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https://www.facebase.org/content/ocdm

To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language.

Proper citation: OCDM - Ontology of Craniofacial Development and Malformation (RRID:SCR_005999) Copy   

•   Source: SciCrunch Registry

http://www.clo-ontology.org/

A community-driven ontology that is developed to standardize and integrate cell line information and support computer-assisted reasoning. Its focus is on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, the Jurkat cell line provides ane xample. Currently CLO contains over 36,000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and bymanual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications. The CLO development has become a community effort with international collaborations. The development consortium includes experts from all over the world: the USA, Europe, and Japan.

Proper citation: Cell Line Ontology (RRID:SCR_005840) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RCTONT

Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.

Proper citation: Randomized Controlled Trials Ontology (RRID:SCR_005992) Copy   

•   Source: SciCrunch Registry

http://purl.org/spar/datacite/

An ontology written in OWL 2 DL to enable the metadata properties of the DataCite Metadata Kernel Specification version 2.2 (http://test.datacite.org/schema/meta/kernel-2.2/index.html) to be described in RDF. This version of the DataCite Ontology has been completely revised and significantly expanded to permit accurate mapping of this new version of the DataCite Metadata Kernel Specification to RDF.

Proper citation: DataCite Ontology (RRID:SCR_006215) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RCD

Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre

Proper citation: Read Codes Clinical Terms Version 3 (RRID:SCR_006055) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/RETO

An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations.

Proper citation: Regulation of Transcription Ontology (RRID:SCR_006238) Copy   

•   Source: SciCrunch Registry

http://obi-ontology.org/

An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project.

Proper citation: Ontology for Biomedical Investigations (RRID:SCR_006266) Copy   

•   Source: SciCrunch Registry

http://www.med.nihon-u.ac.jp/department/physiol1/

Series of MRI slices from 3 male Japanese snow monkeys (Macaca fuscata). Images are provided of 2 mm MRI slices of male monkey brain in the coronal (N = 5), horizontal (N =1) and sagittal (N =1) planes. Slices are presented according to distance from interaural line. The slices are low resolution and no annotations are provided. Would be suitable for low resolution 3D reconstruction of monkey brain, however. Also, there are datasets provided for 5 monkeys total, 3 m.fuscata and 2 m. mulatta.

Proper citation: Stereotaxic MRI Brain Atlas of Monkey (RRID:SCR_007298) Copy   

•   Source: SciCrunch Registry

http://www.sapientaproject.com/

Software to help researchers process scientific papers faster and get the information they are interested in out of them. This is achieved by automating the recognition of core scientific concepts such as Motivation, Method, Result, Conclusion in papers and uses them to generate automatic summaries. This SAPIENTA tool adds additional functionality to the SAPIENT tool, an annotation tool implemented as a web application which enables experts to annotate scientific papers, sentence by sentence manually, according to the Core Scientific Concept (CSC) schema.

Proper citation: Sapienta (RRID:SCR_006993) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm

Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)

Proper citation: POOLSCORE (RRID:SCR_007514) Copy   

•   Source: SciCrunch Registry

http://www.brainnav.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips.

Proper citation: BrainNavigator (RRID:SCR_008289) Copy   

•   Source: SciCrunch Registry

http://digestive.niddk.nih.gov/statistics/statistics.aspx

A collection of statistics about specific digestive diseases, including prevalence, mortality, care delivery and cost.

Proper citation: Digestive Diseases Statistics for the United States (RRID:SCR_006703) Copy   

•   Source: SciCrunch Registry

http://connectivity.brain-map.org/

Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses.

Proper citation: Allen Mouse Brain Connectivity Atlas (RRID:SCR_008848) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/genomic_control/genomic_control.htm

Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software)

Proper citation: GC/GCF (RRID:SCR_009075) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/froi_atlas/

An effort to provide a set of quasi-probabilistic atlases for established functional ROIs in the human neuroimaging literature. Many atlases exist for various anatomical parcellation schemes, such as the Brodmann areas, the structural atlases, tissue segmentation atlases, etc. To date, however, there is no atlas for so-called functional ROIs. Such fROIs are typically associated with an anatomical label of some kind (e.g. the _fusiform_ face area), but these labels are only approximate and can be misleading inasmuch as fROIs are not constrained by anatomical landmarks, whether cytoarchitectonic or based on sulcal and gyral landmarks. The goal of this project is to provide quasi-probabilistic atlases for fROIs that are based on published coordinates in the neuroimaging literature. This is an open-ended enterprise and the atlas can grow as needed. Members of the neuroscience and neuroimaging community interested in contributing to the project are encouraged to do so.

Proper citation: Functional ROI Atlas (RRID:SCR_009481) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/atag/

This atlas takes advantage of ultra-high resolution 7T MRI to provide unprecedented levels of detail on structures of the basal ganglia in-vivo. The atlas includes probability maps of the Subthalamic Nucleus (STh) using T2*-imaging. For now it has been created on 13 young healthy participants with a mean age of 24.38 (range: 22-28, SD: 2.36). We recently also created atlas STh probability maps from 8 middle-aged participants with a mean age of 50.67 (range: 40-59, SD: 6.63), and 9 elderly participants with a mean age of 72.33 (range: 67-77, SD: 2.87). You can find more details about the creation of these maps in the following papers: Young: http://www.ncbi.nlm.nih.gov/pubmed/22227131 Middle-aged & Elderly: http://www.ncbi.nlm.nih.gov/pubmed/23486960 Participating institutions are the Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, and the Cognitive Science Center Amsterdam, University of Amsterdam, the Netherlands.

Proper citation: Atlasing of the basal ganglia (RRID:SCR_009431) Copy   

•   Source: SciCrunch Registry

http://www.neurofly.de

An on-going atlas project of the Virtual Insect Brain Project with the goal of reconstructing and standardizing Gal4 expression patterns in Drosophila brains. Neurofly will be a web-based tool that will enable the online comparison of mutations and Gal4 expression patterns in the Drosophila brain. To this end, a database of reconstructed and standardized Gal4 expression patterns - on the basis of the existing Drosophila StandardBrain - was developed along with tools for 3D image data set processing. Users will be able to evaluate the expression patterns intersections of various Gal4 driver lines and/or mutations.

Proper citation: Neurofly (RRID:SCR_013833) Copy   

•   Source: SciCrunch Registry

http://findlab.stanford.edu/functional_ROIs.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Atlas of functional ROIs (fROIs) containing 499 regions, with extensive gray matter coverage. Atlases are available for download directly from the website.

Proper citation: 499 fROI atlas (RRID:SCR_014756) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/striatalvoimap/

An atlas intended to provide accurate data in terms of specific uptake location to make the BP quantitation. The VOIs were manually drawn with software Analyze 9.0 (Mayo Clinic) in 18F-DOPA brain image after spatial normalization with a 18F-DOPA Template. Each striatum was divided into 6 sub-regions: ventral caudate, anterior dorsal caudate, posterior dorsal caudate, ventral putamen, anterior dorsal putamen and posterior dorsal putamen.

Proper citation: Striatal Subregional VOImap (RRID:SCR_014173) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/cmap/

The Brain Coactivation Map describes all the coactivation networks in the human brain based on the meta-analysis of more than 5,400 neuroimaging articles (from NeuroSynth) containing more than 16,000 individual experiments. The map can be browsed interactively (CoactivationMap.app on GitHub) or queried from a shell using a command line tool (cmtool on GitHub).

Proper citation: Brain Coactivation Map (RRID:SCR_014172) Copy   

•   Source: SciCrunch Registry