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http://www.ebi.ac.uk/asd/aedb/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 27, 2013. A manual generated database for alternative exons and their properties from numerous species - the data is gathered from literature where these exons have been experimentally verified. Most alternative exons are cassette exons and are expressed in more than two tissues. Of all exons whose expression was reported to be specific for a certain tissue, the majority were expressed in the brain. At the moment, AEdb products that are available are sequence (a database of alternative exons), function (a database of functions attributed to constitutive and alternative exon), regulatory sequence (a database of transcript regulatory motifs), minigenes (a table of minigenes and their associations to splicing events), and diseases (a table of diseases associated with splicing and their associations to AltSplice). Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. The continuation and upgrade of the ASD consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs.

Proper citation: Alternative Exon Database (RRID:SCR_008157) Copy   

•   Source: SciCrunch Registry

https://epilepsy.uni-freiburg.de/freiburg-seizure-prediction-project

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 29,2025. Electroencephalogram (EEG) data recorded from invasive and scalp electrodes. The EEG database contains invasive EEG recordings of 21 patients suffering from medically intractable focal epilepsy. The data were recorded during an invasive pre-surgical epilepsy monitoring at the Epilepsy Center of the University Hospital of Freiburg, Germany. In eleven patients, the epileptic focus was located in neocortical brain structures, in eight patients in the hippocampus, and in two patients in both. In order to obtain a high signal-to-noise ratio, fewer artifacts, and to record directly from focal areas, intracranial grid-, strip-, and depth-electrodes were utilized. The EEG data were acquired using a Neurofile NT digital video EEG system with 128 channels, 256 Hz sampling rate, and a 16 bit analogue-to-digital converter. Notch or band pass filters have not been applied. For each of the patients, there are datasets called ictal and interictal, the former containing files with epileptic seizures and at least 50 min pre-ictal data. the latter containing approximately 24 hours of EEG-recordings without seizure activity. At least 24 h of continuous interictal recordings are available for 13 patients. For the remaining patients interictal invasive EEG data consisting of less than 24 h were joined together, to end up with at least 24 h per patient. An interdisciplinary project between: * Epilepsy Center, University Hospital Freiburg * Bernstein Center for Computational Neuroscience (BCCN), Freiburg * Freiburg Center for Data Analysis and Modeling (FDM).

Proper citation: Electroencephalogram Database: Prediction of Epileptic Seizures (RRID:SCR_008032) Copy   

•   Source: SciCrunch Registry

http://dimer.tamu.edu/doodle/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Doodle is a database that was developed to store and distribute information about the protein oligomerization domains that are encoded by various genomes. The protein oligomerization domains described here were found using the lambda repressor fusion system. Doodle uses a schema that is based on EnsEMBL, while also utilizing bioperl modules to both store and retrieve data. The frontend was developed entirely in perl, while the backend utilizes MySQL. GMOD was used to develop the genomic view.

Proper citation: Database of oligomerization domains from lambda experiments (RRID:SCR_008107) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/genomes/plasmid.html

The Plasmid Genome Database aims to collate biological and genomic data for all bacterial plasmids in the hopes of enabling rapid, interrogation of both meta- and genomic data. Data maintained includes access to all plasmid genomes and information on core genomic features obtained from parsing the original EMBL/DDBJ/NCBI submission. In addition a suite of third party analyses has been performed for each genome to supplement the original annotation. This site also links to Genome Atlases provided by the Centre for Biological Sequence Analysis (CBS). The motivation behind the construction of this site derived from observations from genome sequencing projects: the abundance and inferred importance of the horizontal gene pool (HGP) in bacterial adaptation and evolution. In so far as plasmids are autonomously replicating, extrachromosomal elements they are a readily identifiable and accessible component of the HGP. Also plasmids have been identified in almost all bacterial divisions, ranging in size from less than 2 kbp to > 1.5 Mbp and as such represent a defined, yet diverse and complex sample of genes in the HGP.

Proper citation: Plasmid Genome Database (RRID:SCR_008228) Copy   

•   Source: SciCrunch Registry

http://166.111.130.62/portal/root/bi_dbnei/index.jsp

Version 1.0 database for neuro-endocrine-immune (dbNEI) is a web-based knowledge resource specific for the NEI systems. It provides a knowledge environment for understanding the main regulatory systems of NEI in a molecular level. dbNEI provides a knowledge environment for understanding the main regulatory systems of NEI in a molecular level. dbNEI collects 1,058 NEI related signal molecules, their 940 interactions and 72 affiliated tissues from the Cell Signaling Networks database and manually selects 982 NEI papers from PubMed. NEI related information, such as signal transductions, regulations and control subunits, are integrated. Especially, dbNEI represents as graphic visualization, by which control subunits can be automatically obtained according to the inquiring issues. Version 2.0: We updated the database in four aspects. 1. Recruiting new NEI genes and compounds. 2. Adding KEGG,HPRD,Transcription factor and microRNA target relations. 3. Collecting drug-gene and disease-gene relation. 4. Building multi-layer network for drug-NEI-disease.

Proper citation: NEI (neuro-endocrine-immune) Network Database (RRID:SCR_008106) Copy   

•   Source: SciCrunch Registry

http://domine.utdallas.edu/cgi-bin/Domine?page=help

DDIB collects information of domain-domain interactions and domain interactions with biological molecules such as RNA, DNA, peptides, inorganic ions, phospholipids and cholesterols. Most of the data were extracted automatically from publication abstracts in MEDLINE, and the rest were collected from other public databases, research laboratories and individual scientists. In addition, DDIB includes many putative domain-domain interactions inferred from documented protein-protein interactions. To provide comprehensive knowledge of a domain, DDIB also integrates relevant information from PFAM, InterPro, GO and KEGG databases.

Proper citation: Database of Domain Interactions and Bindings (RRID:SCR_008100) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/services/genomes/uwe25/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK.

Proper citation: Protochlamydia amoebophila UWE25 (RRID:SCR_008222) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.mdc-berlin.de/splice/db/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. An online available compendium of alternative splice forms for several organisms (Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Rattus norvegicus, Xenopus laevis). Alternative splice forms are defined by comparing high-scoring ESTs to mRNA sequences (both from GenBank) with known exon-intron information (from ENSEMBL database) using BLAST. Repetitive sequences of all mRNAs have beforehand been masked by MaskerAid. Filtering programs with defined parameters compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which suggest the existence of alternative splice forms. The database is accessible by typing in accession numbers (ACC) or keywords like description, gene names, organism or other keywords. (If more than one hit was found a list of all results is given.) And the result page is divided into 4 major parts. The first part (General Information About The Entry) summarizes the most important information as database ids, organism, and description. The so called alternative splice profile (ASP) of each human sequence is shown in the second part (Alternative Splice Frequency). The ASP indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE corresponds to the EST coverage and can be used as a quality value for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene. Moreover the number of ESTs from cancerous tissues is shown. The histological source and the developmental stages are illustrated with several colors to enables the user to get an overview of the origins of the matching ESTs. Also, the Splice Site View shows graphically all alternative splice sites for the whole transcript.

Proper citation: Extended Alternatively Spliced EST Database (RRID:SCR_008186) Copy   

•   Source: SciCrunch Registry

http://csbdb.mpimp-golm.mpg.de/

CSB.DB presents the results of bio-statistical analysis on gene expression data in association with additional biochemical and physiological knowledge. The main aim of this database platform is to provide tools that support insight into life''s complexity pyramid with a special focus on the integration of data from transcript and metabolite profiling experiments. The main focus of the CSB project is the generation of new easily accessible knowledge about the relationship and the hierarchy of cellular components. Thus new progress towards understanding lifes complexity pyramid is made. For this aim statistical and computational algorithms are applied to organism specific data derived from publicly available multi-parallel technologies, currently such as expression profiles. The underlying data are derived from various research activities. Thus CSB project provides an integrated and centralized public resource allowing universal access on the generated knowledge CSB.DB: A Comprehensive Systems-Biology Database. The derived knowledge should support the formulation of new hypotheses about the respective functional involvement of genes beyond their (inter-) relationships. Another major goal of the CSB project is to supply the researchers with necessary information to formulate these new hypotheses without demanding any a-priori statistical knowledge of the user. The CSB project mainly focuses on application of required statistical tests as well as to assist the user during exploration of results with information / help files to support hypothesis generation

Proper citation: Comprehensive Systems-Biology Database (RRID:SCR_008185) Copy   

•   Source: SciCrunch Registry

http://ucairss.utsa.edu/cgi-bin/Pwebrecon.cgi?DB=local&PAGE=First

CAIRSS is a bibliographic database of older literature (prior to 1993) of music research literature in music education, music psychology, music therapy, and music medicine. Citations have been taken from 1,354 different journal titles; 18 of which are primary journals, meaning that every article ever to appear is included. The primary journals are: * Arts in Psychotherapy * Bulletin of the Council for Research in Music Education * Bulletin of the National Association for Music Therapy * Contributions to Music Education * Hospital Music Newsletter * International Journal of Arts Medicine * Journal of the Association for Music and Imagery * Journal of Music Teacher Education * Journal of Music Therapy * Journal of Research in Music Education * Medical Problems of Performing Artists * Music Perception * Music Therapy * Music Therapy Perspectives * Psychology of Music * Psychomusicology * The Quarterly * Applications of Research to Music Education

Proper citation: Computer-Assisted Information Retrieval Service System for Music (RRID:SCR_008177) Copy   

•   Source: SciCrunch Registry

http://mpr.nci.nih.gov/MPR/BrowseProteins.aspx

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 6/24/13. A repository of information on commercially available phospho-specific antibodies to human phosphorylation sites. It provides a BLAST search for phosphorylation sites using as query the amino acid sequence surrounding the site. It also provides direct links to the relevant antibodies from many companies including BD Pharmingen, Biosource International, Cell Signaling Technology (CST), Santa Cruz Biotechnologies, Upstate Biotechnology.

Proper citation: Mammalian Phosphorylation Resource (RRID:SCR_008210) Copy   

•   Source: SciCrunch Registry

http://chromium.lovd.nl/LOVD2/home.php?select_db=CDKN2A

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The CDKN2A Database presents the germline and somatic variants of the CDKN2A tumor suppressor gene recorded in human disease through June 2003, annotated with evolutionary, structural, and functional information, in a format that allows the user to either download it or manipulate it for their purposes online. The goal is to provide a database that can be used as a resource by researchers and geneticists and that aids in the interpretation of CDKN2A missense variants. Most online mutation databases present flat files that cannot be manipulated, are often incomplete, and have varying degrees of annotation that may or may not help to interpret the data. They hope to use CDKN2A as a prototype for integrating computational and laboratory data to help interpret variants in other cancer-related genes and other single nucleotide polymorphisms (SNPs) found throughout the genome. Another goal of the lab is to interpret the functional and disease significance of missense variants in cancer susceptibility genes. Eventually, these results will be relevant to the interpretation of single nucleotide polymorphisms (SNPs) in general. The CDKN2A locus is a valuable model for assessing relationships among variation, structure, function, and disease because: Variants of this gene are associated with hereditary cancer: Familial Melanoma (and related syndromes); somatic alterations play a role in carcinogenesis; allelic variants occur whose functional consequences are unknown; reliable functional assays exist; and crystal structure is known. All variants in the database are recorded according to the nomenclature guidelines as outlined by the Human Genome Variation Society. This database is currently designed for research purposes only and is not yet recommended as a clinical resource. Many of the mutations reported here have not been tested for disease association and may represent normal, non-disease causing polymorphisms.

Proper citation: CDKN2A Database (RRID:SCR_008179) Copy   

•   Source: SciCrunch Registry

http://www.schematikon.org/Nh3D.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB. It is a dataset of structurally dissimilar proteins. This dataset has been compiled by selecting well resolved representatives from the Topology level of the CATH database which hierarchically classifies all protein structures. These have been been pruned to remove: i) domains that may contain homologous elements (by pairwise sequence comparison and structural superposition of aligned residues) ii) internal duplications (by repeat detection) iii) regions with high B-Factor The statistical analysis of protein structures requires datasets in which structural features can be considered independently distributed, i.e. not related through common ancestry, and that fulfill minimal requirements regarding the experimental quality of the structures it contains. However, non-redundant datasets based on sequence similarity invariably contain distantly related homologues. Here a reference dataset of non-homologous protein domains is provided, assuming that structural dissimilarity at the topology level is incompatible with recognizable common ancestry. It contains the best refined representatives of each Topology level, validates structural dissimilarity and removes internally duplicated fragments. The compilation of Nh3D is fully scripted. The current Nh3D list contains 570 domains with a total of 90780 residues. It covers more than 70% of folds at the Topology level of the CATH database and represents more than 90% of the structures in the PDB that have been classified by CATH. Even though all protein pairs are structurally dissimilar, some pairwise sequence identities after global alignment are greater than 30%. Nh3D is freely available as a reference dataset for the statistical analysis of sequence and structure features of proteins in the PDB.

Proper citation: Nh3D: A Reference Dataset of Structures of Non-homologous Proteins (RRID:SCR_008212) Copy   

•   Source: SciCrunch Registry

http://dtp.nci.nih.gov/docs/3d_database/dis3d.html

The NCI DIS 3D database is a collection of 3D structures for over 400,000 drugs. The database is an extension of the NCI Drug Information System. The structural information stored in the DIS is only the connection table for each drug. The connection table is just a list of which atoms are connected and how they are connected. It is essentially a searcheable database of three-dimensional structures has been developed from the chemistry database of the NCI Drug Information System (DIS), a file of about 450,000 primarily organic compounds which have been tested by NCI for anticancer activity. The DIS database is very similar in size and content to the proprietary databases used in the pharmaceutical industry; its development began in the 1950s; and this history led to a number of problems in the generation of 3D structures. This information can be searched to find drugs that share similar patterns of connections, which can correlate with similar biological activity. But the cellular targets for drug action, as well as the drugs themselves, are 3 dimensional objects and advances in computer hardware and software have reached the point where they can be represented as such. In many cases the important points of interaction between a drug and its target can be represented by a 3D arrangement of a small number of atoms. Such a group of atoms is called a pharmacophore. The pharmacophore can be used to search 3D databases and drugs that match the pharmacophore could have similar biological activity, but have very different patterns of atomic connections. Having a diverse set of lead compounds increases the chances of finding an active compound with acceptable properties for clinical development. Sponsor: The ICBG are supported by the Cooperative Agreement mechanism, with funds from nine components of the NIH, the National Science Foundation, and the Foreign Agricultural Service of the USDA.

Proper citation: National Cancer Institute 3D Structure Database (RRID:SCR_008211) Copy   

•   Source: SciCrunch Registry

http://databases.unesco.org/bioethics/biowebintro.shtml

Bioethics database comprises over 645 bioethics institutions (bioethics committees, commissions, training, research and documentation centres) in over 80 countries, including information on activities and publications. Information is based on replies obtained from a widely distributed questionnaire and has been gathered in cooperation with National Commissions and Permanent Delegations to UNESCO. The Program develops four main action areas: -Intellectual forum -Standard-setting action -Advisory role and capacity-building -Education and awareness raising The Bioethics Program is part of UNESCOs Division of the Ethics of Science and Technology in the Social and Human Sciences Sector. It is primarily responsible for the Secretariat of two advisory bodies: the International Bioethics Committee (IBC), composed of 36 independent experts, and the Intergovernmental Bioethics Committee (IGBC), composed of representatives of 36 Member States. These Committees cooperate to produce advice, recommendations and proposals that each submits to the Director-General for consideration by UNESCOs governing bodies.

Proper citation: Bioethics Institutes Database (RRID:SCR_008173) Copy   

•   Source: SciCrunch Registry

http://jbirc.jbic.or.jp/hinv/ppi/

The PPI view displays H-InvDB human protein-protein interaction (PPI) information. It is constructed by assigning interaction data to H-InvDB proteins which were originally predicted from transcriptional products generated by the H-Invitational project. The PPI view is now providing 32,198 human PPIs comprised of 9,268 H-InvDB proteins. H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups. Sponsors: This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program.

Proper citation: H-Invitational Database: Protein-Protein Interaction Viewer (RRID:SCR_008054) Copy   

•   Source: SciCrunch Registry

http://www3.isrl.uiuc.edu/~TeleNature/bibe/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A facility to help novices and experts find information about plants and animals in digital collections. The objectives of the Project are to facilitate access to online flora and fauna by both novices and experts through enhanced indexing, searching, and visualization techniques. Specific search facility and content will be added to help users with different levels of domain knowledge identify species based on the augmentation of professionally developed taxonomic treatments or species descriptions. This is a novel use of taxonomic descriptions.

Proper citation: Biological Information Browsing Environment (RRID:SCR_008170) Copy   

•   Source: SciCrunch Registry

http://amazonia.montp.inserm.fr/

A web interface and associated tools for easy query of public human transcriptome data by keyword, through thematic pages with list annotations. Amazonia provides a thematic entry to public transcriptomes: users may for instance query a gene on a Stem Cells page, where they will see the expression of their favorite gene across selected microarray experiments related to stem cell biology. This selection of samples can be customized at will among the 6331 samples currently present in the database. Every transcriptome study results in the identification of lists of genes relevant to a given biological condition. In order to include this valuable information in any new query in the Amazonia database, they indicate for each gene in which lists it is included. This is a straightforward and efficient way to synthesize hundreds of microarray publications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: AmaZonia: Explore the Jungle of Microarrays Results (RRID:SCR_008405) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/asd/altextron/indexhtml

THIS RESOURCE IS NO LONGER IN SERVICE. A computer generated high quality dataset of human transcript-confirmed constitutive and alternative exons and introns. The alternative events have been delineated and annotated with various characterizations. AltExtron is the prototype database for the production version AltSplice. AltExtron is more geared towards investigating various aspects of the methodologies used, and focuses in general on the biology behind alternative splicing. The complete data used in this work is available for downloading in several flat files, containing human genes, introns, exons, isoform events, human-mouse comparisons, and additional information on GC-AG introns. Two versions of AltExtron data are available - one as prototype (for human) and another as latest build (for human, drosophila, mouse, and others) based on EMBL/GenBank (Feb 2003).

Proper citation: AltExtron Database (RRID:SCR_008404) Copy   

•   Source: SciCrunch Registry

http://www.gavialliance.org/

Although Haemophilus influenza type b (Hib) diseases and Hepatitis B (Hep B) infections are preventable with one combined life-saving vaccine, both continue to pose risks to the worlds most vulnerable populations, leading to life-long disabilities or even death. Vaccinating against Hib and Hepatitis B represents an essential step towards reaching Millennium Development Goal 4. The Hib bacterium causes meningitis and pneumonia and is considered the third vaccine-preventable cause of death in children aged under five. It is estimated that there are three million cases of serious Hib infection annually, of which 400,000 result in childhood death. The majority of survivors suffer paralysis, deafness, mental retardation and learning disabilities. Babies and young children are most at risk from Hep B, a viral disease, which attacks the liver and can cause both acute and chronic disease. This can lead to chronic liver disease and puts victims at high risk of death from cirrhosis of the liver and liver cancer in later life. More than two billion people are infected by Hep B worldwide of whom 360 million suffer from chronic Hep B infection; the latter is highly prevalent in all countries that GAVI supports. Children are most vulnerable to infection with 90 percent of infants infected in the first months of their lives developing chronic Hep B infection. Infections in the developing world are mostly from mother to child, or from child to child, mainly through cuts, bites, scrapes and scratches. Vaccinating against Hib and Hep B represents an essential step towards reaching Millennium Development Goal 4, which is to reduce the under-five mortality rate by two thirds by 2015. GAVI uses two mechanisms that draw heavily on private-sector thinking to help overcome historic limitations to development funding for immunisation. These mechanisms are the AMC and the IFFIm. The former reflects the need to meet disproportionately high costs in the early stages of implementing aid programmes; the latter developing countries'' need for sustainable predictable funding., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GAVI (RRID:SCR_008528) Copy   

•   Source: SciCrunch Registry