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http://neurolog.i3s.unice.fr/public_namespace/ontology

An ontology for neuroimaging or medical imaging studies based on DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering), as the foundational ontology. Detailed description from web: Our aim is the design of a common semantic model providing a unified view on all data and tools to be shared between NeuroLOG partners. For this purpose, we built a multi-layered and multi-components formal ontology. We chose a design framework that structures the ontology at different levels of abstraction while respecting common conceptualization choices. At the highest level is a top-level ontology that includes abstract concepts and relationships valid across domains. We adopted DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering), as the foundational ontology. We then added Core ontologies, which provide generic, basic and minimal concepts and relations in a specific domain. By minimal we mean that core ontologies should include only the most reusable and widely applicable categories. These kinds of ontologies are essential for sharing intended meaning between different domains. We adopted I& DA (Information and Discourse Acts), a core ontology initially built for classifying documents as a function of their content.We use it to model medical images, which we consider as types of documents. Participant Roles is the core ontology we use to describe the modes of image participation in data processing. I& DA and Participant Roles are built according to DOLCE ontological commitments. On the basis of these two layers, we constructed our Domain ontology dedicated to conceptualizing a specific domain, in this case neuroimaging. Obviously, large domains such as neuroimaging can be divided into sub-domains for the sake of modularization.

Proper citation: OntoNeuroLOG (RRID:SCR_008957) Copy   

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http://www.humanmotorthalamus.com/

A research tool for clinical and experimental neuroscience, which provides images of human thalamus in the stereotactic planes of the coordinate system based on intercommissural line. Images include histological sagittal sections, sagittal maps, coronal maps, horizontal maps, and MRI images all from the same brain. The website also provides materials and methods section, references to the articles and presentations describing research data (on which the maps are based), and a bibliography on the synaptic relationships of subcortical and cortical afferents with projection and local circuit neurons in the motor thalamus.

Proper citation: Human Thalamus in 3D Stereotactic Coordinates (RRID:SCR_014214) Copy   

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http://cbbiweb.uthscsa.edu/KMethylomes/

Datbase and web-based system for visualization and analysis of genome-wide methylation data of human cancers.

Proper citation: Cancer Methylome System (RRID:SCR_012013) Copy   

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http://appris.bioinfo.cnio.es/

A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript.

Proper citation: APPRIS (RRID:SCR_012019) Copy   

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http://jbirc.jbic.or.jp/h-dbas/

A specialized database for human alternative splicing (AS) based on H-Invitational full-length cDNAs. H-DBAS offers unique data and viewer for human Alternative Splicing (AS) analysis. It contains: * Genome-wide representative alternative splicing variants (RASVs) identified from following datasets * H-Inv full-length cDNAs (resource summary): H-Invitational cDNA dataset * H-Inv all transcripts (resource summary): Published human mRNA dataset * Mouse full-length cDNAs (resource summary): Mouse cDNA dataset * RASVs affecting protein functions such as protein motif, GO, subcellular localization signal and transmembrane domain * Conserved RASVs compared with mouse genome and the full-length cDNAs (H-Inv full-length cDNAs only)

Proper citation: Human Transcriptome Database for Alternative Splicing (RRID:SCR_013305) Copy   

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http://bioinf.uta.fi/BTKbase/

A mutation registry for X-linked agammaglobulinemia (XLA). BTKbase lists mutation entries of 1,111 patients from 973 unrelated families showing 602 unique molecular events. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement. Two thirds of cases are familial, and one third of cases are believed to arise from new mutations. Mutations of the BTK gene are found in approximately 80% of patients with agammaglobulinemia. The localization of the mutations on the gene and protein for BTK can be analyzed by clicking sequences on the web pages. It includes a mutation browser, which gives users access to mutations in Bruton tyrosine kinase (BTK) protein sequences, and XLA fact file, and forms for users to submit mutation to the dataset.

Proper citation: BTKbase (RRID:SCR_013101) Copy   

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http://dorina.mdc-berlin.de/rbp_browser/dorina.html

In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.

Proper citation: doRiNA (RRID:SCR_013222) Copy   

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http://agem.cnb.csic.es/VisualOmics/aGEM/

Database platform of an integrated view of eight databases (mouse gene expression resources: EMAGE, GXD, GENSAT, BioGPS, ABA, EUREXPRESS; human gene expression databases: HUDSEN, BioGPS and Human Protein Atlas) that allows the experimentalist to retrieve relevant statistical information relating gene expression, anatomical structure (space) and developmental stage (time). Moreover, general biological information from databases such as KEGG, OMIM and MTB is integrated too. It can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. This is a powerful tool in the gene expression field that makes easy the access to information related to the anatomical pattern of gene expression in human and mouse, so that it can complement many functional genomics studies. The platform allows the integration of gene expression data with spatial-temporal anatomic data by means of an intuitive and user friendly display., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: aGEM (RRID:SCR_013349) Copy   

•   Source: SciCrunch Registry

http://www.deathdomain.org/

A manually curated database of protein-protein interactions for Death Domain Superfamily. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The DD superfamily currently comprises four subfamilies: * Death domain (DD) subfamily * Death effector domain (DED) subfamily * Caspase recruitment domain (CARD) subfamily * Pyrin domain (PYD) subfamily

Proper citation: Death Domain database (RRID:SCR_013231) Copy   

•   Source: SciCrunch Registry

http://db.systemsbiology.net/kaviar/

A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants.

Proper citation: KAVIAR (RRID:SCR_013737) Copy   

•   Source: SciCrunch Registry

http://servers.binf.ku.dk/bloodspot/

Database that provides gene expression profiles of genes and gene signatures in healthy and malignant hematopoiesis and includes data from both humans and mice. In addition to the default plot, which displays an integrated expression plot, two additional levels of visualization are available: an interactive tree showing the hierarchical relationship between the samples, and a Kaplan-Meier survival plot. The database is sub-divided into several datasets that are accessible for browsing.

Proper citation: BloodSpot (RRID:SCR_015563) Copy   

•   Source: SciCrunch Registry

http://compartments.jensenlab.org/Downloads

Web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. All evidence is mapped to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.

Proper citation: COMPARTMENTS Subcellular localization database (RRID:SCR_015561) Copy   

•   Source: SciCrunch Registry

https://www.proteomicsdb.org/

Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository.

Proper citation: ProteomicsDB (RRID:SCR_015562) Copy   

•   Source: SciCrunch Registry

https://senselab.med.yale.edu/MicroCircuitDB/

A database for storing and efficiently retrieving realistic computational models of brain microcircuits and networks. The focus is on microcircuits that are based on experimentally demonstrated properties of neurons and their connectivity.

Proper citation: MicrocircuitDB (RRID:SCR_014577) Copy   

•   Source: SciCrunch Registry

http://www.nihtoolbox.org/WhatAndWhy/Sensation/Taste/Pages/NIH-Toolbox-Regional-Taste-Intensity-Test.aspx

Assessment test that measures the perceived intensity of quinine (a bitter tastant) and salt administered in liquid solutions. The tastants are applied to the tip of the tongue as well as the whole mouth and rated on a generalized labeled magnitude scale (ranging from no sensation at all to strongest sensation of any kind). The test is recommended for administration to participants ages 12-85 and takes approximately six minutes to administer.

Proper citation: NIH Toolbox Regional Taste Intensity Test (RRID:SCR_003637) Copy   

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http://www.nihtoolbox.org/WhatAndWhy/Sensation/Pain/Pages/Pain-Intensity-Survey.aspx

A measure that consists of a single item measuring immediate (i.e., acute) pain in adults. As part of Toolbox, a single pain intensity item measures immediate (a.k.a. acute) pain for use in adults. It takes less than one minute to administer and is recommended for ages 18-85.

Proper citation: NIH Toolbox Pain Intensity Survey (RRID:SCR_003636) Copy   

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http://www.nihtoolbox.org/WhatAndWhy/Sensation/Pain/Pages/NIH-Toolbox-Pain-Interference-Survey.aspx

A self-report scale that measures the degree to which pain interferes with other activities in life in adults. Pain interference items were developed as part of the NIH PROMIS. This measure is administered as a computer-adaptive test and takes approximately three minutes. It is recommended for ages 8-85.

Proper citation: NIH Toolbox Pain Interference Survey (RRID:SCR_003635) Copy   

•   Source: SciCrunch Registry

http://psychology-tools.com/autism-spectrum-quotient/

A 50 question psychological assessment that measures the symptoms of autism in adults, children and adolescents.

Proper citation: Autism-Spectrum Quotient (RRID:SCR_003639) Copy   

•   Source: SciCrunch Registry

http://psychology-tools.com/spin/

A 17-item self-administered assessment questionnaire developed by the Psychiatry and Behavioral Sciences Department at Duke University effective in screening for and measuring the severity of social anxiety disorder. Each question is answered with one of 5 responses ranging from Not at All to Extremely. Each response is assigned a score and then totaled at the end. Scoring: * 0-20 Little or No Anxiety * 21-30 Mild Anxiety * 31-40 Moderate Anxiety * 41-50 Severe Anxiety * 51-68 Very Severe Anxiety

Proper citation: Social Phobia Inventory (RRID:SCR_003673) Copy   

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https://www.onlinetherapyuser.ca/assessment/pdss-sr

A self-administered assessment used to detect possible symptoms of panic disorder and suggest the need for a formal diagnostic assessment. It consists of seven items (which are rated from 0-4). The items assess panic frequency, distress during panic, panic-focused anticipatory anxiety, phobic avoidance of situations, phobic avoidance of physical sensations, impairment in work functioning, and impairment in social functioning. The overall assessment is made by a total score, which is calculated by summing the scores for all seven items. The total scores range from 0 to 28. The PDSS-SR is used for screening and the scores 9 and above suggest the need for a formal diagnostic assessment. (Adapted from Wikipedia)

Proper citation: Panic Disorder Severity Scale - Self-Report (RRID:SCR_003671) Copy   

•   Source: SciCrunch Registry