether it was non-futile to proceed with further study of these agents. The progression of PD was measured by the change in total UPDRS score between the baseline visit and month 12 or the time of sufficient disability to require symptomatic therapy (last visit before subject goes on dopaminergic therapy), whichever occurs first. The additional follow-up of subjects until 18 months addressed the secondary objectives. The FS-1 study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD). | PMID:18520981 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11251 | http://www.pd-doc.org/Databases/LinkedDatabases/NETPDDatabases/FS1Study/tabid/198/Default.aspx | SCR_001153 | FS-1 | 2026-08-10 09:31:21 | 0 | ||||||||
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NeuroPedia Resource Report Resource Website 10+ mentions |
NeuroPedia (RRID:SCR_001551) | NeuroPedia | data or information resource, database | A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species. | proteomics, peptide, neuropeptide, mass spectrometry assay, peptide sequence, spectrum, homolog | has parent organization: Center for Computational Mass Spectrometry | NCRR P41-RR024851; NIDA 5K01DA23065; NINDS R01 NS24553; NIDA R01 DA04271; NIMH R01 MH077305; NHLBI P01 HL58120 |
PMID:21821666 | Free, Freely available | nlx_152894 | SCR_001551 | NeuroPedia: Neuropeptide database and spectra library | 2026-08-10 09:31:27 | 12 | |||||
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Earlier versus Later Levodopa Therapy in Parkinson Disease Resource Report Resource Website |
Earlier versus Later Levodopa Therapy in Parkinson Disease (RRID:SCR_001150) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from the ELLDOPA study: a multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial of 361 early, mild Parkinson's disease (PD) subjects, not requiring symptomatic medications with a duration from time of diagnosis less than 2 years. A NINDS funded study. The multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial, called the Earlier versus Later Levodopa Therapy in Parkinson Disease (ELLDOPA) study was run by the Parkinson Study Group and sponsored by the National Institute of Neurological Disorders and Stroke (NINDS). The subjects (n=361) were enrolled between September 1998 and August 2001 at 33 sites in the United States and 5 sites in Canada. Despite the known benefit of levodopa in reducing the symptoms of Parkinsons disease, concern has been expressed that its use might hasten neurodegeneration. This study assessed the effect of levodopa on the rate of progression of Parkinsons disease.The primary analysis assessed the doseresponse relationship between the assigned doses and the worsening of parkinsonism, as indicated by the changes in the total score on the UPDRS between the baseline visit and week 42. Washout of study drug occurred during weeks 40-42. | ClinicalTrials.Gov: NCT00004733 | Parkinson's Disease | National Institute of Neurological Disorders and Stroke | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11249 | http://www.pd-doc.org/Databases/LinkedDatabases/PSGDatabases/ELLDOPAStudy/tabid/161/Default.aspx | SCR_001150 | 2026-08-10 09:31:21 | 0 | |||||||
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Catalogue for Transmission Genetics in Arabs Resource Report Resource Website 1+ mentions |
Catalogue for Transmission Genetics in Arabs (RRID:SCR_000730) | data or information resource, database | The CTGA database is a database for genetic disorders in Arab populations. It hosts entries for Mendelian disorders and related genes, and currently contains nearly 1290 entries. Its goal is to facilitate further research on Arab genomic diseases. | arab, arab genomic diseases, arab inherited disease, arab inherited disorder, mendelian disorder | PMID:16381941 | nif-0000-02705 | SCR_000730 | CTGA | 2026-08-10 09:31:14 | 7 | |||||||||
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GOLD.db - Genomics Of Lipid-associated Disorders Resource Report Resource Website 10+ mentions |
GOLD.db - Genomics Of Lipid-associated Disorders (RRID:SCR_000736) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database that integrates information on the function and properties of genes and their protein products relevant to lipid-associated disorders. GOLD.db provides information such as the biology, diagnosis management, treatment and prevention of such disorders like non-insulin dependent diabetes, various hyperlipedemias, high blood pressure and atherosclerosis. Resources include the biological pathways, data sets, microarray protocols and other experimental standards, analytical tools, and reagents. | lipid, disorder, diabetes, insulin, hyperlipedemia, blood pressure, athersclerosis, microarray, reagent, biology | PMID:15588328 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02919 | http://gold.tugraz.at | SCR_000736 | Genomics Of Lipid-associated Disorders database, GOLD.db Genomics Of Lipid-associated Disorders, GOLD.db | 2026-08-10 09:31:14 | 25 | |||||||
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BloodExpress Resource Report Resource Website 1+ mentions |
BloodExpress (RRID:SCR_001142) | data or information resource, database | A database of gene expression in mouse haematopoiesis, integrating 271 individual microarray experiments derived from 15 distinct studies done on most characterized mouse blood cell types. Gene expression information has been discretized to absent/present/unknown calls. It supports gene-centric searches to find out where a gene of interest is expressed, and what other genes follow the same (or a similar) pattern of expression. It also supports cell-centric searches to find out what genes are expressed in specific cell types/studies and not others. | blood, hematopoiesis, microarray, red blood cell, gene expression, expression profile, gene, cell, haematopoietic stem cell |
uses: StemBase uses: Gene Expression Omnibus has parent organization: University of Cambridge; Cambridge; United Kingdom |
Leukemia Research Foundation ; Leukemia and Lymphoma Society ; MRC |
PMID:18987008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02615 | SCR_001142 | Blood Express | 2026-08-10 09:31:21 | 1 | ||||||
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ButterflyBase Resource Report Resource Website 1+ mentions |
ButterflyBase (RRID:SCR_000727) | data or information resource, database | An open-access Genomic Database for Lepidoptera. It includes all the Lepidoptera cDNA sequences available in NCBI's dbEST. Support for genomic-DNA sequences such as BACs and the Bombyx mori genome is being generated. Tools available on this website include BLAST search, Annotation search, Primer design, and Microsatellite repeat finders. Users can also download all data and sequences. Within the site, the Expressed Sequence Tag sequences are made with Trace2dbest from raw sequence data if available or downloaded from NCBI. We cluster them using PartiGene into gene-objects to reduce redundancy. Subsequently, we perform hierarchical BLAST searches to provide accurate similarity annotation and a robust protein translation protocol using prot4EST. Putative proteins objects have been further annotated with the Gene Ontology biological vocabulary (GO terms) and InterPro (EBI) domains to facilitate gene-hunters. The repository is open for all Lepidopteran researchers. | bombyx mori, butterfly, moth, lepidoptera, lepidoptera cdna, lepidoptera genome |
is listed by: 3DVC has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:17933781 | Please cite: Papanicolaou A, Gebauer-Jung S, Blaxter ML, Owen McMillan W, Jiggins CD. ButterflyBase: a platform for lepidopteran genomics. Nucleic Acids Res. 2008 Jan;36(Database issue):D582-7. Epub 2007 Oct 12. | nif-0000-02627 | SCR_000727 | ButterflyBase | 2026-08-10 09:31:14 | 3 |
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